@article {pmid30658982,
year = {2019},
author = {Jiao, S and Chen, W and Wei, G},
title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02523-18},
pmid = {30658982},
issn = {1098-5336},
abstract = {Lacking knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of different plant growth were explored via sequencing of the 16S rRNA amplicon and shotgun metagenomics. Soil microbial alpha-diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles compared with functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals strong resilience of soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.Importance Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon-degradation and metal-tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.},
}

@article {pmid30655101,
year = {2018},
author = {Wolters, M and Ahrens, J and Romaní-Pérez, M and Watkins, C and Sanz, Y and Benítez-Páez, A and Stanton, C and Günther, K},
title = {Dietary fat, the gut microbiota, and metabolic health - A systematic review conducted within the MyNewGut project.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnu.2018.12.024},
pmid = {30655101},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: Studies indicate that dietary fat quantity and quality influence the gut microbiota composition which may as a consequence impact metabolic health. This systematic review aims to summarize the results of available studies in humans on dietary fat intake (quantity and quality), the intestinal microbiota composition and related cardiometabolic health outcomes.

METHODS: We performed a systematic review (CRD42018088685) following PRISMA guidelines and searched for literature in Medline, EMBASE, and Cochrane databases.

RESULTS: From 796 records, 765 records were excluded based on title or abstract. After screening of 31 full-text articles six randomized controlled trials (RCT) and nine cross-sectional observational studies were included. Our results of interventional trials do not suggest strong effects of different amounts and types of dietary fat on the intestinal microbiota composition or on metabolic health outcomes while observational studies indicate associations with the microbiota and health outcomes. High intake of fat and saturated fatty acids (SFA) may negatively affect microbiota richness and diversity and diets high in monounsaturated fatty acids (MUFA) may decrease total bacterial numbers whereas dietary polyunsaturated fatty acids (PUFA) had no effect on richness and diversity.

CONCLUSIONS: High fat and high SFA diets can exert unfavorable effects on the gut microbiota and are associated with an unhealthy metabolic state. Also high MUFA diets may negatively affect gut microbiota whereas PUFA do not seem to negatively affect the gut microbiota or metabolic health outcomes. However, data are not consistent and most RCT and observational studies showed risks of bias.},
}

@article {pmid30654982,
year = {2019},
author = {Mandalakis, M and Gavriilidou, A and Polymenakou, PN and Christakis, CA and Nomikou, P and Medvecký, M and Kilias, SP and Kentouri, M and Kotoulas, G and Magoulas, A},
title = {Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics.},
journal = {Marine environmental research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.marenvres.2019.01.002},
pmid = {30654982},
issn = {1879-0291},
abstract = {As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts.},
}

@article {pmid30647456,
year = {2019},
author = {Junghare, M and Spiteller, D and Schink, B},
title = {Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0348-5},
pmid = {30647456},
issn = {1751-7370},
abstract = {Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.},
}

@article {pmid30640580,
year = {2019},
author = {Cornut, J and De Respinis, S and Tonolla, M and Petrini, O and Bärlocher, F and Chauvet, E and Bruder, A},
title = {Rapid characterization of aquatic hyphomycetes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/00275514.2018.1528129},
pmid = {30640580},
issn = {1557-2536},
abstract = {Protein fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI--TOF MS) is a rapid, reliable, and economical method to characterize isolates of terrestrial fungi and other microorganisms. The objective of our study was to evaluate the suitability of MALDI-TOF MS for the identification of aquatic hyphomycetes, a polyphyletic group of fungi that play crucial roles in stream ecosystems. To this end, we used 34 isolates of 21 aquatic hyphomycete species whose identity was confirmed by spore morphology and internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) nuc rDNA sequencing. We tested the efficiency of three protein extraction methods, including chemical and mechanical treatments using 13 different protocols, with the objective of producing high-quality MALDI-TOF mass spectra. In addition to extraction protocols, mycelium age was identified as a key parameter affecting protein extraction efficiency. The dendrogram based on mass-spectrum similarity indicated good and relevant taxonomic discrimination; the tree structure was comparable to that of the phylogram based on ITS sequences. Consequently, MALDI-TOF MS could reliably identify the isolates studied and provided greater taxonomic accuracy than classical morphological methods. MALDI-TOF MS seems suited for rapid characterization and identification of aquatic hyphomycete species.},
}

@article {pmid30636276,
year = {2019},
author = {Zak, DR and Pellitier, PT and Argiroff, WA and Castillo, B and James, TY and Nave, LE and Averill, C and Beidler, K and Bhatnagar, J and Blesh, J and Classen, AT and Craig, M and Fernandez, CW and Gundersen, P and Johansen, R and Koide, RT and Lilleskov, EA and Lindahl, BD and Nadelhoffer, KJ and Phillips, RP and Tunlid, A},
title = {Exploring the role of ectomycorrhizal fungi in soil carbon dynamics.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.15679},
pmid = {30636276},
issn = {1469-8137},
abstract = {The extent to which ectomycorrhizal fungi (ECM) enable plants to access organic nitrogen (N) bound in soil organic matter (SOM) and transfer this growth-limiting nutrient to their plant host, has important implications for our understanding of plant-fungal interactions and the cycling and storage of carbon (C) and N in terrestrial ecosystems. Empirical evidence currently supports a range of perspectives, suggesting that ECM vary in their ability to provide their host with N bound in SOM, and that this capacity can both positively and negatively influence soil C storage. To help resolve the multiplicity of observations, we gathered a group of researchers to explore the role of ECM fungi in soil C dynamics, and propose new directions that hold promise to resolve competing hypotheses and contrasting observations. In this Viewpoint, we summarize these deliberations and identify areas of inquiry that hold promise for increasing our understanding of these fundamental and widespread plant symbionts and their role in ecosystem level biogeochemistry. This article is protected by copyright. All rights reserved.},
}

@article {pmid30635381,
year = {2019},
author = {Yao, Z and Du, S and Liang, C and Zhao, Y and Dini-Andreote, F and Wang, K and Zhang, D},
title = {Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02602-18},
pmid = {30635381},
issn = {1098-5336},
abstract = {Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly are poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high-marsh, using the 16S rRNA gene amplicon sequencing. Bacterial community composition differed significantly between sediment transects. Physico-chemical properties, particularly sediment nutrient levels [i.e., total nitrogen (TN) and available phosphorus (AP)], as well as sediment physical structure and pH (P < 0.05) were strongly associated with the overall community variations. In addition, the topological properties of bacterial co-occurrence networks varied with the distance to the water-land junction. Both node- and network-level topological features revealed the bacterial network of sediments farthest from the junction to be less intense in complexity and interactions compared with other sediments. Phylogenetic null modelling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, this study provides a detailed outline of the distribution pattern of sediment bacterial community across the estuarine marsh and inform on the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCESalt marshes represent highly dynamic ecosystems where the atmosphere, continents and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating the bacterial assembly are poorly understood in salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.},
}

@article {pmid30633563,
year = {2019},
author = {Tomás-Barberán, FA and Espín, JC},
title = {Effect of Food Structure and Processing on (Poly)phenol-Gut Microbiota Interactions and the Effects on Human Health.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-032818-121615},
pmid = {30633563},
issn = {1941-1413},
abstract = {The two-way interaction of food (poly)phenols with the human gut microbiota has been studied throughout the past ten years. Research has shown that this interaction can be relevant to explain the health effects of these phytochemicals. The effect of the food matrix and food processing on this interaction has only been partially studied. In this article, the studies within this field have been critically reviewed, with a special focus on the following groups of phenolic metabolites: citrus flavanones, pomegranate ellagitannins, and cocoa proanthocyanidins. The available research shows that both the food matrix and food processing can be relevant factors for gut microbiota reshaping to reach a healthier microbial ecology and for the conversion of polyphenols to bioactive and bioavailable metabolites. There are, however, some research gaps that indicate a more comprehensive research approach is needed to reach valid conclusions regarding the gut microbiota-mediated effects of polyphenols on human health.},
}

@article {pmid30629579,
year = {2019},
author = {Miranda-CasoLuengo, R and Lu, J and Williams, EJ and Miranda-CasoLuengo, AA and Carrington, SD and Evans, ACO and Meijer, WG},
title = {Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0200974},
doi = {10.1371/journal.pone.0200974},
pmid = {30629579},
issn = {1932-6203},
abstract = {Bacterial overgrowth in the uterus is a normal event after parturition. In contrast to the healthy cow, animals unable to control the infection within 21 days after calving develop postpartum endometritis. Studies on the Microbial Ecology of the bovine reproductive tract have focused on either vaginal or uterine microbiomes. This is the first study that compares both microbiomes in the same animals. Terminal Restriction Fragment Length Polymorphism of the 16S rRNA gene showed that despite large differences associated to individuals, a shared community exist in vagina and uterus during the postpartum period. The largest changes associated with development of endometritis were observed at 7 days postpartum, a time when vaginal and uterine microbiomes were most similar. 16S rRNA pyrosequencing of the vaginal microbiome at 7 days postpartum showed at least three different microbiome types that were associated with later development of postpartum endometritis. All three microbiome types featured reduced bacterial diversity. Taken together, the above findings support a scenario where disruption of the compartmentalization of the reproductive tract during parturition results in the dispersal and mixing of the vaginal and uterine microbiomes, which subsequently are subject to differentiation. This differentiation was observed early postpartum in the healthy cow. In contrast, loss of bacterial diversity and dominance of the microbiome by few bacterial taxa were related to a delayed succession at 7DPP in cows that at 21 DPP or later were diagnosed with endometritis.},
}

@article {pmid30627762,
year = {2019},
author = {Treichel, NS and Prevoršek, Z and Mrak, V and Kostrić, M and Vestergaard, G and Foesel, B and Pfeiffer, S and Stres, B and Schöler, A and Schloter, M},
title = {Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01317-7},
pmid = {30627762},
issn = {1432-184X},
abstract = {The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and β-diversity of the offspring's gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response. The core microbiome transferred from the obese nursing mother showed a higher robustness in comparison to the microbiome transferred from the lean nursing mother. Overall, the nursing mother impacts the gut microbial composition of the offspring during early development and might play an important role for health and disease of the animals at later stages of life.},
}

@article {pmid30627761,
year = {2019},
author = {Fokin, SI and Serra, V and Ferrantini, F and Modeo, L and Petroni, G},
title = {"Candidatus Hafkinia simulans" gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1311-0},
pmid = {30627761},
issn = {1432-184X},
support = {PRA_2018_63//Università di Pisa/ ; },
abstract = {We characterized a novel Holospora-like bacterium (HLB) (Alphaproteobacteria, Holosporales) living in the macronucleus of the brackish water ciliate Frontonia salmastra. This bacterium was morphologically and ultrastructurally investigated, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and performed in situ hybridization experiments with a specifically-designed probe. A new taxon, "Candidatus Hafkinia simulans", was established for this HLB. The phylogeny of the family Holosporaceae based on 16S rRNA gene sequences was inferred, adding to the already available data both the sequence of the novel bacterium and those of other Holospora and HLB species recently characterized. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and placed the new endosymbiont as the sister genus of Holospora. Additionally, the host ciliate F. salmastra, recorded in Europe for the first time, was concurrently described through a multidisciplinary study. Frontonia salmastra's phylogenetic position in the subclass Peniculia and the genus Frontonia was assessed according to 18S rRNA gene sequencing. Comments on the biodiversity of this genus were added according to past and recent literature.},
}

@article {pmid30413475,
year = {2019},
author = {Zerfaß, C and Christie-Oleza, JA and Soyer, OS},
title = {Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {2},
pages = {},
doi = {10.1128/AEM.02129-18},
pmid = {30413475},
issn = {1098-5336},
abstract = {Manganese biomineralization is a widespread process among bacteria and fungi. To date, there is no conclusive experimental evidence for how and if this process impacts microbial fitness in the environment. Here, we show how a model organism for manganese oxidation is growth inhibited by nitrite, and that this inhibition is mitigated in the presence of manganese. We show that such manganese-mediated mitigation of nitrite inhibition is dependent on the culture inoculum size, and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (nontoxic) nitrate under physiological conditions and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e., mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS.IMPORTANCE We present here a direct fitness benefit (i.e., growth advantage) for manganese oxide biomineralization activity in Roseobacter sp. strain AzwK-3b, a model organism used to study this process. We find that strain AzwK-3b in a laboratory culture experiment is growth inhibited by nitrite in manganese-free cultures, while the inhibition is considerably relieved by manganese supplementation and manganese oxide (MnOX) formation. We show that biogenic MnOX interacts directly with nitrite and possibly with reactive oxygen species and find that its beneficial effects are established through formation of dispersed MnOX granules in a manner dependent on the population size. These experiments raise the possibility that manganese biomineralization could confer protection against nitrite toxicity to a population of cells. They open up new avenues of interrogating this process in other species and provide possible routes to their biotechnological applications, including in metal recovery, biomaterials production, and synthetic community engineering.},
}

@article {pmid30625192,
year = {2019},
author = {Ramírez-Fernández, L and Trefault, N and Carú, M and Orlando, J},
title = {Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0209887},
doi = {10.1371/journal.pone.0209887},
pmid = {30625192},
issn = {1932-6203},
abstract = {Seabirds and pinnipeds play an important role in biogeochemical cycling by transferring nutrients from aquatic to terrestrial environments. Indeed, soils rich in animal depositions have generally high organic carbon, nitrogen and phosphorus contents. Several studies have assessed bacterial diversity in Antarctic soils influenced by marine animals; however most have been conducted in areas with significant human impact. Thus, we chose Cape Shirreff, Livingston Island, an Antarctic Specially Protected Area designated mainly to protect the diversity of marine vertebrate fauna, and selected sampling sites with different types of animals coexisting in a relatively small space, and where human presence and impact are negligible. Using 16S rRNA gene analyses through massive sequencing, we assessed the influence of animal concentrations, via their modification of edaphic characteristics, on soil bacterial diversity and composition. The nutrient composition of soils impacted by Antarctic fur seals and kelp gulls was more similar to that of control soils (i.e. soils without visible presence of plants or animals), which may be due to the more active behaviour of these marine animals compared to other species. Conversely, the soils from concentrations of southern elephant seals and penguins showed greater differences in soil nutrients compared to the control. In agreement with this, the bacterial communities of the soils associated with these animals were most different from those of the control soils, with the soils of penguin colonies also possessing the lowest bacterial diversity. However, all the soils influenced by the presence of marine animals were dominated by bacteria belonging to Gammaproteobacteria, particularly those of the genus Rhodanobacter. Therefore, we conclude that the modification of soil nutrient composition by marine vertebrates promotes specific groups of bacteria, which could play an important role in the recycling of nutrients in terrestrial Antarctic ecosystems.},
}

@article {pmid30625112,
year = {2019},
author = {Brooks, LE and Kaze, M and Sistrom, M},
title = {Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges.},
journal = {Microbial genomics},
volume = {},
number = {},
pages = {},
doi = {10.1099/mgen.0.000244},
pmid = {30625112},
issn = {2057-5858},
abstract = {Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.},
}

