About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot

About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot


Bibliography Options Menu

24 Feb 2020 at 01:38
Hide Abstracts   |   Hide Additional Links
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Microbial Ecology


Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 24 Feb 2020 at 01:38 Created: 

Microbial Ecology

Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

Created with PubMed® Query: "microbial ecology" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2020-02-23

Zhang S, Shao Y, Zhao X, et al (2020)

Indole contributes to tetracycline resistance via the outer membrane protein OmpN in Vibrio splendidus.

World journal of microbiology & biotechnology, 36(3):36 pii:10.1007/s11274-020-02813-6.

As an interspecies and interkingdom signaling molecule, indole has recently received attention for its diverse effects on the physiology of both bacteria and hosts. In this study, indole increased the tetracycline resistance of Vibrio splendidus. The minimal inhibitory concentration of tetracycline was 10 μg/mL, and the OD600 of V. splendidus decreased by 94.5% in the presence of 20 μg/mL tetracycline; however, the OD600 of V. splendidus with a mixture of 20 μg/mL tetracycline and 125 μM indole was 10- or 4.5-fold higher than that with only 20 μg/mL tetracycline at different time points. The percentage of cells resistant to 10 μg/mL tetracycline was 600-fold higher in the culture with an OD600 of approximately 2.0 (higher level of indole) than that in the culture with an OD600 of 0.5, which also meant that the level of indole was correlated to the tetracycline resistance of V. splendidus. Furthermore, one differentially expressed protein, which was identified as the outer membrane porin OmpN using SDS-PAGE combined with MALDI-TOF/TOF MS, was upregulated. Consequently, the expression of the ompN gene in the presence of either tetracycline or indole and simultaneously in the presence of indole and tetracycline was upregulated by 1.8-, 2.54-, and 6.01-fold, respectively, compared to the control samples. The combined results demonstrated that indole enhanced the tetracycline resistance of V. splendidus, and this resistance was probably due to upregulation of the outer membrane porin OmpN.

RevDate: 2020-02-23

Law CKY, De Henau R, J De Vrieze (2020)

Feedstock thermal pretreatment selectively steers process stability during the anaerobic digestion of waste activated sludge.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10472-8 [Epub ahead of print].

Strategies to enhance process performance of anaerobic digestion remain of key importance to promote wider usage of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e. organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process stability of the digesters fed sterile WAS, with a 92 ± 45% decrease in methane production, compared to a 42 ± 31% increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process stability between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na+ L-1. Feedstock sterilization through thermal pretreatment strongly impacted the microbial community in the digesters. In conclusion, feedstock thermal pretreatment strongly impacted anaerobic digestion process stability, due to feedstock inoculation and compositional modification.

RevDate: 2020-02-22

Bao G, Song M, Wang Y, et al (2020)

Does Epichloë Endophyte Enhance Host Tolerance to Root Hemiparasite?.

Microbial ecology pii:10.1007/s00248-020-01496-8 [Epub ahead of print].

Epichloë endophytes have been shown to be mutualistic symbionts of cool-season grasses under most environmental conditions. Although pairwise interactions between hemiparasites and their hosts are heavily affected by host-associated symbiotic microorganisms, little attention has been paid to the effects of microbe-plant interactions, particularly endophytic symbiosis, in studies examining the effects of parasitic plants on host performance. In this study, we performed a greenhouse experiment to examine the effects of hereditary Epichloë endophyte symbiosis on the growth of two host grasses (Stipa purpurea and Elymus tangutorum) in the presence or absence of a facultative root hemiparasite (Pedicularis kansuensis Maxim). We observed parasitism of both hosts by P. kansuensis: when grown with a host plant, the hemiparasite decreased the performance of the host while improving its own biomass and survival rate of the hemiparasite. Parasitized endophyte-infected S. purpurea plants had higher biomass, tillers, root:shoot ratio, and photosynthetic parameters and a lower number of functional haustoria than the endophyte-free S. purpurea conspecifics. By contrast, parasitized endophyte-infected E. tangutorum had a lower biomass, root:shoot ratio, and photosynthetic parameters and a higher number of haustoria and functional haustoria than their endophyte-free counterparts. Our results reveal that the interactions between the endophytes and the host grasses are context dependent and that plant-plant interactions can strongly affect their mutualistic interactions. Endophytes originating from S. purpurea alleviate the host biomass reduction by P. kansuensis and growth depression in the hemiparasite. These findings shed new light on using grass-endophyte symbionts as biocontrol methods for the effective and sustainable management of this weedy hemiparasite.