@article {pmid30625109,
year = {2019},
author = {van der Aart, LT and Nouioui, I and Kloosterman, A and Ingual, JM and Willemse, J and Goodfellow, M and van Wezel, GP},
title = {Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1099/ijsem.0.003215},
pmid = {30625109},
issn = {1466-5034},
abstract = {A polyphasic study was designed to establish the taxonomic status of a Streptomyces strain isolated from soil from the QinLing Mountains, Shaanxi Province, China, and found to be the source of known and new specialized metabolites. Strain MBT76T was found to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. The strain formed a distinct branch in the Streptomyces16S rRNA gene tree and was closely related to the type strains of Streptomyces hiroshimensis and Streptomycesmobaraerensis. Multi-locus sequence analyses based on five conserved house-keeping gene alleles showed that strain MBT76T is closely related to the type strain of S. hiroshimensis, as was the case in analysis of a family of conserved proteins. The organism was also distinguished from S. hiroshimensis using cultural and phenotypic features. Average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain MBT76T and S. hiroshimensis DSM 40037T were 88.96 and 28.4±2.3%, respectively, which is in line with their assignment to different species. On the basis of this wealth of data it is proposed that strain MBT76T (=DSM 106196T=NCCB 100637T), be classified as a new species, Streptomycesroseifaciens sp. nov.},
}

@article {pmid30624643,
year = {2019},
author = {Baldrian, P},
title = {The known and the unknown in soil microbial ecology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz005},
pmid = {30624643},
issn = {1574-6941},
abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.},
}

@article {pmid30623212,
year = {2019},
author = {de Sousa, AGG and Tomasino, MP and Duarte, P and Fernández-Méndez, M and Assmy, P and Ribeiro, H and Surkont, J and Leite, RB and Pereira-Leal, JB and Torgo, L and Magalhães, C},
title = {Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-01314-2},
pmid = {30623212},
issn = {1432-184X},
support = {244646//Research Council of Norway/ ; NORTE-01-0145-FEDER-000031//Structured Program of R&D&I MarInfo/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; NITROLIMIT - PTDC 2017 - PTDC/CTA-AMB/30997/2017//Funda??o para a Ci?ncia e a Tecnologia/ ; },
abstract = {One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.},
}

@article {pmid30620427,
year = {2019},
author = {Pasulka, A and Hu, SK and Countway, PD and Coyne, KJ and Cary, SC and Heidelberg, KB and Caron, DA},
title = {SSU-rRNA Gene Sequencing Survey of Benthic Microbial Eukaryotes from Guaymas Basin Hydrothermal Vent.},
journal = {The Journal of eukaryotic microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeu.12711},
pmid = {30620427},
issn = {1550-7408},
abstract = {Microbial eukaryotes have important roles in marine food webs, but their diversity and activities in hydrothermal vent ecosystems are poorly characterized. In this study, we analyzed microbial eukaryotic communities associated with bacterial (Beggiatoa) mats in the 2,000 m deep-sea Guaymas Basin hydrothermal vent system using 18S rRNA gene high-throughput sequencing of the V4 region. We detected 6,954 distinct Operational Taxonomic Units (OTUs) across various mat systems. Of the sequences that aligned with known protistan phylotypes, most were affiliated with alveolates, especially dinoflagellates and ciliates, and cercozoans. OTU richness and community structure differed among sediment habitats (e.g., different mat types and cold sediments away from mats). Additionally, full-length 18S rRNA genes amplified and cloned from single-cells revealed the identities of some of the most commonly encountered, active ciliates in this hydrothermal vent ecosystem. Observations and experiments were also conducted to demonstrate that ciliates were trophically active and ingesting fluorescent bacteria or Beggiatoa trichomes. Our work suggests that the active and diverse protistan community at the Guaymas Basin hydrothermal vent ecosystem likely consumes substantial amounts of bacterial biomass, and that the different habitats, often defined by distances of just a few 10s of cm, select for particular assemblages and levels of diversity. This article is protected by copyright. All rights reserved.},
}

@article {pmid30619557,
year = {2018},
author = {Duplouy, A and Minard, G and Lähteenaro, M and Rytteri, S and Saastamoinen, M},
title = {Silk properties and overwinter survival in gregarious butterfly larvae.},
journal = {Ecology and evolution},
volume = {8},
number = {24},
pages = {12443-12455},
doi = {10.1002/ece3.4595},
pmid = {30619557},
issn = {2045-7758},
abstract = {All organisms are challenged by encounters with parasites, which strongly select for efficient escape strategies in the host. The threat is especially high for gregarious species entering immobile periods, such as diapause. Larvae of the Glanville fritillary butterfly, Melitaea cinxia, spend the winter in diapause in groups of conspecifics each sheltered in a silk nest. Despite intensive monitoring of the population, we have little understanding of the ecological factors influencing larval survival over the winter in the field. We tested whether qualitative and quantitative properties of the silk nest contribute to larval survival over diapause. We used comparative proteomics, metabarcoding analyses, microscopic imaging, and in vitro experiments to compare protein composition of the silk, community composition of the silk-associated microbiota, and silk density from both wild-collected and laboratory-reared families, which survived or died in the field. Although most traits assessed varied across families, only silk density was correlated with overwinter survival in the field. The silk nest spun by gregarious larvae before the winter acts as an efficient breathable physical shield that positively affects larval survival during diapause. Such benefit may explain how this costly trait is conserved across populations of this butterfly species and potentially across other silk-spinning insect species.},
}

@article {pmid30619545,
year = {2018},
author = {Alessi, AM and Redeker, KR and Chong, JPJ},
title = {A practical introduction to microbial molecular ecology through the use of isolation chips.},
journal = {Ecology and evolution},
volume = {8},
number = {24},
pages = {12286-12298},
doi = {10.1002/ece3.4748},
pmid = {30619545},
issn = {2045-7758},
abstract = {In the context of antimicrobial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a 4 year undergraduate Masters Program, in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness/diversity indices as well as principal coordinate analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.},
}

@article {pmid30619197,
year = {2018},
author = {Dyksma, S and Lenk, S and Sawicka, JE and Mußmann, M},
title = {Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3124},
doi = {10.3389/fmicb.2018.03124},
pmid = {30619197},
issn = {1664-302X},
abstract = {Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with 14C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of 14C-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31-62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover.},
}

@article {pmid30619181,
year = {2018},
author = {Simonin, M and Cantarel, AAM and Crouzet, A and Gervaix, J and Martins, JMF and Richaume, A},
title = {Negative Effects of Copper Oxide Nanoparticles on Carbon and Nitrogen Cycle Microbial Activities in Contrasting Agricultural Soils and in Presence of Plants.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3102},
doi = {10.3389/fmicb.2018.03102},
pmid = {30619181},
issn = {1664-302X},
abstract = {Metal-oxide nanoparticles (NPs) such as copper oxide (CuO) NPs offer promising perspectives for the development of novel agro-chemical formulations of pesticides and fertilizers. However, their potential impact on agro-ecosystem functioning still remains to be investigated. Here, we assessed the impact of CuO-NPs (0.1, 1, and 100 mg/kg dry soil) on soil microbial activities involved in the carbon and nitrogen cycles in five contrasting agricultural soils in a microcosm experiment over 90 days. Additionally, in a pot experiment, we evaluated the influence of plant presence on the toxicity of CuO-NPs on soil microbial activities. CuO-NPs caused significant reductions of the three microbial activities measured (denitrification, nitrification, and soil respiration) at 100 mg/kg dry soil, but the low concentrations (0.1 and 1 mg/kg) had limited effects. We observed that denitrification was the most sensitive microbial activity to CuO-NPs in most soil types, while soil respiration and nitrification were mainly impacted in coarse soils with low organic matter content. Additionally, large decreases in heterotrophic microbial activities were observed in soils planted with wheat, even at 1 mg/kg for soil substrate-induced respiration, indicating that plant presence did not mitigate or compensate CuO-NP toxicity for microorganisms. These two experiments show that CuO-NPs can have detrimental effects on microbial activities in soils with contrasting physicochemical properties and previously exposed to various agricultural practices. Moreover, we observed that the negative effects of CuO-NPs increased over time, indicating that short-term studies (hours, days) may underestimate the risks posed by these contaminants in soils.},
}

@article {pmid30619134,
year = {2018},
author = {Porcar, M and Louie, KB and Kosina, SM and Van Goethem, MW and Bowen, BP and Tanner, K and Northen, TR},
title = {Microbial Ecology on Solar Panels in Berkeley, CA, United States.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3043},
doi = {10.3389/fmicb.2018.03043},
pmid = {30619134},
issn = {1664-302X},
abstract = {Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.},
}

@article {pmid30619117,
year = {2018},
author = {López-García, A and Pineda-Quiroga, C and Atxaerandio, R and Pérez, A and Hernández, I and García-Rodríguez, A and González-Recio, O},
title = {Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3010},
doi = {10.3389/fmicb.2018.03010},
pmid = {30619117},
issn = {1664-302X},
abstract = {Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.},
}

@article {pmid30618066,
year = {2019},
author = {Flores-Uribe, J and Hevroni, G and Ghai, R and Pushkarev, A and Inoue, K and Kandori, H and Béjà, O},
title = {Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12730},
pmid = {30618066},
issn = {1758-2229},
abstract = {Microbial heliorhodopsins are a new type of rhodopsins, currently believed to engage in light sensing, with an opposite membrane topology compared to type-1 and type-2 rhodopsins. We determined heliorhodopsins presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater metagenomes as well as metagenome assembled genome collections. Heliorhodopsins are absent in diderms, confirming our previous observations in cultured Proteobacteria. We do not rule out the possibility that heliorhodopsins serve as light sensors. However, this does not easily explain their absence from diderms. Based on these observations, we speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules. This article is protected by copyright. All rights reserved.},
}

@article {pmid30613848,
year = {2019},
author = {Ye, S and Bhattacharjee, M and Siemann, E},
title = {Thermal Tolerance in Green Hydra: Identifying the Roles of Algal Endosymbionts and Hosts in a Freshwater Holobiont Under Stress.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-01315-1},
pmid = {30613848},
issn = {1432-184X},
abstract = {It has been proposed that holobionts (host-symbiont units) could swap endosymbionts, rapidly alter the hologenome (host plus symbiont genome), and increase their stress tolerance. However, experimental tests of individual and combined contributions of hosts and endosymbionts to holobiont stress tolerance are needed to test this hypothesis. Here, we used six green hydra (Hydra viridissima) strains to tease apart host (hydra) and symbiont (algae) contributions to thermal tolerance. Heat shock experiments with (1) hydra with their original symbionts, (2) aposymbiotic hydra (algae removed), (3) novel associations (a single hydra strain hosting different algae individually), and (4) control hydra (aposymbiotic hydra re-associated with their original algae) showed high variation in thermal tolerance in each group. Relative tolerances of strains were the same within original, aposymbiotic, and control treatments, but reversed in the novel associations group. Aposymbiotic hydra had similar or higher thermal tolerance than hydra with algal symbionts. Selection on the holobiont appears to be stronger than on either partner alone, suggesting endosymbiosis could become an evolutionary trap under climate change. Our results suggest that green hydra thermal tolerance is strongly determined by the host, with a smaller, non-positive role for the algal symbiont. Once temperatures exceed host tolerance limits, swapping symbionts is unlikely to allow these holobionts to persist. Rather, increases in host tolerance through in situ adaptation or migration of pre-adapted host strains appear more likely to increase local thermal tolerance. Overall, our results indicate green hydra is a valuable system for studying aquatic endosymbiosis under changing environmental conditions, and demonstrate how the host and the endosymbiont contribute to holobiont stress tolerance.},
}

@article {pmid30612185,
year = {2019},
author = {Murphy, AE and Kolkmeyer, R and Song, B and Anderson, IC and Bowen, J},
title = {Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-01312-4},
pmid = {30612185},
issn = {1432-184X},
support = {OCE 1062882//National Science Foundation/ ; OCE 1233801//National Science Foundation/ ; LTER 0080381//National Science Foundation/ ; NA10OAR4170085//Virginia Sea Grant, Virginia Institute of Marine Science/ ; },
abstract = {Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.},
}

@article {pmid30612184,
year = {2019},
author = {Pan, J and Chen, Y and Wang, Y and Zhou, Z and Li, M},
title = {Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1309-7},
pmid = {30612184},
issn = {1432-184X},
support = {41506163,31622002,91851105//National Natural Science Foundation of China/ ; 31600093//National Natural Science Foundation of China/ ; },
abstract = {Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.},
}

@article {pmid30612183,
year = {2019},
author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY},
title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-01313-3},
pmid = {30612183},
issn = {1432-184X},
abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.},
}

@article {pmid30612083,
year = {2018},
author = {Zhu, X and Campanaro, S and Treu, L and Kougias, PG and Angelidaki, I},
title = {Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics.},
journal = {Water research},
volume = {151},
number = {},
pages = {271-279},
doi = {10.1016/j.watres.2018.12.041},
pmid = {30612083},
issn = {1879-2448},
abstract = {In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.},
}

@article {pmid30610256,
year = {2019},
author = {Mikhailov, IS and Zakharova, YR and Bukin, YS and Galachyants, YP and Petrova, DP and Sakirko, MV and Likhoshway, YV},
title = {Correction to: Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1307-9},
pmid = {30610256},
issn = {1432-184X},
abstract = {The original version of this article unfortunately contained mistakes in the legends of figures.},
}

@article {pmid30610255,
year = {2019},
author = {Xia, X and Cheung, S and Endo, H and Suzuki, K and Liu, H},
title = {Latitudinal and Vertical Variation of Synechococcus Assemblage Composition Along 170° W Transect From the South Pacific to the Arctic Ocean.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1308-8},
pmid = {30610255},
issn = {1432-184X},
support = {JPMJCR11A5//JST CREST program/ ; 24121004//JSPS Grant-in-Aid for Scientific Research on Innovative Areas/ ; 16128416 and 16101917//Research Grant Council of Hong Kong/ ; },
abstract = {Synechococcus is one of the most widely distributed and abundant picocyanobacteria in the global oceans. Although latitudinal variation of Synechococcus assemblage in marine surface waters has been observed, few studies compared Synechococcus assemblage composition in surface and subsurface waters at the basin scale. Here, we report marine Synechococcus diversity in the surface and deep chlorophyll maximum (DCM) layers along 170° W from the South Pacific to the Arctic Ocean in summer. Along the transect, spatial niche partitioning of Synechococcus lineages in the surface waters was clearly observed. Species richness of surface Synechococcus assemblage was positively correlated with water temperature. Clade CRD1 was dominant in the areas (15° S-10° N and 35-40° N) associated with upwelling, and there were 3 different subclades with distinct distribution. CRD1-A was restricted in the North Equatorial Current (5-10° N), CRD1-B dominated in the equatorial upwelling region (15° S-0.17° N), and CRD1-C was only distributed in the North Pacific Current (35-40° N). Similarities between the Synechococcus assemblages in the surface and DCM layers were high at the upwelling regions and areas where the mixed layer was deep, while low in the Subtropical Gyres with strong stratification. Clade I, CRD1-B, and CRD1-C were major Synechococcus lineages in the DCM layer. In particular, clade I, which is composed of 7 subclades with distinct thermal niches, was widely distributed in the DCM layer. Overall, our results provide new insights into not only the latitudinal distribution of Synechococcus assemblages, but also their vertical variation in the central Pacific.},
}