RevDate: 2020-02-22

Elhalis H, Cox J, J Zhao (2020)

Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans.

International journal of food microbiology, 321:108544 pii:S0168-1605(20)30038-6 [Epub ahead of print].

The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.

RevDate: 2020-02-21

Lories B, Roberfroid S, Dieltjens L, et al (2020)

Biofilm Bacteria Use Stress Responses to Detect and Respond to Competitors.

Current biology : CB pii:S0960-9822(20)30109-3 [Epub ahead of print].

Bacteria use complex regulatory networks to cope with stress, but the function of these networks in natural habitats is poorly understood. The competition sensing hypothesis states that bacterial stress response systems can serve to detect ecological competition, but studying regulatory responses in diverse communities is challenging. Here, we solve this problem by using differential fluorescence induction to screen the Salmonella Typhimurium genome for loci that respond, at the single-cell level, to life in biofilms with competing strains of S. Typhimurium and Escherichia coli. This screening reveals the presence of competing strains drives up the expression of genes associated with biofilm matrix production (CsgD pathway), epithelial invasion (SPI1 invasion system), and, finally, chemical efflux and antibiotic tolerance (TolC efflux pump and AadA aminoglycoside 3-adenyltransferase). We validate that these regulatory changes result in the predicted phenotypic changes in biofilm, mammalian cell invasion, and antibiotic tolerance. We further show that these responses arise via activation of major stress responses, providing direct support for the competition sensing hypothesis. Moreover, inactivation of the type VI secretion system (T6SS) of a competitor annuls the responses to competition, indicating that T6SS-derived cell damage activates these stress response systems. Our work shows that bacteria use stress responses to detect and respond to competition in a manner important for major phenotypes, including biofilm formation, virulence, and antibiotic tolerance.

RevDate: 2020-02-21

Xu J, Ma Z, Li X, et al (2020)

A more pronounced effect of type III resistant starch vs. type II resistant starch on ameliorating hyperlipidemia in high fat diet-fed mice is associated with its supramolecular structural characteristics.

Food & function [Epub ahead of print].

The anti-obesity effects of two categories of resistant starch (RS) including RS2 (isolated from untreated lentil starch, URS) and RS3 (isolated from autoclaved and retrograded lentil starch, ARS) on mice with high-fat (HF) diet-induced obesity and the supramolecular structure-in vivo physiological functionality relationship of RS were investigated. Following 6 consecutive weeks, the obese mice in the two RS administered groups displayed suppression of body/liver weight gain and an improvement in serum glucose/lipid profile, antioxidant status, and gut microbiota structure. Compared with the URS intervention group, the ARS administration resulted in a more pronounced effect in controlling body weight, together with a more prominent reduction in blood glucose and triglyceride concentration, as well as a significant increase in the HDL-c level in obese mice. The ARS group also showed an absolute advantage over URS in suppressing the oxidative stress and regulating the liver function induced by the HF diet. Simultaneously, the administration of URS and ARS efficiently suppressed the HF-diet induced alterations in gut microbial ecology, with an obviously decreased ratio of Firmicutes to Bacteroidetes, especially for the ARS group, suggesting its beneficial role in gastrointestinal tract health. The structural characterization results revealed that ARS and URS differed significantly in their supramolecular structural characteristics, where ARS exhibited a higher proportion of crystallinity and double helix content with an X-ray diffraction pattern of a CB type crystal polymorph and a low proportion of molecular inhomogeneity. This study suggested that the difference in the anti-obesity effect of resistant starches was a consequence of the diversity in their structural features.

RevDate: 2020-02-20

Chen H, Wang M, S Chang (2020)

Disentangling Community Structure of Ecological System in Activated Sludge: Core Communities, Functionality, and Functional Redundancy.

Microbial ecology pii:10.1007/s00248-020-01492-y [Epub ahead of print].

The microbial ecosystems of the sludge were characterized in terms of the core community structure, functional pathways, and functional redundancy through Illumina MiSeq sequencing and PICRUSt analysis on the activated sludge (AS) samples from an extended activated aeration process. Based on the identified OTU distribution, we identified 125 core community genera, including 3 abundant core genera and 21 intermittent abundant core genera. Putative genera Nitrosomonas, Nitrotoga, Zoogloea, Novosphingobium, Thermomonas, Amaricoccus, Tetrasphaera, Candidatus Microthrix, and Haliscomenobacter, which are associated with functions of nitrifying, denitrifying, phosphorus accumulating, and bulking and foaming, were found to present as the core community organisms in the AS sampled from the conventional extended aeration AS processes. The high-abundant nitrogen metabolic pathways were associated with nitrate reduction to ammonium (DNRA and ANRA), denitrification, and nitrogen fixation, while the ammonia oxidation-related genes (amo) were rarely annotated in the AS samples. Strict functional redundancy was not found with the AS ecosystem as it showed a high correlation between the community composition similarity and function similarity. In addition, the classified dominant core genera community was found to be sufficient to characterize the functionality of AS, which could invigorate applications of 16S rDNA MiSeq sequencing and PICRUSt for the prediction of functions of AS ecosystems.

RevDate: 2020-02-20

Aubé J, Senin P, Bonin P, et al (2020)

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning.

Microbial ecology pii:10.1007/s00248-020-01493-x [Epub ahead of print].

Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.

RevDate: 2020-02-20

Hernandez-Sanabria E, Heiremans E, Calatayud Arroyo M, et al (2020)

Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation.

NPJ biofilms and microbiomes, 6(1):9 pii:10.1038/s41522-020-0119-0.

Celecoxib has been effective in the prevention and treatment of chronic inflammatory disorders through inhibition of altered cyclooxygenase-2 (COX-2) pathways. Despite the benefits, continuous administration may increase risk of cardiovascular events. Understanding microbiome-drug-host interactions is fundamental for improving drug disposition and safety responses of colon-targeted formulations, but little information is available on the bidirectional interaction between individual microbiomes and celecoxib. Here, we conducted in vitro batch incubations of human faecal microbiota to obtain a mechanistic proof-of-concept of the short-term impact of celecoxib on activity and composition of colon bacterial communities. Celecoxib-exposed microbiota shifted metabolic activity and community composition, whereas total transcriptionally active bacterial population was not significantly changed. Butyrate production decreased by 50% in a donor-dependent manner, suggesting that celecoxib impacts in vitro fermentation. Microbiota-derived acetate has been associated with inhibition of cancer markers and our results suggest uptake of acetate for bacterial functions when celecoxib was supplied, which potentially favoured bacterial competition for acetyl-CoA. We further assessed whether colon microbiota modulates anti-inflammatory efficacy of celecoxib using a simplified inflammation model, and a novel in vitro simulation of the enterohepatic metabolism. Celecoxib was responsible for only 5% of the variance in bacterial community composition but celecoxib-exposed microbiota preserved barrier function and decreased concentrations of IL-8 and CXCL16 in a donor-dependent manner in our two models simulating gut inflammatory milieu. Our results suggest that celecoxib-microbiome-host interactions may not only elicit adaptations in community composition but also in microbiota functionality, and these may need to be considered for guaranteeing efficient COX-2 inhibition.

RevDate: 2020-02-20

Dhakar K, A Pandey (2020)

Microbial Ecology from the Himalayan Cryosphere Perspective.

Microorganisms, 8(2): pii:microorganisms8020257.

Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.

RevDate: 2020-02-19

Junges DSB, Delabeneta MF, Rosseto LRB, et al (2020)

Antibiotic Activity of Wickerhamomyces anomalus Mycocins on Multidrug-Resistant Acinetobacter baumannii.

Microbial ecology pii:10.1007/s00248-020-01495-9 [Epub ahead of print].