@article {pmid30610231,
year = {2019},
author = {Andrei, AŞ and Salcher, MM and Mehrshad, M and Rychtecký, P and Znachor, P and Ghai, R},
title = {Niche-directed evolution modulates genome architecture in freshwater Planctomycetes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0332-5},
pmid = {30610231},
issn = {1751-7370},
support = {MSM200961801//Akademie Věd České Republiky (Academy of Sciences of the Czech Republic)/ ; PPPLZ: L200961651//Akademie Věd České Republiky (Academy of Sciences of the Czech Republic)/ ; 17-04828S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 17-04828S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; },
abstract = {Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche).},
}

@article {pmid30607437,
year = {2019},
author = {Lupatini, M and Suleiman, AKA and Jacques, RJS and Lemos, LN and Pylro, VS and Van Veen, JA and Kuramae, EE and Roesch, LFW},
title = {Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1310-1},
pmid = {30607437},
issn = {1432-184X},
abstract = {Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.},
}

@article {pmid30604790,
year = {2019},
author = {De Paepe, K and Verspreet, J and Rezaei, MN and Martinez, SH and Meysman, F and Van de Walle, D and Dewettinck, K and Courtin, CM and Van de Wiele, T},
title = {Modification of wheat bran particle size and tissue composition affects colonisation and metabolism by human faecal microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c8fo01272e},
pmid = {30604790},
issn = {2042-650X},
abstract = {Dietary modulation can alter the gut microbiota composition and activity, in turn affecting health. Particularly, dietary fibre rich foods, such as wheat bran, are an important nutrient source for the gut microbiota. Several processing methods have been developed to modify the functional, textural and breadmaking properties of wheat bran, which can affect the gut microbiota. We therefore studied the effect of enzyme treatment, particle size reduction and wheat kernel pearling on the faecal microbiota of ten healthy individuals. The most commonly studied health marker, associated to the gut microbiota activity is Short Chain Fatty Acid (SCFA) production. This study shows that modifying wheat bran physicochemical properties allows control over the extent and the rate of SCFA production by the faecal microbiota. Wheat bran pericarp fractions, depleted in starch and enriched in cellulose and highly branched arabinoxylans, were poorly fermentable compared to unmodified wheat bran, thus resulting in a reduced SCFA production with up to 20 mM. The nature of the SCFA, however, largely depends on the donor and can be linked to the individual's gut microbiota composition. The latter changed in an individually dependent manner in response to wheat bran modification. Some product dependent significant differences could still be identified across the ten donors. This product effect is more pronounced in the microbial community attached to the wheat bran residue as compared to the luminal microbial community. Generally, we find lower levels of Firmicutes, Bacteroidetes and Bifidobacterium and a higher abundance of Proteobacteria in the pericarp enriched wheat bran fractions, compared to unmodified wheat bran.},
}

@article {pmid30603770,
year = {2019},
author = {Ishizawa, H and Kuroda, M and Inoue, K and Inoue, D and Morikawa, M and Ike, M},
title = {Colonization and Competition Dynamics of Plant Growth-Promoting/Inhibiting Bacteria in the Phytosphere of the Duckweed Lemna minor.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1306-x},
pmid = {30603770},
issn = {1432-184X},
support = {JPJMAL1108//Advanced Low Carbon Technology Research and Development Program/ ; JP18J10181//Japan Society for the Promotion of Science/ ; },
abstract = {Despite the considerable role of aquatic plant-associated bacteria in host plant growth and nutrient cycling in aquatic environments, the mode of their plant colonization has hardly been understood. This study examined the colonization and competition dynamics of a plant growth-promoting bacterium (PGPB) and two plant growth-inhibiting bacteria (PGIB) in the aquatic plant Lemna minor (common duckweed). When inoculated separately to L. minor, each bacterial strain quickly colonized at approximately 106 cells per milligram (plant fresh weight) and kept similar populations throughout the 7-day cultivation time. The results of two-membered co-inoculation assays revealed that the PGPB strain Aquitalea magnusonii H3 consistently competitively excluded the PGIB strain Acinetobacter ursingii M3, and strain H3 co-existed at almost 1:1 proportion with another PGIB strain, Asticcacaulis excentricus M6, regardless of the inoculation ratios (99:1-1:99) and inoculation order. We also found that A. magnusonii H3 exerted its growth-promoting effect over the negative effects of the two PGIB strains even when only a small amount was inoculated, probably due to its excellent competitive colonization ability. These experimental results demonstrate that there is a constant ecological equilibrium state involved in the bacterial colonization of aquatic plants.},
}

@article {pmid30603713,
year = {2018},
author = {Nakato, GV and Wicker, E and Coutinho, TA and Mahuku, G and Studholme, DJ},
title = {A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences.},
journal = {Heliyon},
volume = {4},
number = {12},
pages = {e01080},
doi = {10.1016/j.heliyon.2018.e01080},
pmid = {30603713},
issn = {2405-8440},
abstract = {Xanthomonas vasicola pv. musacearum (Xvm) is a bacterial pathogen responsible for the economically important Xanthomonas wilt disease on banana and enset crops in Sub-Saharan Africa. Given that the symptoms are similar to those of other diseases, molecular diagnosis is essential to unambiguously identify this pathogen and distinguish it from closely related strains not pathogenic on these hosts. Currently, Xvm identification is based on polymerase chain reaction (PCR) with GspDm primers, targeting the gene encoding general secretory protein D. Experimental results and examination of genomic sequences revealed poor specificity of the GspDm PCR. Here, we present and validate five new Xvm-specific primers amplifying only Xvm strains.},
}

@article {pmid30602074,
year = {2016},
author = {Nemchenko, UM and Rakova, EB and Savelkaieva, MV and Serdiuk, LV and Ivanova, EI and Shabanova, NM and Bukharova, EV},
title = {[The complex evaluation of condition of intestinal and nasopharyngeal microbiocenosis in alumni of children's home].},
journal = {Klinicheskaia laboratornaia diagnostika},
volume = {61},
number = {8},
pages = {508-512},
pmid = {30602074},
issn = {0869-2084},
abstract = {The examination of nasopharyngeal and intestinal microbiocenoses was implemented in orphan children aged 1-3 years residing in children;s home of Cheremkhovo of the Irkutskaia oblast. All children had compromised anamnesis: prematurity, hypotrophy, chicken pox, frequent acute respiratory viral infections, intestinal infections, atopic dermatitis. The study was carried out to comprehensively evaluate conditions of intestinal and nasopharyngeal biotops in children residing in closed children’s institution - children’s home. The microbiological analysis of qualitative and quantitative composition of content of intestine and nasopharynx was implemented according standard techniques. The analysis established in 81.2±6.90% of examined children deficiency of Bifidobacterium flora, decreasing of level of population density of bifidobacteria up to 6.9±1.53% lg KOE/g, in 31.2±8.1% - deficiency of normal colibacillus, in 78.1±7.3% - increased level of opportunistic flora. The analysis also established high rate of isolation of Escherichia coli with decreased enzyme activity and in 28.1±7.9% - Escherichia coli with hemolytic activity. The enterococci were permanent participants of nasopharyngeal and intestinal biotop (58.6±8.7%). From opportunistic flora, in nasopharynx were registered pathogenic streptococci - S.pyogenes, S.pneumonia and also pathogenic fungi Candida andpoly-resistant strains S. aureus. The study results demonstrated characteristics of microbial ecology of intestinal and nasopharyngeal biotops of orphan children in conditions of children institution of closed type where the circulation of pathogenic and opportunistic microorganisms occurs intensively, including strains with high medicinal resistance. All this determines necessity to attribute alumni of children’s homes to risk group of infectious pathology and requires constant micro-ecological monitoring for timely correction of microbiocenoses.},
}

@article {pmid30602082,
year = {2018},
author = {Jeon, SJ and Galvão, KN},
title = {An Advanced Understanding of Uterine Microbial Ecology Associated with Metritis in Dairy Cows.},
journal = {Genomics & informatics},
volume = {16},
number = {4},
pages = {e21},
doi = {10.5808/GI.2018.16.4.e21},
pmid = {30602082},
issn = {1598-866X},
abstract = {Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although the antibiotic ceftiofur is widely used for the treatment of metritis, endometrium and ovary function is compromised, resulting in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica. Recent studies using high-throughput sequencing claimed that metritis is a microbiota-associated disease. Herein, we propose that metritis is associated with uterine microbiota with high abundance of Bacteroides, Porphyromonas, and Fusobacterium, but rare bacteria such as Escherichia coli and Helcococcus ovis cannot be ignored.},
}

@article {pmid30599206,
year = {2018},
author = {Zwaenepoel, A and Li, Z and Lohaus, R and Van de Peer, Y},
title = {Finding evidence for whole genome duplications: a reappraisal.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2018.12.019},
pmid = {30599206},
issn = {1752-9867},
}

@article {pmid30598728,
year = {2019},
author = {Rafeek, R and Carrington, CVF and Gomez, A and Harkins, D and Torralba, M and Kuelbs, C and Addae, J and Moustafa, A and Nelson, KE},
title = {Xylitol and sorbitol effects on the microbiome of saliva and plaque.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1536181},
doi = {10.1080/20002297.2018.1536181},
pmid = {30598728},
issn = {2000-2297},
abstract = {Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and plaque following short-term consumption of xylitol and sorbitol containing chewing gum. Participants (n = 30) underwent a washout period and were randomly assigned to one of two groups. Each group chewed either xylitol or sorbitol gum for three weeks, before undergoing a second four-week washout period after which they switched to the alternate gum for three weeks. Analysis of samples collected before and after each intervention identified distinct plaque and saliva microbial communities that altered dependent on the order in which gum treatments were given. Neither the xylitol nor sorbitol treatments significantly affected the bacterial composition of plaque. Lactobacilli were undetected and the number of Streptococcus mutans sequence reads was very low and unaffected by either xylitol or sorbitol. However, sorbitol affected several other streptococcal species in saliva including increasing the abundance of S. cristatus, an oral commensal shown to inhibit bacteria associated with chronic periodontitis.},
}

@article {pmid30595029,
year = {2018},
author = {Tian, L and Tan, Y and Chen, G and Wang, G and Sun, J and Ou, S and Chen, W and Bai, W},
title = {Metabolism of anthocyanins and consequent effects on the gut microbiota.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/10408398.2018.1533517},
pmid = {30595029},
issn = {1549-7852},
abstract = {Anthocyanins are natural water-soluble polyphenols present in fruits and vegetables. Health-promoting effects attributed to anthocyanins are mainly associated with oxidative stress inhibition and gut microbiota modulation. Dietary anthocyanins undergo a complex metabolism after ingestion and interact with endogenous and microbial enzymes, leading to the production of a large number of circulating and excreted anthocyanin metabolites and catabolic products. To date, the bioavailability and health benefits of anthocyanins have been widely documented. Although there are several papers that illustrated the metabolism of anthocyanins, the effects of dietary anthocyanins on the modulation of the gut microbial ecology and on the growth of certain microbial species are still poorly understood. The present paper summarizes the recent data on the absorption of anthocyanins in the upper gastrointestine and the metabolism of anthocyanins by gut microbiota. The modulatory effects of anthocyanins from different sources on gut microbiota are also discussed.},
}

@article {pmid30594092,
year = {2018},
author = {Garner, E and Inyang, M and Garvey, E and Parks, J and Glover, C and Grimaldi, A and Dickenson, E and Sutherland, J and Salveson, A and Edwards, MA and Pruden, A},
title = {Impact of blending for direct potable reuse on premise plumbing microbial ecology and regrowth of opportunistic pathogens and antibiotic resistant bacteria.},
journal = {Water research},
volume = {151},
number = {},
pages = {75-86},
doi = {10.1016/j.watres.2018.12.003},
pmid = {30594092},
issn = {1879-2448},
abstract = {Little is known about how introducing recycled water intended for direct potable reuse (DPR) into distribution systems and premise plumbing will affect water quality at the point of use, particularly with respect to effects on microbial communities and regrowth. The examination of potential growth of opportunistic pathogens (OPs) and spread of antibiotic resistance genes (ARGs), each representing serious and growing public health concerns, by introducing DPR water has not previously been evaluated. In this study, the impact of blending purified DPR water with traditional drinking water sources was investigated with respect to treatment techniques, blending location, and blending ratio. Water from four U.S. utility partners was treated in bench- and pilot-scale treatment trains to simulate DPR with blending. Water was incubated in simulated premise plumbing rigs made of PVC pipe containing brass coupons to measure regrowth of total bacteria (16S rRNA genes, heterotrophic plate count), OPs (Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa), ARGs (qnrA, vanA), and an indicator of horizontal gene transfer and multi-drug resistance (intI1). The microbial community composition was profiled and the resistome (i.e., all ARGs present) was characterized in select samples using next generation sequencing. While regrowth of total bacteria (16S rRNA genes) from the start of the incubation through week eight consistently occurred across tested scenarios (Wilcoxon, p ≤ 0.0001), total bacteria were not more abundant in the water or biofilm of any DPR scenario than in the corresponding conventional potable condition (p ≥ 0.0748). Regrowth of OP marker genes, qnrA, vanA, and intI1 were not significantly greater in water or biofilm for any DPR blends treated with advanced oxidation compared to corresponding potable water (p ≥ 0.1047). This study of initial bacteria colonizing pipes after introduction of blended DPR water revealed little evidence (i.e., one target in one water type) of exacerbated regrowth of total bacteria, OPs, or ARGs in premise plumbing.},
}

@article {pmid30593603,
year = {2018},
author = {Bachran, M and Kluge, S and Lopez-Fernandez, M and Cherkouk, A},
title = {Microbial Diversity in an Arid, Naturally Saline Environment.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1301-2},
pmid = {30593603},
issn = {1432-184X},
abstract = {The Arava Valley in is a rock desert within the Great African Rift valley. Soil from this area is covered with a salt crust. Here, we report microbial diversity from arid, naturally saline samples collected near Ein Yahav from the Arava Valley by culture-independent as well as culture-dependent analysis. High-throughput sequencing of the hypervariable region V4 of the 16S rRNA gene revealed that the microbial community consists of halophiles from the domain Bacteria as well as Archaea. Bacterial diversity was mainly represented by the genus Salinimicrobium of the order Flavobacteriales within the phylum Bacteroidetes, from the gammaproteobacterial orders Alteromonadales and Oceanospirillales as well as representatives from the order Bacillales of the phylum Firmicutes. Archaeal diversity was dominated by euryarchaeal Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales. But more than 40% of the sequences affiliated with Archaea were assigned to unknown or unclassified archaea. Even if taxonomic resolution of the 16S rRNA gene V4 region for Archaea is limited, this study indicates the need of further and more detailed studies of Archaea. By using culture-dependent analysis, bacteria of the order Bacillales as well as archaea from all three halobacterial orders Halobacteriales, Haloferacales, and Natrialbales including potentially novel species from the genera Halorubrum and Haloparvum were isolated.},
}

@article {pmid30593565,
year = {2018},
author = {Vallespir Lowery, N and Ursell, T},
title = {Structured environments fundamentally alter dynamics and stability of ecological communities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1811887116},
pmid = {30593565},
issn = {1091-6490},
abstract = {The dynamics and stability of ecological communities are intimately linked with the specific interactions-like cooperation or predation-between constituent species. In microbial communities, like those found in soils or the mammalian gut, physical anisotropies produced by fluid flow and chemical gradients impact community structure and ecological dynamics, even in structurally isotropic environments. Although natural communities existing in physically unstructured environments are rare, the role of environmental structure in determining community dynamics and stability remains poorly studied. To address this gap, we used modified Lotka-Volterra simulations of competitive microbial communities to characterize the effects of surface structure on community dynamics. We find that environmental structure has profound effects on communities, in a manner dependent on the specific pattern of interactions between community members. For two mutually competing species, eventual extinction of one competitor is effectively guaranteed in isotropic environments. However, addition of environmental structure enables long-term coexistence of both species via local "pinning" of competition interfaces, even when one species has a significant competitive advantage. In contrast, while three species competing in an intransitive loop (as in a game of rock-paper-scissors) coexist stably in isotropic environments, structural anisotropy disrupts the spatial patterns on which coexistence depends, causing chaotic population fluctuations and subsequent extinction cascades. These results indicate that the stability of microbial communities strongly depends on the structural environment in which they reside. Therefore, a more complete ecological understanding, including effective manipulation and interventions in natural communities of interest, must account for the physical structure of the environment.},
}

@article {pmid30586832,
year = {2019},
author = {Yang, S and Zheng, Q and Yuan, M and Shi, Z and Chiariello, NR and Docherty, KM and Dong, S and Field, CB and Gu, Y and Gutknecht, J and Hungate, BA and Le Roux, X and Ma, X and Niboyet, A and Yuan, T and Zhou, J and Yang, Y},
title = {Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials.},
journal = {The Science of the total environment},
volume = {652},
number = {},
pages = {1474-1481},
doi = {10.1016/j.scitotenv.2018.10.353},
pmid = {30586832},
issn = {1879-1026},
abstract = {The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.},
}

@article {pmid30585386,
year = {2018},
author = {Cholet, F and Ijaz, UZ and Smith, CJ},
title = {Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14516},
pmid = {30585386},
issn = {1462-2920},
abstract = {Reliability and reproducibility of transcriptomics-based studies are dependent on RNA integrity. In microbial ecology, microfluidics-based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here we present an integrity index, the Ratio Amplicon, Ramp , adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly-degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT-Q-PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study. This article is protected by copyright. All rights reserved.},
}

@article {pmid30581429,
year = {2018},
author = {Brenzinger, K and Drost, SM and Korthals, G and Bodelier, PLE},
title = {Organic Residue Amendments to Modulate Greenhouse Gas Emissions From Agricultural Soils.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3035},
doi = {10.3389/fmicb.2018.03035},
pmid = {30581429},
issn = {1664-302X},
abstract = {Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH4 oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO2 and N2O differed considerably between the treatments, CH4 fluxes remained stable. In contrast, in vitro CH4 oxidation showed a clear increase for all amendments over time. CO2 fluxes were mostly dependent on the amount of organic residue that was used, while N2O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO2, CH4, and/or N2O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.},
}

@article {pmid30580396,
year = {2019},
author = {Williams, MR and Hashsham, SA},
title = {Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1918},
number = {},
pages = {21-33},
doi = {10.1007/978-1-4939-9000-9_2},
pmid = {30580396},
issn = {1940-6029},
abstract = {The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.},
}

@article {pmid30579209,
year = {2018},
author = {Bains, W and Petkowski, JJ and Sousa-Silva, C and Seager, S},
title = {New environmental model for thermodynamic ecology of biological phosphine production.},
journal = {The Science of the total environment},
volume = {658},
number = {},
pages = {521-536},
doi = {10.1016/j.scitotenv.2018.12.086},
pmid = {30579209},
issn = {1879-1026},
abstract = {We present a new model for the biological production of phosphine (PH3). Phosphine is found globally, in trace amounts, in the Earth's atmosphere. It has been suggested as a key molecule in the phosphorus cycle, linking atmospheric, lithospheric and biological phosphorus chemistry. Phosphine's production is strongly associated with marshes, swamps and other sites of anaerobic biology. However the mechanism of phosphine's biological production has remained controversial, because it has been believed that reduction of phosphate to phosphine is endergonic. In this paper we show through thermodynamic calculations that, in specific environments, the combined action of phosphate reducing and phosphite disproportionating bacteria can produce phosphine. Phosphate-reducing bacteria can capture energy from the reduction of phosphate to phosphite through coupling phosphate reduction to NADH oxidation. Our hypothesis describes how the phosphate chemistry in an environmental niche is coupled to phosphite generation in ground water, which in turn is coupled to the phosphine production in water and atmosphere, driven by a specific microbial ecology. Our hypothesis provides clear predictions on specific complex environments where biological phosphine production could be widespread. We propose tests of our hypothesis in fieldwork.},
}

@article {pmid30577137,
year = {2018},
author = {Abreu-Junior, CH and de Lima Brossi, MJ and Monteiro, RT and Cardoso, PHS and da Silva Mandu, T and Nogueira, TAR and Ganga, A and Filzmoser, P and de Oliveira, FC and Firme, LP and He, Z and Capra, GF},
title = {Effects of sewage sludge application on unfertile tropical soils evaluated by multiple approaches: A field experiment in a commercial Eucalyptus plantation.},
journal = {The Science of the total environment},
volume = {655},
number = {},
pages = {1457-1467},
doi = {10.1016/j.scitotenv.2018.11.334},
pmid = {30577137},
issn = {1879-1026},
abstract = {Sewage sludge (SS) reuse in forest plantation as soil fertilizer/amendment has tremendously increased in recent years. However, SS may have high concentrations of potentially toxic elements (PTE), representing a potential risk for soil and the whole ecosystem. This paper was aimed to assess the toxicity of PTE in unfertile tropical soils amended with SS in a commercial Eucalyptus plantation, with an integrated multiple approaches combining: i) the use of a battery of bioassays (Daphnia magna, Pseudokcrichirella subcapitata, Lactuca sativa, and Allium cepa); and ii) the evaluation of some PTE (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) and their availability into the pedoenvironment. Differences in total and available PTE between SS doses and time of treatments were evaluated using ANOVA; correlations between PTE and bioassays by a sparse partial robust M-regression (SPRM), while multiple correlations among parameters were performed by principal factor analysis (PFA). Results show that PTE contents in soils tended to increase with SS application doses. However this cannot be assumed as a general rule since in all the investigated treatments the PTE concentrations were consistently below both soil natural background concentrations and quality reference values. Bioassays showed a generalized low eco- and genotoxicity of SS with an increase in toxicity at increasing SS doses but with a clear decreasing trend as time went by. A. cepa was the most sensitive bioassay followed by P. subcapitata > D. magna > L. sativa. Overall, the results indicate that in realistic open field conditions SS risk may be lower than expected due to dynamic decrease in PTE toxicity with time after application. This study has an important implication that open-field trials should be strongly encouraged for evaluating environmental risk of SS application in forestry.},
}

@article {pmid30577127,
year = {2018},
author = {Wang, D and Li, T and Huang, K and He, X and Zhang, XX},
title = {Roles and correlations of functional bacteria and genes in the start-up of simultaneous anammox and denitrification system for enhanced nitrogen removal.},
journal = {The Science of the total environment},
volume = {655},
number = {},
pages = {1355-1363},
doi = {10.1016/j.scitotenv.2018.11.321},
pmid = {30577127},
issn = {1879-1026},
abstract = {Simultaneous anammox and denitrification (SAD) is a newly developed wastewater treatment process efficient in nitrogen removal, but its underlying microbiological mechanisms during start-up remains unknown. This study investigated the changing patterns of functional bacteria and genes, as well as their correlation during the start-up (260 d) of the SAD systems in two lab-scale up-flow anaerobic sludge blanket bioreactors separately inoculated with anaerobic granular sludge (R1) and aerobic floccular sludge (R2). Results showed that high total nitrogen removal was achieved in the SAD systems of both R1 (88.25%) and R2 (89.42%). High-throughput sequencing of 16S rRNA gene amplicons revealed that Armatimonadetes phylum had a high abundance (44.34%) in R2, while was not detectable in R1 during the anammox stage. However, the SAD bioreactors retained inherent microbial community and the inoculation with different sludge showed less notable effects on their microbial composition. In the SAD systems, Candidatus Brocadia had high abundance in R1 (2.93%) and R2 (4.64%) and played important role in anammox. Network analysis indicated that Denitratisoma and Dokdonella were positively correlated with nitrite reductase genes nirS and nirK (p < 0.05), while Thermomonas and Pseudomonas showing a positive correlation with nitrate reductase gene narG (p < 0.05) were mainly responsible for the nitrate reduction in the SAD systems. Moreover, the overwhelming dominance of narG v.s. napA revealed the crucial roles of respiratory nitrate reduction in the bioreactors. The results extend our knowledge regarding the microbial ecology of the SAD system, which might be practically helpful for application of the process in wastewater treatment.},
}

@article {pmid30574650,
year = {2018},
author = {Weiss, R and Palatinszky, M and Wagner, M and Niessner, R and Elsner, M and Seidel, M and Ivleva, NP},
title = {Surface-enhanced Raman spectroscopy of microorganisms: limitations and applicability on the single-cell level.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/c8an02177e},
pmid = {30574650},
issn = {1364-5528},
abstract = {Detection and characterization of microorganisms is essential for both clinical diagnostics and environmental studies. An emerging technique to analyse microbes at single-cell resolution is surface-enhanced Raman spectroscopy (surface-enhanced Raman scattering: SERS). Optimised SERS procedures enable fast analytical read-outs with specific molecular information, providing insight into the chemical composition of microbiological samples. Knowledge about the origin of microbial SERS signals and parameter(s) affecting their occurrence, intensity and/or reproducibility is crucial for reliable SERS-based analyses. In this work, we explore the feasibility and limitations of the SERS approach for characterizing microbial cells and investigate the applicability of SERS for single-cell sorting as well as for three-dimensional visualization of microbial communities. Analyses of six different microbial species (an archaeon, two Gram-positive bacteria, three Gram-negative bacteria) showed that for several of these organisms distinct features in their SERS spectra were lacking. As additional confounding factor, the physiological conditions of the cells (as influenced by e.g., storage conditions or deuterium-labelling) were systematically addressed, for which we conclude that the respective SERS signal at the single-cell level is strongly influenced by the metabolic activity of the analysed cells. While this finding complicates the interpretation of SERS data, it may on the other hand enable probing of the metabolic state of individual cells within microbial populations of interest.},
}

@article {pmid30574135,
year = {2018},
author = {Vander Roost, J and Daae, FL and Steen, IH and Thorseth, IH and Dahle, H},
title = {Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3008},
doi = {10.3389/fmicb.2018.03008},
pmid = {30574135},
issn = {1664-302X},
abstract = {Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.},
}

@article {pmid30572962,
year = {2018},
author = {Du Preez, S and Corbitt, M and Cabanas, H and Eaton, N and Staines, D and Marshall-Gradisnik, S},
title = {A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis.},
journal = {Systematic reviews},
volume = {7},
number = {1},
pages = {241},
doi = {10.1186/s13643-018-0909-0},
pmid = {30572962},
issn = {2046-4053},
abstract = {BACKGROUND: Chronic fatigue syndrome or myalgic encephalomyelitis (CFS/ME) is an illness characterised by profound and pervasive fatigue in addition to a heterogeneous constellation of symptoms. The aetiology of this condition remains unknown; however, it has been previously suggested that enteric dysbiosis is implicated in the pathogenesis of CFS/ME. This review examines the evidence currently available for the presence of abnormal microbial ecology in CFS/ME in comparison to healthy controls, with one exception being probiotic-supplemented CFS/ME patients, and whether the composition of the microbiome plays a role in symptom causation.

METHODS: EMBASE, Medline (via EBSCOhost), Pubmed and Scopus were systematically searched from 1994 to March 2018. All studies that investigated the gut microbiome composition of CFS/ME patients were initially included prior to the application of specific exclusion criteria. The association between these findings and patient-centred outcomes (fatigue, quality of life, gastrointestinal symptoms, psychological wellbeing) are also reported.

RESULTS: Seven studies that met the inclusion criteria were included in the review. The microbiome composition of CFS/ME patients was compared with healthy controls, with the exception of one study that compared to probiotic-supplemented CFS/ME patients. Differences were reported in each study; however, only three were considered statistically significant, and the findings across all studies were inconsistent. The quality of the studies included in this review scored between poor (< 54%), fair (54-72%) and good (94-100%) using the Downs and Black checklist.

CONCLUSIONS: There is currently insufficient evidence for enteric dysbiosis playing a significant role in the pathomechanism of CFS/ME. Recommendations for future research in this field include the use of consistent criteria for the diagnosis of CFS/ME, reduction of confounding variables by controlling factors that influence microbiome composition prior to sample collection and including more severe cases of CFS/ME.},
}

@article {pmid30568671,
year = {2018},
author = {Bardin, M and Leyronas, C and Troulet, C and Morris, CE},
title = {Striking Similarities Between Botrytis cinerea From Non-agricultural and From Agricultural Habitats.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1820},
doi = {10.3389/fpls.2018.01820},
pmid = {30568671},
issn = {1664-462X},
abstract = {Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.},
}

@article {pmid30565880,
year = {2018},
author = {Thorn, CE and Bergesch, C and Joyce, A and Sambrano, G and McDonnell, K and Brennan, F and Heyer, R and Benndorf, D and Abram, F},
title = {A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes, and pure cultures.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12979},
pmid = {30565880},
issn = {1755-0998},
abstract = {The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the sub-millimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules i.e. nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5 to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures. This article is protected by copyright. All rights reserved.},
}

@article {pmid30565684,
year = {2018},
author = {Wang, JC and Bergeron, M and Andersen, H and Tikhtman, R and Haslam, D and Hunter, T and Herr, AB and de Alarcon, A},
title = {Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.27356},
pmid = {30565684},
issn = {1531-4995},
abstract = {OBJECTIVE: Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs.

METHODS: Four TTs were collected from pediatric patients (1.4-10.2 years) with (n = 2) and without (n = 2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA.

RESULTS: Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome.

CONCLUSION: This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs.