To evaluate the susceptibility of multidrug-resistant Acinetobacter baumannii to mycocins produced by Wickerhamomyces anomalus and to verify the cytotoxicity of these compounds. Three culture supernatants of W. anomalus (WA40, WA45, and WA92), containing mycocins (WA40M1, WA45M2, and WA92M3), were tested on A. baumannii using broth microdilution methods, solid medium tests, and cytotoxicity tests in human erythrocytes and in Artemia saline Leach. W. anomalus was able to produce high antimicrobial mycocins, as even at high dilutions, they inhibited A. baumannii. In a solid medium, it was possible to observe the inhibition of A. baumannii, caused by the diffusion of mycocins between agar. Finally, the three supernatants were not cytotoxic when tested on human erythrocytes and Artemia salina. According to the evidence in this study, the mycocins of W. anomalus have been effective and could be used in the development of new antimicrobial substances.

RevDate: 2020-02-19

Klimenko NS, Tyakht AV, Toshchakov SV, et al (2020)

Co-occurrence patterns of bacteria within microbiome of Moscow subway.

Computational and structural biotechnology journal, 18:314-322 pii:S2001-0370(19)30410-6.

Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, "shotgun" metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.

RevDate: 2020-02-19

Chen X, Krug L, Yang H, et al (2020)

Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars.

Computational and structural biotechnology journal, 18:287-295 pii:S2001-0370(19)30250-8.

Seed endophytes of crop plants have recently received increased attention due to their implications in plant health and the potential to be included in agro-biotechnological applications. While previous studies indicated that plants from the Solanaceae family harbor a highly diverse seed microbiome, genotype-specific effects on the community composition and structure remained largely unexplored. The present study revealed Enterobacteriaceae-dominated seed-endophytic communities in four Nicotiana tabacum L. cultivars originating from Brazil, China, and the USA. When the dissimilarity of bacterial communities was assessed, none of the cultivars showed significant differences in microbial community composition. Various unusual endophyte signatures were represented by Spirochaetaceae family members and the genera Mycobacterium, Clostridium, and Staphylococcus. The bacterial fraction shared by all cultivars was dominated by members of the phyla Proteobacteria and Firmicutes. In total, 29 OTUs were present in all investigated cultivars and accounted for 65.5% of the combined core microbiome reads. Cultivars from the same breeding line were shown to share a higher number of common OTUs than more distant lines. Moreover, the Chinese cultivar Yunyan 87 contained the highest number (33 taxa) of unique signatures. Our results indicate that a distinct proportion of the seed microbiome of N. tabacum remained unaffected by breeding approaches of the last century, while a substantial proportion co-diverged with the plant genotype. Moreover, they provide the basis to identify plant-specific endophytes that could be addressed for upcoming biotechnological approaches in agriculture.

RevDate: 2020-02-19

Röttjers L, K Faust (2020)

manta: a Clustering Algorithm for Weighted Ecological Networks.

mSystems, 5(1): pii:5/1/e00903-19.

Microbial network inference and analysis have become successful approaches to extract biological hypotheses from microbial sequencing data. Network clustering is a crucial step in this analysis. Here, we present a novel heuristic network clustering algorithm, manta, which clusters nodes in weighted networks. In contrast to existing algorithms, manta exploits negative edges while differentiating between weak and strong cluster assignments. For this reason, manta can tackle gradients and is able to avoid clustering problematic nodes. In addition, manta assesses the robustness of cluster assignment, which makes it more robust to noisy data than most existing tools. On noise-free synthetic data, manta equals or outperforms existing algorithms, while it identifies biologically relevant subcompositions in real-world data sets. On a cheese rind data set, manta identifies groups of taxa that correspond to intermediate moisture content in the rinds, while on an ocean data set, the algorithm identifies a cluster of organisms that were reduced in abundance during a transition period but did not correlate strongly to biochemical parameters that changed during the transition period. These case studies demonstrate the power of manta as a tool that identifies biologically informative groups within microbial networks.IMPORTANCE manta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.

RevDate: 2020-02-19

Clark CM, Murphy BT, LM Sanchez (2020)

A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination.

mSystems, 5(1): pii:5/1/e00813-19.

RevDate: 2020-02-19

McAllister SM, Polson SW, Butterfield DA, et al (2020)

Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents.

mSystems, 5(1): pii:5/1/e00553-19.

Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.

RevDate: 2020-02-19

Ossowicki A, Tracanna V, Petrus MLC, et al (2020)

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat.

Proceedings. Biological sciences, 287(1921):20192527.