LEVEL OF EVIDENCE: 2c. Laryngoscope, 2018.},
}

@article {pmid30565024,
year = {2018},
author = {Lee, JC and Song, JS and Whang, KS},
title = {Sphingobium pinisoli sp. nov., isolated from the rhizosphere soil of a Korean native pine tree.},
journal = {Antonie van Leeuwenhoek},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10482-018-01215-x},
pmid = {30565024},
issn = {1572-9699},
support = {PJ01287601//Department of Agriculture and Rural Development/ ; },
abstract = {A Gram-stain negative, aromatic compound degrading bacterium, designated strain ASA28T, was isolated from the rhizosphere soil of a pine tree at Anmyon island, Taean in Korea. Strain ASA28T was found to be strictly aerobic, non-motile, short rods which can grow at 15-28 °C (optimum, 25-28 °C), at pH 5.0-11.0 (optimum, pH 7.0) and at salinities of 0-1.0% (w/v) NaCl (optimum, 0% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain ASA28T belongs to the genus Sphingobium, showing high sequence similarity to Sphingobium scionense WP01T (97.8%), Sphingobium vermicocomposti VC-230T (96.8%), Sphingobium yanoikuyae ATCC 51230T (96.5%) and Sphingobium herbicidovorans MHT (95.6%). The predominant ubiquinone and polyamine components were identified as Q-10 and spermidine, respectively. The major fatty acids were identified as C18:1ω7c, C16:0, C14:0 2-OH and C16:1ω7c and/or C15:0 iso 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, phosphoglycolipid, four unidentified aminophospholipids, an unidentified aminolipid, two unidentified phospholipids and six unidentified lipids. The DNA G+C content of this novel isolate was determined to be 63.0 mol%. DNA-DNA relatedness between strain ASA28T and S. herbicidovorans KCTC 2939T, S. vermicocomposti DSM 21299T and S. scionense DSM 19371T was determined to be 32 ± 5%, 30 ± 4% and 25 ± 5%, respectively. On the basis of the phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain ASA28T is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium pinisoli sp. nov. is proposed. The type strain is ASA28T (= KACC 18700T = NBRC 112246T).},
}

@article {pmid30564217,
year = {2018},
author = {Ramírez, GA and Jørgensen, SL and Zhao, R and D'Hondt, S},
title = {Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2969},
doi = {10.3389/fmicb.2018.02969},
pmid = {30564217},
issn = {1664-302X},
abstract = {Extracellular DNA has been reported to comprise a large fraction of total DNA in near-seafloor sediment. However, the potential effect of extracellular DNA, arising from dead or moribund cells, on sequencing surveys is a critical concern that has largely not been addressed for marine sedimentary habitats. To address this concern, we interrogated freshly collected Arctic and Pacific sediment for extracellular 16S rRNA genes using the photoactive DNA-binding dye Propidium Monoazide. Significant differences between relative abundances of total (intracellular + extracellular) Bacterial 16S rRNA genes and relative abundances of intracellular Bacterial 16S rRNA genes are only detected in three of twelve shallow [10 cm below seafloor (cmbsf)] samples. Relative abundances of total Bacterial 16S rRNA genes are statistically indistinguishable from relative abundances of intracellular Bacterial 16S rRNA genes in all interrogated samples from depths greater than 10 cmbsf. 16S rRNA gene sequencing shows that even where significantly higher abundances of extracellular genes are detected, they have little or no influence on prokaryote community composition. Taxon-level analyses suggest that extracellular DNA, arising from in situ death, may be sourced from different organisms in sediment of different ages. However, the overall effect of extracellular genes on sequencing surveys of marine sedimentary prokaryotes is minimal.},
}

@article {pmid30564202,
year = {2018},
author = {Too, CC and Keller, A and Sickel, W and Lee, SM and Yule, CM},
title = {Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2859},
doi = {10.3389/fmicb.2018.02859},
pmid = {30564202},
issn = {1664-302X},
abstract = {Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.},
}

@article {pmid30562060,
year = {2018},
author = {Arora, T and Rudenko, O and Egerod, KL and Husted, AS and Kovatcheva-Datchary, P and Akrami, R and Kristensen, M and Schwartz, TW and Bäckhed, F},
title = {Microbial fermentation of flaxseed fibers modulates the transcriptome of GPR41-expressing enteroendocrine cells and protects mice against diet-induced obesity.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00391.2018},
pmid = {30562060},
issn = {1522-1555},
abstract = {Dietary fibers, an integral part of the human diet, require the enzymatic activity of the gut microbiota for complete metabolism into short chain fatty acids (SCFAs). SCFAs are important modulators of host metabolism and physiology and act in part as signaling molecules by activating G-protein coupled receptors (GPR) such as GPR41. Flaxseed fibers improve metabolism in rodents and mice, but their fermentation profiles, effects on enteroendocrine cells and associated metabolic benefits are unknown. We fed GPR41-RFP mice, an enteroendocrine reporter mouse strain, chow, high fat diet (HFD) or HFD supplemented either with 10% non-fermentable fiber cellulose or fermentable flaxseed fibers for 12 weeks to assess changes in cecal gut microbiota, enteroendocrine cell transcriptome in ileum and colon, and physiological parameters. We observed that flaxseed fibers restructured the gut microbiota and promoted proliferation of the genera Bifidobacterium and Akkermansia compared with HFD. The shifts in cecal bacterial composition restored levels of the SCFAs butyrate similar to the chow diet, resulting in colonic, but not ileal, enteroendocrine cell transcriptional changes in genes related to cell cycle, mRNA and protein transport compared with HFD. Consistent with effects on enteroendocrine functions, flaxseed fibers also protected mice from diet-induced obesity, potentially by preventing reduction in energy expenditure induced by HFD. Our study shows that flaxseed fibers alter cecal microbial ecology, are fermented to SCFAs in cecum, and modulate enteroendocrine cell transcriptome in colon, which may contribute to their metabolically favorable phenotype.},
}

@article {pmid30559748,
year = {2018},
author = {Guyonnet, JP and Guillemet, M and Dubost, A and Simon, L and Ortet, P and Barakat, M and Heulin, T and Achouak, W and Haichar, FEZ},
title = {Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1662},
doi = {10.3389/fpls.2018.01662},
pmid = {30559748},
issn = {1664-462X},
abstract = {Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.},
}

@article {pmid30403856,
year = {2018},
author = {Calatayud, M and Xiong, C and Du Laing, G and Raber, G and Francesconi, K and van de Wiele, T},
title = {Salivary and Gut Microbiomes Play a Significant Role in in Vitro Oral Bioaccessibility, Biotransformation, and Intestinal Absorption of Arsenic from Food.},
journal = {Environmental science & technology},
volume = {52},
number = {24},
pages = {14422-14435},
doi = {10.1021/acs.est.8b04457},
pmid = {30403856},
issn = {1520-5851},
abstract = {The release of a toxicant from a food matrix during the gastrointestinal digestion is a crucial determinant of the toxicant's oral bioavailability. We present a modified setup of the human simulator of the gut microbial ecosystem (SHIME), with four sequential gastrointestinal reactors (oral, stomach, small intestine, and colon), including the salivary and colonic microbiomes. Naturally arsenic-containing rice, mussels, and nori seaweed were digested in the presence of microorganisms and in vitro oral bioaccessibility, bioavailability, and metabolism of arsenic species were evaluated following analysis by using HPLC/mass spectrometry. When food matrices were digested with salivary bacteria, the soluble arsenic in the gastric digestion stage increased for mussel and nori samples, but no coincidence impact was found in the small intestinal and colonic digestion stages. However, the simulated small intestinal absorption of arsenic was increased in all food matrices (1.2-2.7 fold higher) following digestion with salivary microorganisms. No significant transformation of the arsenic species occurred except for the arsenosugars present in mussels and nori. In those samples, conversions between the oxo arsenosugars were observed in the small intestinal digestion stage whereupon the thioxo analogs became major metabolites. These results expand our knowledge on the likely metabolism and oral bioavailabiltiy of arsenic during human digestion, and provide valuable information for future risk assessments of dietary arsenic.},
}

@article {pmid30555445,
year = {2018},
author = {Ilgrande, C and Leroy, B and Wattiez, R and Vlaeminck, SE and Boon, N and Clauwaert, P},
title = {Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2914},
doi = {10.3389/fmicb.2018.02914},
pmid = {30555445},
issn = {1664-302X},
abstract = {Typically, nitrification is a two-stage microbial process and is key in wastewater treatment and nutrient recovery from waste streams. Changes in salinity represent a major stress factor that can trigger response mechanisms, impacting the activity and the physiology of bacteria. Despite its pivotal biotechnological role, little information is available on the specific response of nitrifying bacteria to varying levels of salinity. In this study, synthetic communities of ammonia-oxidizing bacteria (AOB Nitrosomonas europaea and/or Nitrosomonas ureae) and nitrite-oxidizing bacteria (NOB Nitrobacter winogradskyi and/or Nitrobacter vulgaris) were tested at 5, 10, and 30 mS cm-1 by adding sodium chloride to the mineral medium (0, 40, and 200 mM NaCl, respectively). Ammonia oxidation activity was less affected by salinity than nitrite oxidation. AOB, on their own or in combination with NOB, showed no significant difference in the ammonia oxidation rate among the three conditions. However, N. winogradskyi improved the absolute ammonia oxidation rate of both N. europaea and N. ureae. N. winogradskyi's nitrite oxidation rate decreased to 42% residual activity upon exposure to 30 mS cm-1, also showing a similar behavior when tested with Nitrosomonas spp. The nitrite oxidation rate of N. vulgaris, as a single species, was not affected when adding sodium chloride up to 30 mS cm-1, however, its activity was completely inhibited when combined with Nitrosomonas spp. in the presence of ammonium/ammonia. The proteomic analysis of a co-culture of N. europaea and N. winogradskyi revealed the production of osmolytes, regulation of cell permeability and an oxidative stress response in N. europaea and an oxidative stress response in N. winogradskyi, as a result of increasing the salt concentration from 5 to 30 mS cm-1. A specific metabolic response observed in N. europaea suggests the role of carbon metabolism in the production of reducing power, possibly to meet the energy demands of the stress response mechanisms, induced by high salinity. For the first time, metabolic modifications and response mechanisms caused by the exposure to salinity were described, serving as a tool toward controllability and predictability of nitrifying systems exposed to salt fluctuations.},
}

@article {pmid30555443,
year = {2018},
author = {Tanaka, K and Yokoe, S and Igarashi, K and Takashino, M and Ishikawa, M and Hori, K and Nakanishi, S and Kato, S},
title = {Extracellular Electron Transfer via Outer Membrane Cytochromes in a Methanotrophic Bacterium Methylococcus capsulatus (Bath).},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2905},
doi = {10.3389/fmicb.2018.02905},
pmid = {30555443},
issn = {1664-302X},
abstract = {Electron exchange reactions between microbial cells and solid materials, referred to as extracellular electron transfer (EET), have attracted attention in the fields of microbial physiology, microbial ecology, and biotechnology. Studies of model species of iron-reducing, or equivalently, current-generating bacteria such as Geobacter spp. and Shewanella spp. have revealed that redox-active proteins, especially outer membrane c-type cytochromes (OMCs), play a pivotal role in the EET process. Recent (meta)genomic analyses have revealed that diverse microorganisms that have not been demonstrated to have EET ability also harbor OMC-like proteins, indicating that EET via OMCs could be more widely preserved in microorganisms than originally thought. A methanotrophic bacterium Methylococcus capsulatus (Bath) was reported to harbor multiple OMC genes whose expression is elevated by Cu starvation. However, the physiological role of these genes is unknown. Therefore, in this study, we explored whether M. capsulatus (Bath) displays EET abilities via OMCs. In electrochemical analysis, M. capsulatus (Bath) generated anodic current only when electron donors such as formate were available, and could reduce insoluble iron oxides in the presence of electron donor compounds. Furthermore, the current-generating and iron-reducing activities of M. capsulatus (Bath) cells that were cultured in a Cu-deficient medium, which promotes high levels of OMC expression, were higher than those cultured in a Cu-supplemented medium. Anodic current production by the Cu-deficient cells was significantly suppressed by disruption of MCA0421, a highly expressed OMC gene, and by treatment with carbon monoxide (CO) gas (an inhibitor of c-type cytochromes). Our results provide evidence of EET in M. capsulatus (Bath) and demonstrate the pivotal role of OMCs in this process. This study raises the possibility that EET to solid compounds is a novel survival strategy of methanotrophic bacteria.},
}

@article {pmid30554808,
year = {2018},
author = {Sutherland, WJ and Broad, S and Butchart, SHM and Clarke, SJ and Collins, AM and Dicks, LV and Doran, H and Esmail, N and Fleishman, E and Frost, N and Gaston, KJ and Gibbons, DW and Hughes, AC and Jiang, Z and Kelman, R and LeAnstey, B and le Roux, X and Lickorish, FA and Monk, KA and Mortimer, D and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Seymour, CL and Spalding, MD and Wentworth, J and Ockendon, N},
title = {A Horizon Scan of Emerging Issues for Global Conservation in 2019.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2018.11.001},
pmid = {30554808},
issn = {1872-8383},
abstract = {We present the results of our tenth annual horizon scan. We identified 15 emerging priority topics that may have major positive or negative effects on the future conservation of global biodiversity, but currently have low awareness within the conservation community. We hope to increase research and policy attention on these areas, improving the capacity of the community to mitigate impacts of potentially negative issues, and maximise the benefits of issues that provide opportunities. Topics include advances in crop breeding, which may affect insects and land use; manipulations of natural water flows and weather systems on the Tibetan Plateau; release of carbon and mercury from melting polar ice and thawing permafrost; new funding schemes and regulations; and land-use changes across Indo-Malaysia.},
}

@article {pmid30554770,
year = {2018},
author = {Cordier, T and Lanzén, A and Apothéloz-Perret-Gentil, L and Stoeck, T and Pawlowski, J},
title = {Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2018.10.012},
pmid = {30554770},
issn = {1878-4380},
abstract = {Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioindicator taxa. While prokaryotic and eukaryotic microbial diversity is of key importance in ecosystem functioning, its implementation in biomonitoring programs is still largely unappreciated, mainly because of difficulties in identifying microbes and limited knowledge of their ecological functions. Here, we argue that the combination of massive environmental genomics microbial data with machine learning algorithms can be extremely powerful for biomonitoring programs and pave the way to fill important gaps in our understanding of microbial ecology.},
}

@article {pmid30554323,
year = {2018},
author = {Jiang, N and Liu, H and Wang, P and Huang, J and Han, H and Wang, Q},
title = {Illumina MiSeq Sequencing Investigation of Microbiota in Bronchoalveolar Lavage Fluid and Cecum of the Swine Infected with PRRSV.},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00284-018-1613-y},
pmid = {30554323},
issn = {1432-0991},
support = {No. 81172777//the National Natural Science Foundation of China under Grant/ ; No. 2014B11NC096//the Dalian Science and Technological Project under Grant/ ; },
abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant animal morbidity and mortality and economic losses worldwide. In this study, we analyzed the microbiota in bronchoalveolar lavage fluid (BAL), mucosa, and feces in cecum of the PRRSV-challenged pigs using the Illumina MiSeq sequencing platform, to investigate the role of microbiota in the pathogenesis and development of porcine reproductive and respiratory syndrome (PRRS). Quantitative insights into microbial ecology analyses indicated that the dominant bacterial groups in the lung from the PRRSV-challenged pigs were Haemophilus parasuis and Mycoplasma hyorhinis, with a relative abundance of 35-48% and 27-41%, respectively. Our results were consistent with the clinical observation that the PRRSV-infected pigs are always co-infected with other bacteria, such as Haemophilus and Mycoplasma. On the other hand, Campylobacter and Clostridium became the two most abundant bacteria in the mucosal and luminal microbiota of the cecum of the PRRSV-challenged pigs, and the relative abundance was four times higher than that in the healthy pigs. This suggested that Campylobacter and Clostridium might be associated with the pathogenesis of diarrhea in PRRS. Linear discriminant analysis effect size reveals significant microbial dysbiosis of BAL, mucosa, and feces in cecum of the PRRSV-challenged pigs. We have identified a structural imbalance of the microbiota, characterized by a reduced diversity of microbiota and abundance alterations of certain bacteria in the PRRSV-challenged pigs. The observed microbiota dysbiosis in this study provides insight into the roles of the microbiota in the complications of the PRRSV infection.},
}

@article {pmid30552443,
year = {2018},
author = {Rothman, JA and Andrikopoulos, C and Cox-Foster, D and McFrederick, QS},
title = {Floral and Foliar Source Affect the Bee Nest Microbial Community.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1300-3},
pmid = {30552443},
issn = {1432-184X},
support = {NNX15AP99A//National Aeronautics and Space Administration/ ; 2018-67011-28123//National Institute of Food and Agriculture/ ; CA-R-ENT-5109-H//National Institute of Food and Agriculture/ ; },
abstract = {Managed pollinators such as the alfalfa leafcutting bee, Megachile rotundata, are essential to the production of a wide variety of agricultural crops. These pollinators encounter a diverse array of microbes when foraging for food and nest-building materials on various plants. To test the hypothesis that food and nest-building source affects the composition of the bee-nest microbiome, we exposed M. rotundata adults to treatments that varied both floral and foliar source in a 2 × 2 factorial design. We used 16S rRNA gene and internal transcribed spacer (ITS) sequencing to capture the bacterial and fungal diversity of the bee nests. We found that nest microbial communities were significantly different between treatments, indicating that bee nests become inoculated with environmentally derived microbes. We did not find evidence of interactions between the fungi and bacteria within our samples. Furthermore, both the bacterial and fungal communities were quite diverse and contained numerous exact sequence variants (ESVs) of known plant and bee pathogens that differed based on treatment. Our research indicates that bees deposit plant-associated microbes into their nests, including multiple plant pathogens such as smut fungi and bacteria that cause blight and wilt. The presence of plant pathogens in larval pollen provisions highlights the potential for bee nests to act as disease reservoirs across seasons. We therefore suggest that future research should investigate the ability of bees to transmit pathogens from nest to host plant.},
}

@article {pmid30547761,
year = {2018},
author = {Morales-Cruz, A and Figueroa-Balderas, R and García, JF and Tran, E and Rolshausen, PE and Baumgartner, K and Cantu, D},
title = {Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {214},
doi = {10.1186/s12866-018-1343-0},
pmid = {30547761},
issn = {1471-2180},
support = {2016-1798//American Vineyard Foundation/ ; 2017-1798//American Vineyard Foundation/ ; 2018-1798//American Vineyard Foundation/ ; 2012-51181-19954//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Profiling of pathogen communities associated with grapevine trunk diseases is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the fungal kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology.

RESULTS: We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were over- or under-estimated with universal primers.

CONCLUSIONS: Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.},
}

@article {pmid30547194,
year = {2018},
author = {Visvalingam, J and Zhang, P and Ells, TC and Yang, X},
title = {Dynamics of Biofilm Formation by Salmonella Typhimurium and Beef Processing Plant Bacteria in Mono- and Dual-Species Cultures.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1304-z},
pmid = {30547194},
issn = {1432-184X},
support = {A-1603 and A-1637//Agriculture and Agri-Food Canada/ ; },
abstract = {This study aimed to determine the impact of bacteria from a beef plant conveyor belt on the biofilm formation of Salmonella in dual-species cultures. Beef plant isolates (50) including 18 Gram-negative aerobes (GNA), 8 Gram-positive aerobes (GPA), 5 lactic acid bacteria (LAB), 9 Enterobacteriaceae (EB), and 10 generic Escherichia coli (GEC) were included for developing biofilms in mono- and co-culture with S. Typhimurium at 15 °C for 6 days. Five selected cultures in planktonic form and in biofilms were tested for susceptibility to two commonly used sanitizers (i.e. E-San and Perox-E Plus). In mono-cultures, ≥ 80, 67, 61, 20, and 13% of GEC, EB, GNA, LAB, and GPA, respectively, developed measurable biofilms after 2 days, while all co-culture pairings with S. Typhimurium achieved some level of biofilm production. The predominant effect of EB and only effect of GEC strains on the biofilm formation of S. Typhimurium was antagonistic, while that of Gram-positive bacteria was synergistic, with the effect being more prominent on day 6. The effect was highly variable for the GNA isolates. Six aerobic isolates that formed moderate/strong biofilms by day 2 greatly boosted the co-culture biofilm formation. Seven Gram-negative bacteria were antagonistic against the biofilm formation of the co-cultures. Both sanitizers completely inactivated the selected planktonic cultures, but were largely ineffective against biofilms. In conclusion, all beef plant isolates assessed formed biofilms when paired with S. Typhimurium. Aerobic biofilm formers may create a more favorable condition for Salmonella biofilm formation, while some beef plant isolates have potential as a biocontrol strategy for Salmonella biofilms.},
}

@article {pmid30545051,
year = {2018},
author = {Haro, C and Villatoro, M and Vaquero, L and Pastor, J and Giménez, MJ and Ozuna, CV and Sánchez-León, S and García-Molina, MD and Segura, V and Comino, I and Sousa, C and Vivas, S and Landa, BB and Barro, F},
title = {The Dietary Intervention of Transgenic Low-Gliadin Wheat Bread in Patients with Non-Celiac Gluten Sensitivity (NCGS) Showed No Differences with Gluten Free Diet (GFD) but Provides Better Gut Microbiota Profile.},
journal = {Nutrients},
volume = {10},
number = {12},
pages = {},
doi = {10.3390/nu10121964},
pmid = {30545051},
issn = {2072-6643},
support = {Projects AGL2013-48946-C3-1-R, AGL2013-48946-C and AGL2016-80566-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; },
abstract = {The study evaluated the symptoms, acceptance, and digestibility of bread made from transgenic low-gliadin wheat, in comparison with gluten free bread, in Non-coeliac gluten sensitivity (NCGS) patients, considering clinical/sensory parameters and gut microbiota composition. This study was performed in two phases of seven days each, comprising a basal phase with gluten free bread and an E82 phase with low-gliadin bread. Gastrointestinal clinical symptoms were evaluated using the Gastrointestinal Symptom Rating Scale (GSRS) questionnaire, and stool samples were collected for gluten immunogenic peptides (GIP) determination and the extraction of gut microbial DNA. For the basal and E82 phases, seven and five patients, respectively, showed undetectable GIPs content. The bacterial 16S rRNA gene V1-V2 hypervariable regions were sequenced using the Illumina MiSeq platform and downstream analysis was done using a Quantitative Insights into Microbial Ecology (QIIME) pipeline. No significant differences in the GSRS questionnaires were observed between the two phases. However, we observed a significantly lower abundance of some gut genera Oscillospira, Dorea, Blautia, Bacteroides, Coprococcus, and Collinsella, and a significantly higher abundance of Roseburia and Faecalibacterium genera during the E82 phase compared with the basal phase. The consumption of low-gliadin bread E82 by NCGS subjects induced potentially positive changes in the gut microbiota composition, increasing the butyrate-producing bacteria and favoring a microbial profile that is suggested to have a key role in the maintenance or improvement of gut permeability.},
}

@article {pmid30544668,
year = {2018},
author = {Kaboré, WAD and Dembélé, R and Bagré, TS and Konaté, A and Boisramé, S and Chevalier, V and Konsem, T and Traoré, AS and Barro, N},
title = {Characterization and Antimicrobial Susceptibility of Lactococcus lactis Isolated from Endodontic Infections in Ouagadougou, Burkina Faso.},
journal = {Dentistry journal},
volume = {6},
number = {4},
pages = {},
doi = {10.3390/dj6040069},
pmid = {30544668},
issn = {2304-6767},
abstract = {BACKGROUND: This study aimed to characterize and test the antimicrobial susceptibility of Lactococcus lactis isolated in endodontic infections in Burkina Faso.

MATERIAL AND METHODS: This was a prospective study conducted at the Municipal Oral Health Center of Ouagadougou, Burkina Faso, from June to October 2014. Clinical data were collected using a questionnaire form. The method of streaking on selective medium was used to isolate bacteria. Identification was made using the API 20 Strep gallery. Antibiotic susceptibility was performed by the diffusion method on solid medium.

RESULTS: One hundred and twenty-five (125) patients were received with a significant proportion from the age group of 19 to 40 years (55.2%). Apical periodontitis accounted for 50.4% and cellulitis for 49.6% of cases. Lactococcus lactis ssp. lactis was identified in five exudate samples. Isolates were 100% resistant to cefixime and metronidazole, 80% to ceftriaxone, cefuroxime, cefotaxime, chloramphenicol and 60% to penicillin G, amoxicillin, amoxicillin clavulanic acid. A multidrug resistance of more than three families of antibiotics was noticed. No strains produced extended spectrum ß-lactamases.

CONCLUSION: Lactococcus lactis is part of endodontic biofilm. The reported strong antibiotic resistance involving endodontic therapy will focus on the effect of the disinfectant solution and the mechanical action of the canal instruments.},
}

@article {pmid30544592,
year = {2018},
author = {Bosmans, L and Pozo, MI and Verreth, C and Crauwels, S and Wäckers, F and Jacquemyn, H and Lievens, B},
title = {Hibernation Leads to Altered Gut Communities in Bumblebee Queens (Bombus terrestris).},
journal = {Insects},
volume = {9},
number = {4},
pages = {},
doi = {10.3390/insects9040188},
pmid = {30544592},
issn = {2075-4450},
abstract = {Many reptiles, amphibians, mammals, and insects practice some form of hibernation during which their metabolic rate is drastically reduced. This allows them to conserve energy and survive the harsh winter conditions with little or no food. While it can be expected that a reduction in host metabolism has a substantial influence on the gut microbial community, little is known about the effects of hibernation on the composition of the microbial gut community, especially for insects. In this study, we assessed and compared the bacterial gut community composition within the midgut and ileum of indoor-reared queens of Bombus terrestris before and after an artificial hibernation period of 16 weeks. Deep sequencing of 16S ribosomal RNA gene amplicons and clustering of sequence reads into operational taxonomic units (OTUs) at a similarity threshold of 97% revealed several bacterial taxa that are known to be strongly associated with corbiculate bees. Bacterial community composition after hibernation compared to before hibernation was characterized by higher OTU richness and evenness, with decreased levels of the core bacteria Gilliamella (Proteobacteria, Orbaceae) and Snodgrassella (Proteobacteria, Neisseriaceae), and increased relative abundance of non-core bacteria, including several psychrophilic and psychrotrophic taxa.},
}

@article {pmid30542336,
year = {2018},
author = {Okazaki, Y and Salcher, MM and Callieri, C and Nakano, SI},
title = {The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2891},
doi = {10.3389/fmicb.2018.02891},
pmid = {30542336},
issn = {1664-302X},
abstract = {CL500-11 (phylum Chloroflexi) is one of the most ubiquitous and abundant bacterioplankton lineages in deep freshwater lakes inhabiting the oxygenated hypolimnion. While metagenomics predicted possible eco-physiological characteristics of this uncultured lineage, no consensus on their ecology has so far been reached, partly because their niche is not clearly understood due to a limited number of quantitative field observations. This study investigated the abundance and distribution of CL500-11 in seven deep perialpine lakes using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken vertically (5-12 depths in each lake) and temporally (in two lakes) at the deepest point of the lakes located in Switzerland, Italy, and Austria with varying depth, trophic state, mixing regime, and water retention time. The results showed a dominance of CL500-11 in all the lakes; their proportion to total prokaryotes ranged from 4.3% (Mondsee) to 24.3% (Lake Garda) and their abundance ranged from 0.65 × 105 (Mondsee) to 1.77 × 105 (Lake Garda) cells mL-1. By summarizing available information on CL500-11 occurrence to date, we demonstrated their broad habitat spectrum, ranging from ultra-oligotrophic to meso-eutrophic lakes, while low abundances or complete absence was observed in lakes with shallow depth, low pH, and/or short water retention time (<1 year). Together with available metagenomic and geochemical evidences from literatures, here we reviewed potential substrates supporting growth of CL500-11. Overall, the present study further endorsed ubiquity and quantitative significance of CL500-11 in deep freshwater systems and narrowed the focus on their physiological characteristics and ecological importance.},
}

@article {pmid30542078,
year = {2018},
author = {Scoma, A and Heyer, R and Rifai, R and Dandyk, C and Marshall, I and Kerckhof, FM and Marietou, A and Boshker, HTS and Meysman, FJR and Malmos, KG and Vosegaard, T and Vermeir, P and Banat, IM and Benndorf, D and Boon, N},
title = {Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0324-5},
pmid = {30542078},
issn = {1751-7370},
abstract = {Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO2 production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea.},
}

@article {pmid30524385,
year = {2018},
author = {Rilling, JI and Acuña, JJ and Sadowsky, MJ and Jorquera, MA},
title = {Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2710},
doi = {10.3389/fmicb.2018.02710},
pmid = {30524385},
issn = {1664-302X},
abstract = {Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g-1 sample in rhizosphere and 104~105 and 104 CFU g-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.},
}

@article {pmid30522433,
year = {2018},
author = {Mohr, T and Aliyu, H and Küchlin, R and Zwick, M and Cowan, D and Neumann, A and de Maayer, P},
title = {Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {880},
doi = {10.1186/s12864-018-5302-9},
pmid = {30522433},
issn = {1471-2164},
support = {031B0180//Bundesministerium für Bildung und Forschung/ ; },
abstract = {BACKGROUND: The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this species, these organisms offer a potentially viable process for the synthesis of this alternative energy source.

RESULTS: The WGS-catalyzed H2 production capacities of four distinct P. thermoglucosidasius strains were determined by cultivation and gas analysis. Three strains (DSM 2542T, DSM 2543 and DSM 6285) were hydrogenogenic, while the fourth strain (DSM 21625) was not. Furthermore, in one strain (DSM 6285) H2 production commenced earlier in the cultivation than the other hydrogenogenic strains. Comparative genomic analysis of the four strains identified extensive differences in the protein complement encoded on the genomes, some of which are postulated to contribute to the different hydrogenogenic capacities of the strains. Furthermore, polymorphisms and deletions in the CODH-NiFe hydrogenase loci may also contribute towards this variable phenotype.