In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

RevDate: 2020-02-18

Pratama AA, Jiménez DJ, Chen Q, et al (2020)

Delineation of a subgroup of the genus Paraburkholderia, including P. terrae DSM 17804T, P. hospita DSM 17164T and four soil-isolated fungiphiles, reveals remarkable genomic and ecological features - Proposal for the definition of a P. hospita species cluster.

Genome biology and evolution pii:5739963 [Epub ahead of print].

The fungal-interactive (fungiphilic) strains BS001, BS007, BS110 and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around P. hospita (containing the species P. terrae, P. hospita and P. caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared to the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110 and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T and strains BS001, BS007, BS110 and BS437), being clearly divergent from the closely related species P. caribiensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili and diverse secretion systems were found.

RevDate: 2020-02-18

Ghosh TS, Rampelli S, Jeffery IB, et al (2020)

Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries.

Gut pii:gutjnl-2019-319654 [Epub ahead of print].

OBJECTIVE: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty.

DESIGN: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet).

RESULTS: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks.

CONCLUSION: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.

RevDate: 2020-02-17

Orr JN, Neilson R, Freitag TE, et al (2019)

Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils.

Frontiers in plant science, 10:1763.

Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly species-specific nematode suppression may be observed in soils containing a sufficiently high density of Pasteuria spp. spores. This suppression is enacted by the bacteria via inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of Pasteuria spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile Pasteuria spp. and nematode communities in parallel. We have investigated Pasteuria spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the Pasteuria spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that Pasteuria spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to Pasteuria hartismeri, a species first described parasitizing Meloidogyne ardenensis, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a Pasteuria-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and Pratylenchus spp. encumbered by Pasteuria spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the Pasteuria spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of Pasteuria species from eDNA.

RevDate: 2020-02-16

Nkongolo KK, R Narendrula-Kotha (2020)

Advances in monitoring soil microbial community dynamic and function.

Journal of applied genetics pii:10.1007/s13353-020-00549-5 [Epub ahead of print].

Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.

RevDate: 2020-02-18

Iacumin L, Osualdini M, Bovolenta S, et al (2020)

Microbial, chemico-physical and volatile aromatic compounds characterization of Pitina PGI, a peculiar sausage-like product of North East Italy.

Meat science, 163:108081 pii:S0309-1740(19)30925-8 [Epub ahead of print].

Pitina is a fermented sausage-like produced in the mountainous area of the North-East Italy by artisanal plants without the use of both selected starters and casing (Slow Food Presidium). Originally, Pitina has been a way of preserving meat and it is manifactured by meat from ungulates mixed with pork lard, smoked, dryed and ripened. In this study, microbial ecology, physic-chemical parameters, and volatile aromatic compounds of Pitina SR and LR, which differ by the duration of ripening processes, were investigated. Results showed the good hygienic quality. Staphylococcus xylosus and Lactobacillus sakei were responsible for the ripening. Other Coagulase-negative Catalase-positive Cocci (CNCPC) and LAB species were identified: S. equorum, S. warneri, S. succinus and Carnobacterium divergens, Streptococcus equinus, Kocuria rhizophila. Giberella moniliformis and Penicillium turbatum were the only mould species isolated. Strain characterization demonstrated a high genetic variability. Raw meat, environment and ripening conditions seemed to affect strains distribution, which had an impact on the aromatic profile of the product.

RevDate: 2020-02-18

Stopelli E, Duyen VT, Mai TT, et al (2020)

Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes.

The Science of the total environment, 717:137143 pii:S0048-9697(20)30653-7 [Epub ahead of print].

Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010-2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5-510 μg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 μg/L for the studied period of 2010-2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations.

RevDate: 2020-02-16

Zhu X, Campanaro S, Treu L, et al (2020)

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem.

Microbiome, 8(1):22 pii:10.1186/s40168-019-0780-9.

Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.

RevDate: 2020-02-15

Walter JM, Coutinho FH, Leomil L, et al (2020)

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.

Microbial ecology pii:10.1007/s00248-019-01480-x [Epub ahead of print].

Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.

RevDate: 2020-02-15

Louca P, Menni C, S Padmanabhan (2020)

Genomic determinants of hypertension with a focus on metabolomics and the gut microbiome.