CONCLUSIONS: Disparities in the hydrogenogenic capacities of different P. thermoglucosidasius strains were identified, which may be correlated to variability in their global proteomes and genetic differences in their CODH-NiFe hydrogenase loci. The data from this study may contribute towards an improved understanding of WGS-catalysed hydrogenogenesis by P. thermoglucosidasius.},
}

@article {pmid30538275,
year = {2018},
author = {Nicolás, C and Martin-Bertelsen, T and Floudas, D and Bentzer, J and Smits, M and Johansson, T and Troein, C and Persson, P and Tunlid, A},
title = {The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0331-6},
pmid = {30538275},
issn = {1751-7370},
support = {2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; },
abstract = {Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.},
}

@article {pmid30536130,
year = {2018},
author = {Wilpiszeski, RL and Zhang, Z and House, CH},
title = {Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters.},
journal = {Extremophiles : life under extreme conditions},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00792-018-1066-z},
pmid = {30536130},
issn = {1433-4909},
support = {NAI Cooperative agreement #NNA09DA76A//National Aeronautics and Space Administration/ ; },
abstract = {Built systems such as water heaters can harbor extremophiles similar to those residing in natural hot springs, but the extent of colonization is not well understood. To address this, we conducted a survey of thermophilic microorganisms in household water heaters across the United States. Filter samples and inoculated cultures were collected by citizen-scientists from 101 homes. Draft genomes were assembled from cultured isolates and 16S rRNA genes were sequenced from filter samples. 28% of households harbored communities with unambiguous DNA signatures of thermophilic organisms, 36% of households provided viable inocula, and 21% of households had both. All of the recovered cultures as well as the community sequencing results revealed Thermus scotoductus to be the dominant thermophile in domestic water heaters, with a minority of water heaters also containing Meiothermus species and a few containing Aquificae. Sequence distance comparisons show that allopatric speciation does not appear to be a strong control on T. scotoductus distribution. Our results demonstrate that thermophilic organisms are widespread in hot tap water, and that Thermus scotoductus preferentially colonizes water heaters at the expense of local environmental Thermus strains.},
}

@article {pmid30535916,
year = {2018},
author = {Albecker, MA and Belden, LK and McCoy, MW},
title = {Comparative Analysis of Anuran Amphibian Skin Microbiomes Across Inland and Coastal Wetlands.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1295-9},
pmid = {30535916},
issn = {1432-184X},
support = {DEB 1136640//National Science Foundation/ ; Project No. 2014-R/14-HCE-3//North Carolina SeaGrant/ ; },
abstract = {Amphibians host a community of microbes on their skin that helps resist infectious disease via the dual influence of anti-pathogenic microbial species and emergent community dynamics. Many frogs rely on freshwater habitats, but salinization is rapidly increasing saltwater concentrations in wetlands around the globe, increasing the likelihood that frogs will come into contact with salt-contaminated habitats. Currently, we know little about how increased salt exposure will affect the symbiotic relationship between the skin microbes and frog hosts. To better understand how salt exposure in a natural context affects the frog skin microbiome, we use Hyla cinerea, a North American treefrog species that can inhabit brackish wetlands, to explore three questions. First, we determine the extent that microbial communities in the environment and on frog skin are similar across populations. Second, we assess the microbial species richness and relative abundance on frogs from habitats with different salinity levels to determine how salinity affects the microbiome. Third, we test whether the relative abundances of putatively pathogen-resistant bacterial species differ between frogs from inland and coastal environments. We found that the frog microbiome is more similar among frogs than to the microbial communities found in surface water and soil, but there is overlap between frog skin and the environmental samples. Skin microbial community richness did not differ among populations, but the relative abundances of microbes were different across populations and salinities. We found no differences in the relative abundances of the anti-fungal bacteria Janthinobacterium lividum, the genus Pseudomonas, and Serratia marcescens, suggesting that environmental exposure to saltwater has a limited influence on these putatively beneficial bacterial taxa.},
}

@article {pmid30535915,
year = {2018},
author = {Chamizo, S and Adessi, A and Mugnai, G and Simiani, A and De Philippis, R},
title = {Soil Type and Cyanobacteria Species Influence the Macromolecular and Chemical Characteristics of the Polysaccharidic Matrix in Induced Biocrusts.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1305-y},
pmid = {30535915},
issn = {1432-184X},
support = {706351//H2020 Marie Skłodowska-Curie Actions/ ; },
abstract = {Inoculation of soils with cyanobacteria is proposed as a sustainable biotechnological technique for restoration of degraded areas in drylands due to the important role that cyanobacteria and their exopolysaccharides (EPS) play in the environment. So far, few studies have analyzed the macromolecular and chemical characteristics of the polysaccharidic matrix in induced cyanobacterial biocrusts and the scarce existing studies have mainly focused on sandy soil textures. However, the characteristics of the cyanobacterial polysaccharidic matrix may greatly depend on soil type. The objective of this study was to examine the macromolecular distribution and monosaccharidic composition of the polysaccharidic matrix induced by inoculation of two cyanobacterial species common in arid environments, Phormidium ambiguum (non N-fixing) and Scytonema javanicum (N-fixing) in different soil types. S. javanicum promoted a higher release in the soil of the more soluble and less condensed EPS fraction (i.e., the loosely bound EPS fraction, LB-EPS), while P. ambiguum showed a higher release of the less soluble and more condensed EPS fraction (i.e., the tightly bound EPS fraction, TB-EPS). LB-EPSs were mainly composed of low MW molecules (< 50 kDa), while TB-EPSs were mainly composed of high MW molecules (1100-2000 kDa). The two EPS fractions showed a complex monosaccharidic composition (from 11 to 12 different types of monosaccharides), with glucose as the most abundant monosaccharide, in particular in the poorer soils characterized by lower organic C contents. In more C-rich soils, high abundances of galactose, mannose, and xylose were also found. Low abundance of uronic acids and hydrophobic monosaccharides, such as fucose and rhamnose, was found in the EPS extracted from the inoculated soils. Our results point to the influence of soil type on the macromolecular distribution and monosaccharide composition of the polysaccharidic matrix in induced biocrusts, which is likely to affect biocrust development and their role in soil structure and nutrient cycling in restored dryland soils.},
}

@article {pmid30535914,
year = {2018},
author = {Muthukrishnan, T and Al Khaburi, M and Abed, RMM},
title = {Fouling Microbial Communities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific?.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1303-0},
pmid = {30535914},
issn = {1432-184X},
support = {SQU-GCC/CL/17/02//Sultan Qaboos University/ ; },
abstract = {Although marine biofouling has been widely studied on different substrates, information on biofouling on plastics in the Arabian Gulf is limited. Substrate- and location-specific effects were investigated by comparing the microbial communities developed on polyethylene terephthalate (PET) and polyethylene (PE) with those on steel and wood, at two locations in the Sea of Oman. Total biomass was lower on PET and PE than on steel and wood. PET had the highest bacterial abundance at both locations, whereas chlorophyll a concentrations did not vary between substrates. MiSeq 16S ribosomal RNA sequencing revealed comparable operational taxonomic unit (OTU) richness on all substrates at one location but lower numbers on PET and PE at the other location. Non-metric multidimensional scaling (NMDS) showed distinct clusters of the bacterial communities based on substrate (analysis of similarity (ANOSIM), R = 0.45-0.97, p < 0.03) and location (ANOSIM, R = 0.56, p < 0.0001). The bacterial genera Microcystis and Hydrogenophaga and the diatoms Licmophora and Mastogloia were specifically detected on plastics. Desulfovibrio and Pseudomonas spp. exhibited their highest abundance on steel and Corynebacterium spp. on wood. Scanning electron microscopy (SEM) revealed fissure formation on PET and PE, indicating physical degradation. The presence of free radicals on PET and carbonyl bonds (C=O) on PE, as revealed by Fourier transform infrared (FTIR) spectroscopy, indicated abiotic degradation while hydroxyl groups and spectral peaks for proteins and polysaccharides on PE indicated biotic degradation. We conclude that fouling microbial communities are not only substrate-specific but also location-specific and microbes developing on plastics could potentially contribute to their degradation in the marine environment.},
}

@article {pmid30535652,
year = {2018},
author = {Whittle, A and Amesbury, MJ and Charman, DJ and Hodgson, DA and Perren, BB and Roberts, SJ and Gallego-Sala, AV},
title = {Salt-Enrichment Impact on Biomass Production in a Natural Population of Peatland Dwelling Arcellinida and Euglyphida (Testate Amoebae).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1296-8},
pmid = {30535652},
issn = {1432-184X},
support = {NE/L002434/1//Natural Environment Research Council/ ; },
abstract = {Unicellular free-living microbial eukaryotes of the order Arcellinida (Tubulinea; Amoebozoa) and Euglyphida (Cercozoa; SAR), commonly termed testate amoebae, colonise almost every freshwater ecosystem on Earth. Patterns in the distribution and productivity of these organisms are strongly linked to abiotic conditions-particularly moisture availability and temperature-however, the ecological impacts of changes in salinity remain poorly documented. Here, we examine how variable salt concentrations affect a natural community of Arcellinida and Euglyphida on a freshwater sub-Antarctic peatland. We principally report that deposition of wind-blown oceanic salt-spray aerosols onto the peatland surface corresponds to a strong reduction in biomass and to an alteration in the taxonomic composition of communities in favour of generalist taxa. Our results suggest novel applications of this response as a sensitive tool to monitor salinisation of coastal soils and to detect salinity changes within peatland palaeoclimate archives. Specifically, we suggest that these relationships could be used to reconstruct millennial scale variability in salt-spray deposition-a proxy for changes in wind-conditions-from sub-fossil communities of Arcellinida and Euglyphida preserved in exposed coastal peatlands.},
}

@article {pmid30535561,
year = {2018},
author = {Rydzanicz, K and Golab, E and Rozej-Bielicka, W and Masny, A},
title = {Screening of mosquitoes for filarioid helminths in urban areas in south western Poland-common patterns in European Setaria tundra xenomonitoring studies.},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00436-018-6134-x},
pmid = {30535561},
issn = {1432-1955},
abstract = {In recent years, numerous studies screening mosquitoes for filarioid helminths (xenomonitoring) have been performed in Europe. The entomological monitoring of filarial nematode infections in mosquitoes by molecular xenomonitoring might serve as the measure of the rate at which humans and animals expose mosquitoes to microfilariae and the rate at which animals and humans are exposed to the bites of the infected mosquitoes. We hypothesized that combining the data obtained from molecular xenomonitoring and phenological studies of mosquitoes in the urban environment would provide insights into the transmission risk of filarial diseases. In our search for Dirofilaria spp.-infected mosquitoes, we have found Setaria tundra-infected ones instead, as in many other European studies. We have observed that cross-reactivity in PCR assays for Dirofilaria repens, Dirofilaria immitis, and S. tundra COI gene detection was the rule rather than the exception. S. tundra infections were mainly found in Aedes mosquitoes. The differences in the diurnal rhythm of Aedes and Culex mosquitoes did not seem a likely explanation for the lack of S. tundra infections in Culex mosquitoes. The similarity of S. tundra COI gene sequences found in Aedes vexans and Aedes caspius mosquitoes and in roe deer in many European studies, supported by data on Ae. vexans biology, suggested host preference as the most likely cause of the mosquito genus-biased infections. High diversity of the COI gene sequences isolated in the city of Wroclaw in south western Poland and the presence of identical or almost identical sequences in mosquitoes and roe deer across Europe suggests that S. tundra has been established in most of Europe for a very long time.},
}

@article {pmid30534614,
year = {2018},
author = {Rampelli, S and Guenther, K and Turroni, S and Wolters, M and Veidebaum, T and Kourides, Y and Molnár, D and Lissner, L and Benitez-Paez, A and Sanz, Y and Fraterman, A and Michels, N and Brigidi, P and Candela, M and Ahrens, W},
title = {Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity.},
journal = {Communications biology},
volume = {1},
number = {},
pages = {222},
doi = {10.1038/s42003-018-0221-5},
pmid = {30534614},
issn = {2399-3642},
abstract = {It is widely accepted that the intestinal microbiome is connected to obesity, as key mediator of the diet impact on the host metabolic and immunological status. To investigate whether the individual gut microbiome has a potential in predicting the onset and progression of diseases, here we characterized the faecal microbiota of 70 children in a two-time point prospective study, within a four-year window. All children had normal weight at the beginning of this study, but 36 of them gained excessive weight at the subsequent check-up. Microbiome data were analysed together with the hosts' diet information, physical activity, and inflammatory parameters. We find that the gut microbiota structures were stratified into a discrete number of groups, characterized by different biodiversity that correlates with inflammatory markers and dietary habits, regardless of age, gender, and body weight. Collectively, our data underscore the importance of the microbiome-host-diet configuration as a possible predictor of obesity.},
}

@article {pmid30534120,
year = {2018},
author = {Heijboer, A and de Ruiter, PC and Bodelier, PLE and Kowalchuk, GA},
title = {Modulation of Litter Decomposition by the Soil Microbial Food Web Under Influence of Land Use Change.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2860},
doi = {10.3389/fmicb.2018.02860},
pmid = {30534120},
issn = {1664-302X},
abstract = {Soil microbial communities modulate soil organic matter (SOM) dynamics by catalyzing litter decomposition. However, our understanding of how litter-derived carbon (C) flows through the microbial portion of the soil food web is far from comprehensive. This information is necessary to facilitate reliable predictions of soil C cycling and sequestration in response to a changing environment such as land use change in the form of agricultural abandonment. To examine the flow of litter-derived C through the soil microbial food web and it's response to land use change, we carried out an incubation experiment with soils from six fields; three recently abandoned and three long term abandoned fields. In these soils, the fate of 13C-labeled plant litter was followed by analyzing phospholipid fatty acids (PLFA) over a period of 56 days. The litter-amended soils were sampled over time to measure 13CO2 and mineral N dynamics. Microbial 13C-incorporation patterns revealed a clear succession of microbial groups during litter decomposition. Fungi were first to incorporate 13C-label, followed by G- bacteria, G+ bacteria, actinomycetes and micro-fauna. The order in which various microbial groups responded to litter decomposition was similar across all the fields examined, with no clear distinction between recent and long-term abandoned soils. Although the microbial biomass was initially higher in long-term abandoned soils, the net amount of 13C-labeled litter that was incorporated by the soil microbial community was ultimately comparable between recent and long-term abandoned fields. In relative terms, this means there was a higher efficiency of litter-derived 13C-incorporation in recent abandoned soil microbial communities compared to long-term abandoned soils, most likely due to a net shift from SOM-derived C toward root-derived C input in the soil microbial food web following land-abandonment.},
}

@article {pmid30533919,
year = {2018},
author = {Kim, SJ and Park, SJ and Kim, JG and Jung, MY and Gwak, JH and Rhee, SK},
title = {Draft Genome Sequence of "Candidatus Izimaplasma sp." Strain ZiA1, Obtained from a Toluene-Degrading and Iron-Reducing Enrichment Culture.},
journal = {Microbiology resource announcements},
volume = {7},
number = {8},
pages = {},
doi = {10.1128/MRA.00861-18},
pmid = {30533919},
issn = {2576-098X},
abstract = {Here, we report the draft genome sequence of "Candidatus Izimaplasma sp." strain ZiA1 (1.88 Mb and 29.6% G+C content). Strain ZiA1 was cocultured with iron-reducing and toluene-degrading bacteria in an enrichment culture from tidal flat sediment. Like the genomes of other strains of "Ca. Izimaplasma," the ZiA1 genome contained genes required for anaerobic fermentation.},
}