American journal of hypertension pii:5736356 [Epub ahead of print].

Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of mendelian forms of syndromic hypotension and HTN have all been linked to mutations in genes whose encoded proteins regulate salt-water balance in the kidney, supporting the primacy of the kidneys in BP regulation. There are over 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet and microbial ecology in humans in the causation of essential hypertension.

RevDate: 2020-02-15

Costa OYA, Zerillo MM, Zühlke D, et al (2020)

Responses of AcidobacteriaGranulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses.

Microorganisms, 8(2): pii:microorganisms8020244.

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.

RevDate: 2020-02-14

Smirnova E, Puri P, Muthiah MD, et al (2020)

Fecal microbiome distinguishes alcohol consumption from alcoholic hepatitis but does not discriminate disease severity.

Hepatology (Baltimore, Md.) [Epub ahead of print].

BACKGROUND AND AIMS: The role of the intestinal microbiome in alcoholic hepatitis is not established. The aims of this study were to: (1) characterize the fecal microbial ecology associated with alcoholic hepatitis, (2) relate microbiome changes to disease severity and (3) infer the functional relevance of shifts in microbial ecology.

METHODS: The fecal microbiome in patients with moderate or severe alcoholic hepatitis (MAH and SAH) was compared to healthy (HC) and heavy drinking controls (HDC). Microbial taxa were identified by 16S pyrosequencing. Functional metagenomics was performed using PICRUSt. Fecal short chain fatty acids (SCFA) were measured using an LC/MS platform.

RESULTS: 78 participants (HC, n=24; HDC, n=20; MAH, n=10; SAH, n=24) were studied. Heavy drinking had a distinct signature compared to healthy controls with depletion of Bacteroidetes (46% vs 26%; p=0.01). Alcoholic hepatitis was associated with a distinct microbiome signature compared to heavy drinking controls (AUC=0.826); differential abundance of Ruminococcaceae, Veillonellaceae, Lachnospiraceae, Porphyromonadaceae, and Rikenellaceae families were the key contributors to these differences. The beta diversity was significantly different amongst the groups (PERMANOVA p < 0.001). Severe alcoholic hepatitis was associated with increased Proteobacteria (SAH 14% vs. HDC 7% and SAH vs. HC 2%, p=0.20 and 0.01 respectively). Firmicutes abundance declined from HDC to MAH to SAH (63% vs. 53% vs. 48% respectively, p=0.09 HDC vs. SAH). Microbial taxa did not distinguish between moderate and severe alcoholic hepatitis (PERMANOVA p= 0.785). SCFA producing bacteria (Lachnospiraceae and Ruminococcaceae) were decreased in alcoholic hepatitis, and a similar decrease was observed in fecal short chain fatty acids among alcoholic hepatitis patients.

CONCLUSIONS: There are distinct changes in fecal microbiome associated with development of but not severity of alcoholic hepatitis.

RevDate: 2020-02-14

Marlow JJ, Colocci I, Jungbluth SP, et al (2020)

Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment.

FEMS microbiology letters pii:5736014 [Epub ahead of print].

Interactions among microorganisms and their mineralogical substrates govern the structure, function, and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset, and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2, and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities 'as they really are' and explore determinants of metabolic activity across a range of microbiomes.

RevDate: 2020-02-14

Hatzenpichler R, Krukenberg V, Spietz RL, et al (2020)

Next-generation physiology approaches to study microbiome function at single cell level.

Nature reviews. Microbiology pii:10.1038/s41579-020-0323-1 [Epub ahead of print].

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.

RevDate: 2020-02-14

Park J, EB Kim (2019)

Differences in microbiome and virome between cattle and horses in the same farm.

Asian-Australasian journal of animal sciences pii:ajas.19.0267 [Epub ahead of print].

Objective: The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal's health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated.

Methods: Here, we collected feces and dust samples (4 groups. Cattle feces; C_F, Horse feces; H_F, Cattle dust; C_D, and Horse dust; H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing.

Results: Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% - max 42.8%), Firmicutes (19.1% - 24.9%), Bacteroidetes (10.6% - 22.1%), and Actinobacteria (6.1% - 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease (FMD) virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected.

Conclusions: Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.