@article {pmid30532746,
year = {2018},
author = {Bachmann, J and Heimbach, T and Hassenrück, C and Kopprio, GA and Iversen, MH and Grossart, HP and Gärdes, A},
title = {Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2836},
doi = {10.3389/fmicb.2018.02836},
pmid = {30532746},
issn = {1664-302X},
abstract = {Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2-3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.},
}

@article {pmid30532651,
year = {2018},
author = {Haruta, S and Yamamoto, K},
title = {Model Microbial Consortia as Tools for Understanding Complex Microbial Communities.},
journal = {Current genomics},
volume = {19},
number = {8},
pages = {723-733},
doi = {10.2174/1389202919666180911131206},
pmid = {30532651},
issn = {1389-2029},
abstract = {A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.},
}

@article {pmid30532562,
year = {2018},
author = {Eze, EC and Chenia, HY and Zowalaty, MEE},
title = {Acinetobacter baumannii biofilms: effects of physicochemical factors, virulence, antibiotic resistance determinants, gene regulation, and future antimicrobial treatments.},
journal = {Infection and drug resistance},
volume = {11},
number = {},
pages = {2277-2299},
doi = {10.2147/IDR.S169894},
pmid = {30532562},
issn = {1178-6973},
abstract = {Acinetobacter baumannii is a leading cause of nosocomial infections due to its increased antibiotic resistance and virulence. The ability of A. baumannii to form biofilms contributes to its survival in adverse environmental conditions including hospital environments and medical devices. A. baumannii has undoubtedly propelled the interest of biomedical researchers due to its broad range of associated infections especially in hospital intensive care units. The interplay among microbial physicochemistry, alterations in the phenotype and genotypic determinants, and the impact of existing ecological niche and the chemistry of antimicrobial agents has led to enhanced biofilm formation resulting in limited access of drugs to their specific targets. Understanding the triggers to biofilm formation is a step towards limiting and containing biofilm-associated infections and development of biofilm-specific countermeasures. The present review therefore focused on explaining the impact of environmental factors, antimicrobial resistance, gene alteration and regulation, and the prevailing microbial ecology in A. baumannii biofilm formation and gives insights into prospective anti-infective treatments.},
}

@article {pmid30530153,
year = {2018},
author = {Macintosh, KA and Chin, J and Jacobs, B and Cordell, D and McDowell, RW and Butler, P and Haygarth, PM and Williams, P and Quinn, JP and O'Flaherty, V and McGrath, JW},
title = {Transforming phosphorus use on the island of Ireland: A model for a sustainable system.},
journal = {The Science of the total environment},
volume = {656},
number = {},
pages = {852-861},
doi = {10.1016/j.scitotenv.2018.11.389},
pmid = {30530153},
issn = {1879-1026},
abstract = {Phosphorus is an essential part of the world food web and a non-substitutable nutrient in all biological systems. Losses of phosphorus occur along the food-supply chain and cause environmental degradation and eutrophication. A key global challenge is to meet rising worldwide food demand while protecting water and environmental quality, and seeking to manage uncertainty around potential future phosphorus price or supply shocks. This paper presents a stakeholder-generated conceptual model of potential transformative change for implementing phosphorus sustainability on the island of Ireland via an 'All-Island Phosphorus Sustainability' workshop. Key transition pathways identified by stakeholders included: incentivising phosphorus recovery, developing collaborative networks to facilitate change, developing markets and value chains for recovered products; implementing data-informed practices on-farm to prevent losses and increase efficiencies, and harmonisation of technologies with end-user needs. A comparable model was previously produced for the North American region. We describe consensus and differences around key priorities between the two regions' conceptual models, and assess how the model produced for the island of Ireland can effect system-wide change and policy moving forward. Many of the transitional pathways and future aspirations presented in both models resonate globally and are highly pertinent to other jurisdictions.},
}

@article {pmid30530129,
year = {2018},
author = {Christiaens, MER and Udert, KM and Arends, JBA and Huysman, S and Vanhaecke, L and McAdam, E and Rabaey, K},
title = {Membrane stripping enables effective electrochemical ammonia recovery from urine while retaining microorganisms and micropollutants.},
journal = {Water research},
volume = {150},
number = {},
pages = {349-357},
doi = {10.1016/j.watres.2018.11.072},
pmid = {30530129},
issn = {1879-2448},
abstract = {Ammonia recovery from urine avoids the need for nitrogen removal through nitrification/denitrification and re-synthesis of ammonia (NH3) via the Haber-Bosch process. Previously, we coupled an alkalifying electrochemical cell to a stripping column, and achieved competitive nitrogen removal and energy efficiencies using only electricity as input, compared to other technologies such as conventional column stripping with air. Direct liquid-liquid extraction with a hydrophobic gas membrane could be an alternative to increase nitrogen recovery from urine into the absorbent while minimizing energy requirements, as well as ensuring microbial and micropollutant retention. Here we compared a column with a membrane stripping reactor, each coupled to an electrochemical cell, fed with source-separated urine and operated at 20 A m-2. Both systems achieved similar nitrogen removal rates, 0.34 ± 0.21 and 0.35 ± 0.08 mol N L-1 d-1, and removal efficiencies, 45.1 ± 18.4 and 49.0 ± 9.3%, for the column and membrane reactor, respectively. The membrane reactor improved nitrogen recovery to 0.27 ± 0.09 mol N L-1 d-1 (38.7 ± 13.5%) while lowering the operational (electrochemical and pumping) energy to 6.5 kWhe kg N-1 recovered, compared to the column reactor, which reached 0.15 ± 0.06 mol N L-1 d-1 (17.2 ± 8.1%) at 13.8 kWhe kg N-1. Increased cell concentrations of an autofluorescent E. coli MG1655 + prpsM spiked in the urine influent were observed in the absorbent of the column stripping reactor after 24 h, but not for the membrane stripping reactor. None of six selected micropollutants spiked in the urine were found in the absorbent of both technologies. Overall, the membrane stripping reactor is preferred as it improved nitrogen recovery with less energy input and generated an E. coli- and micropollutant-free product for potential safe reuse. Nitrogen removal rate and efficiency can be further optimized by increasing the NH3 vapor pressure gradient and/or membrane surface area.},
}

@article {pmid30529486,
year = {2018},
author = {Labarthe, S and Polizzi, B and Phan, T and Goudon, T and Ribot, M and Laroche, B},
title = {A mathematical model to investigate the key drivers of the biogeography of the colon microbiota.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtbi.2018.12.009},
pmid = {30529486},
issn = {1095-8541},
abstract = {The gut microbiota, mainly located in the colon, is engaged in a complex dialogue with the large intestinal epithelium through which important regulatory processes for the health and well-being of the host take place. Imbalances of the microbial populations, called dysbiosis, are related to several pathological status, emphasizing the importance of understanding the gut bacterial ecology. Among the ecological drivers of the microbiota, the spatial structure of the colon is of special interest: spatio-temporal mechanisms can lead to the constitution of spatial interactions among the bacterial populations and of environmental niches that impact the overall colonization of the colon. In the present study, we introduce a mathematical model of the colon microbiota in its fluid environment, based on the explicit coupling of a population dynamics model of microbial populations involved in fibre degradation with a fluid dynamics model of the luminal content. This modeling framework is used to study the main drivers of the spatial structure of the microbiota, specially focusing on the dietary fibre inflow, the epithelial motility, the microbial active swimming and viscosity gradients in the digestive track. We found 1) that the viscosity gradients allow the creation of favorable niches in the vicinity of the mucus layer; 2) that very low microbial active swimming in the radial direction is enough to promote bacterial growth, which sheds a new light on microbial motility in the colon and 3) that dietary fibres are the main driver of the spatial structure of the microbiota in the distal bowel whereas epithelial motility is preponderant for the colonization of the proximal colon; in the transverse colon, fibre levels and chemotaxis have the strongest impact on the distribution of the microbial communities.},
}

@article {pmid30521380,
year = {2018},
author = {Calatayud, M and Dezutter, O and Hernandez-Sanabria, E and Hidalgo-Martinez, S and Meysman, FJR and Van de Wiele, T},
title = {Development of a host-microbiome model of the small intestine.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {fj201801414R},
doi = {10.1096/fj.201801414R},
pmid = {30521380},
issn = {1530-6860},
abstract = {The intestinal epithelium plays an essential role in the balance between tolerant and protective immune responses to infectious agents. In vitro models do not typically consider the innate immune response and gut microbiome in detail, so these models do not fully mimic the physiologic aspects of the small intestine. We developed and characterized a long-term in vitro model containing enterocyte, goblet, and immune-like cells exposed to a synthetic microbial community representative of commensal inhabitants of the small intestine. This model showed differential responses toward a synthetic microbial community of commensal bacterial inhabitants of the small intestine in the absence or presence of LPS from Escherichia coli O111:B4. Simultaneous exposure to LPS and microbiota induced impaired epithelial barrier function; increased production of IL-8, IL-6, TNF-α, and C-X-C motif chemokine ligand 16; and augmented differentiation and adhesion of macrophage-like cells and the overexpression of dual oxidase 2 and TLR-2 and -4 mRNA. In addition, the model demonstrated the ability to assess the adhesion of specific bacterial strains from the synthetic microbial community-more specifically, Veillonella parvula-to the simulated epithelium. This novel in vitro model may assist in overcoming sampling and retrieval difficulties when studying host-microbiome interactions in the small intestine.-Calatayud, M., Dezutter, O., Hernandez-Sanabria, E., Hidalgo-Martinez, S., Meysman, F. J. R., Van de Wiele, T. Development of a host-microbiome model of the small intestine.},
}

@article {pmid30520189,
year = {2018},
author = {Andeta, AF and Vandeweyer, D and Teffera, FE and Woldesenbet, F and Verreth, C and Crauwels, S and Lievens, B and Vancampenhout, K and Van Campenhout, L},
title = {Effect of fermentation system on the physicochemical and microbial community dynamics during enset (Ensete ventricosum) fermentation.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.14173},
pmid = {30520189},
issn = {1365-2672},
abstract = {AIMS: The present study was conducted to assess the effect of three different fermentation systems on fermentation of enset into kocho.

METHODS AND RESULTS: Nine enset plants were processed, mixed and fermented in either a pit, a bamboo basket or a Sauerkraut jar. Samples were taken on days 1, 7, 15, 31, 60 and 90. Moisture content and pH generally decreased and titratable acidity increased during fermentation. Total viable aerobic counts were generally high for all samples and Enterobacteriaceae counts were reduced to below the detectable level after day 1 for the pits and jars and after day 7 for the baskets. Illumina MiSeq sequencing of 16S ribosomal RNA genes revealed that Leuconostoc and Lactococcus spp. were the most abundant lactic acid bacteria in the initial phases of the fermentation. Later on, Lactobacillus, Weissella and Bifidobacterium dominated.

CONCLUSIONS: The type of fermentation system used had an effect on the microbial dynamics and the effect increased towards the end of fermentation.

Millions of people in Ethiopia daily consume kocho prepared in either a pit or a basket. These systems show practical problems, but this study shows that fermentation is also possible in a Sauerkraut jar. This article is protected by copyright. All rights reserved.},
}

@article {pmid30518818,
year = {2018},
author = {Rosado, PM and Leite, DCA and Duarte, GAS and Chaloub, RM and Jospin, G and Nunes da Rocha, U and P Saraiva, J and Dini-Andreote, F and Eisen, JA and Bourne, DG and Peixoto, RS},
title = {Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0323-6},
pmid = {30518818},
issn = {1751-7370},
abstract = {Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora damicornis and surrounding seawater) putatively beneficial microorganisms for corals (pBMCs), including five Pseudoalteromonas sp., a Halomonas taeanensis and a Cobetia marina-related species strains. The results from a controlled aquarium experiment in two temperature regimes (26 °C and 30 °C) and four treatments (pBMC; pBMC with pathogen challenge - Vibrio coralliilyticus, VC; pathogen challenge, VC; and control) revealed the ability of the pBMC consortium to partially mitigate coral bleaching. Significantly reduced coral-bleaching metrics were observed in pBMC-inoculated corals, in contrast to controls without pBMC addition, especially challenged corals, which displayed strong bleaching signs as indicated by significantly lower photopigment contents and Fv/Fm ratios. The structure of the coral microbiome community also differed between treatments and specific bioindicators were correlated with corals inoculated with pBMC (e.g., Cobetia sp.) or VC (e.g., Ruegeria sp.). Our results indicate that the microbiome in corals can be manipulated to lessen the effect of bleaching, thus helping to alleviate pathogen and temperature stresses, with the addition of BMCs representing a promising novel approach for minimizing coral mortality in the face of increasing environmental impacts.},
}

@article {pmid30506480,
year = {2018},
author = {Ascunce, MS and Shin, K and Huguet-Tapia, JC and Poudel, R and Garrett, KA and van Bruggen, AHC and Goss, EM},
title = {Penicillin Trunk Injection Affects Bacterial Community Structure in Citrus Trees.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1302-1},
pmid = {30506480},
issn = {1432-184X},
support = {N/A//Florida Department of Agriculture and Consumer Services/ ; N/A//Institute of Food and Agricultural Sciences/ ; N/A//Esther B. O'Keeffe Foundation/ ; },
abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), an uncultured α-proteobacterium, is the most destructive disease of citrus trees worldwide. In previous studies, trunk injections of penicillin reduced CLas titers and HLB symptoms in citrus. However, antibiotic effects on the whole plant microbial community, which include effects on taxa that interact with CLas, have not yet been addressed. In this study, we investigated the effects of penicillin injection (0, 1000, and 6000 mg L-1) on rhizospheric and endophytic bacterial communities of grapefruit trees in field and greenhouse experiments through culture-independent high-throughput sequencing. DNA extractions from petioles and roots were subjected to 16S rRNA high-throughput sequencing, and reads were clustered by sequence similarity into operational taxonomic units (OTUs). Principal coordinates analysis based on weighted-UniFrac distances did not reveal differences in bacterial communities among treatments in any of the sample sources. However, pairwise linear discriminant analysis indicated significant differences in relative abundance of some taxa (including CLas) among treatments. Network analysis showed that penicillin produced major changes in root bacterial community structure by affecting interspecific microbial associations. This study provides new knowledge of the effect of antimicrobial treatments on interspecific relationships in citrus microbial communities.},
}

@article {pmid30505703,
year = {2018},
author = {Ellis, S and Ritz, K},
title = {A modified high-throughput analysis of PLFAs in soil.},
journal = {MethodsX},
volume = {5},
number = {},
pages = {1491-1497},
doi = {10.1016/j.mex.2018.10.022},
pmid = {30505703},
issn = {2215-0161},
abstract = {Microbial community profiling via phospholipid fatty-acid (PLFA) analysis is an insightful technique which elucidates the phenotypic structure of microbial assemblages within soil. Previous iterations of PLFA analysis have used large quantities of chemicals and can take extended periods of time to perform. Another barrier to the implementation of this method is the cost and availability of specialised machinery. We report on a high-throughput method which reduces both the time to extract PLFAs from soil and reduces the quantity of chemicals required.},
}