RevDate: 2020-02-13

Nakabachi A, Malenovský I, Gjonov I, et al (2020)

16S rRNA Sequencing Detected Profftella, Liberibacter, Wolbachia, and Diplorickettsia from Relatives of the Asian Citrus Psyllid.

Microbial ecology pii:10.1007/s00248-020-01491-z [Epub ahead of print].

The Asian citrus psyllid Diaphorina citri (Hemiptera: Psylloidea) is a serious pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria: Rhizobiales), the causative agents of the incurable citrus disease, huanglongbing or greening disease. Diaphorina citri possesses a specialized organ called a bacteriome, which harbors vertically transmitted intracellular mutualists, Ca. Carsonella ruddii (Gammaproteobacteria: Oceanospirillales) and Ca. Profftella armatura (Gammaproteobacteria: Betaproteobacteriales). Whereas Carsonella is a typical nutritional symbiont, Profftella is an unprecedented type of toxin-producing defensive symbiont, unusually sharing organelle-like features with nutritional symbionts. Additionally, many D. citri strains are infected with Wolbachia, which manipulate reproduction in various arthropod hosts. In the present study, in an effort to obtain insights into the evolution of symbioses between Diaphorina and bacteria, microbiomes of psyllids closely related to D. citri were investigated. Bacterial populations of Diaphorina cf. continua and Diaphorina lycii were analyzed using Illumina sequencing of 16S rRNA gene amplicons and compared with data obtained from D. citri. The analysis revealed that all three Diaphorina spp. harbor Profftella as well as Carsonella lineages, implying that Profftella is widespread within the genus Diaphorina. Moreover, the analysis identified Ca. Liberibacter europaeus and Diplorickettsia sp. (Gammaproteobacteria: Diplorickettsiales) in D. cf. continua, and a total of four Wolbachia (Alphaproteobacteria: Rickettsiales) lineages in the three psyllid species. These results provide deeper insights into the interactions among insects, bacteria, and plants, which would eventually help to better manage horticulture.

RevDate: 2020-02-13

Glendinning L, Stewart RD, Pallen MJ, et al (2020)

Assembly of hundreds of novel bacterial genomes from the chicken caecum.

Genome biology, 21(1):34 pii:10.1186/s13059-020-1947-1.

BACKGROUND: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.

RESULTS: We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.

CONCLUSIONS: This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

RevDate: 2020-02-11

Boreczek J, Litwinek D, Żylińska-Urban J, et al (2020)

Bacterial community dynamics in spontaneous sourdoughs made from wheat, spelt, and rye wholemeal flour.

MicrobiologyOpen [Epub ahead of print].

Sourdough fermentation is a traditional process that is used to improve bread quality. A spontaneous sourdough ecosystem consists of a mixture of flour and water that is fermented by endogenous lactic acid bacteria (LAB) and yeasts. The aim of this study was to identify bacterial diversity during backslopping of spontaneous sourdoughs prepared from wheat, spelt, or rye wholemeal flour. Culture-dependent analyses showed that the number of LAB (109 CFU/ml) was higher by three orders of magnitude than the number of yeasts (106 CFU/ml), irrespective of the flour type. These results were complemented by next-generation sequencing of the 16S rDNA V3 and V4 variable regions. The dominant phylum in all sourdough samples was Firmicutes, which was represented exclusively by the Lactobacillales order. The two remaining and less abundant phyla were Proteobacteria and Bacteroidetes. The culture-independent approach allowed us to detect changes in microbial ecology during the 72-hr fermentation period. Weissella sp. was the most abundant genus after 24 hr of fermentation of the rye sourdough, but as the process progressed, its abundance decreased in favor of the Lactobacillus genus similarly as in wheat and spelt sourdoughs. The Lactobacillus genus was dominant in all sourdoughs after 72 hr, which was consistent with our results obtained using culture-dependent analyses. This work was carried out to determine the microbial biodiversity of sourdoughs that are made from wheat, spelt, and rye wholemeal flour and can be used as a source of strains for specific starter cultures to produce functional bread.

RevDate: 2020-02-11

Hofmann K, Huptas C, Doll EV, et al (2020)

Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

Two strains, WS 5063T and WS 5067, isolated from raw cow's milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown, Pseudomonas species by 16S rRNA and rpoD gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel Pseudomonas species. It was most closely related to Pseudomonas synxantha DSM 18928T with an ANIm of 91.4 %. The DNA G+C content of WS 5063T was 60.0 mol %. Phenotypic characterizations showed that the isolates are rod-shaped, motile, catalase- and oxidase-positive, and aerobic. Growth occurred at 4-34 °C and at pH values of pH 5.5-8.0. Both strains showed strong β-haemolysis on blood agar. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant quinone was Q-9 (90 %), but noticeable amounts of Q-8 (9 %) and traces of Q-7 were also detected. Fatty acid profiles were typical for Pseudomonas species and exhibited C16 : 0 as a major component. Based on these results, we conclude that both strains belong to a novel species, for which the name Pseudomonas haemolytica sp. nov. is proposed. The type strain is WS 5063T (=DSM 108987T=LMG 31232T) and an additional strain is WS 5067 (=DSM 108988=LMG 31233).

RevDate: 2020-02-11

Wenning M, Breitenwieser F, Huptas C, et al (2020)

Brevilactibacter flavus gen. nov., sp. nov., a novel bacterium of the family Propionibacteriaceae isolated from raw milk and dairy products and reclassification of Propioniciclava sinopodophylli as Brevilactibacter sinopodophylli comb. nov.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

Eight facultatively anaerobic rod-shaped bacteria were isolated from raw milk and two other dairy products. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates are placed in a distinct lineage within the family Propionibacteriaceae with Propioniciclava sinopodophylli and Propioniciclava tarda as the closest relatives (94.6 and 93.5 % similarity, respectively). The cell-wall peptidoglycan contained meso-diaminopimelic acid, alanine and glutamic acid and was of the A1γ type (meso-DAP-direct). The major cellular fatty acid was anteiso-C15 : 0 and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and three unidentified glycolipids. The quinone system contained predominantly menaquinone MK-9(H4). The G+C content of the genomic DNA of strain VG341T was 67.7 mol%. The whole-cell sugar pattern contained ribose, rhamnose, arabinose and galactose. On the basis of phenotypic and genetic data, eight strains (VG341T, WS4684, WS4769, WS 4882, WS4883, WS4901, WS4902 and WS4904) are proposed to be classified as members of a novel species in a new genus of the family Propionibacteriaceae, for which the name Brevilactibacter flavus gen. nov., sp. nov. is proposed. The type strain is VG341T (=WS4900T=DSM 100885T=LMG 29089T) and seven additional strains are WS4684, WS4769, WS4882, WS4883, WS4901, WS4902 and WS4904. Furthermore, we propose the reclassification of P. sinopodophylli as Brevilactibacter sinopodophylli comb. nov.

RevDate: 2020-02-11

Zhang J, Fu XX, Li RQ, et al (2020)

The hornwort genome and early land plant evolution.

Nature plants pii:10.1038/s41477-019-0588-4 [Epub ahead of print].

Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.

RevDate: 2020-02-11

VanInsberghe D, Elsherbini JA, Varian B, et al (2020)

Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms.

Nature microbiology pii:10.1038/s41564-020-0668-2 [Epub ahead of print].

Although Clostridium difficile is widely considered an antibiotic- and hospital-associated pathogen, recent evidence indicates that this is an insufficient depiction of the risks and reservoirs. A common thread that links all major risk factors of infection is their association with gastrointestinal disturbances, but this relationship to C. difficile colonization has never been tested directly. Here, we show that disturbances caused by diarrhoeal events trigger susceptibility to C. difficile colonization. Using survey data of the human gut microbiome, we detected C. difficile colonization and blooms in people recovering from food poisoning and Vibrio cholerae infections. Carriers remained colonized for year-long time scales and experienced highly variable patterns of C. difficile abundance, where increased shedding over short periods of 1-2 d interrupted week-long periods in which C. difficile was undetectable. Given that short shedding events were often linked to gastrointestinal disturbances, our results help explain why C. difficile is frequently detected as a co-infecting pathogen in patients with diarrhoea. To directly test the impact of diarrhoea on susceptibility to colonization, we developed a mouse model of variable disturbance intensity, which allowed us to monitor colonization in the absence of disease. As mice exposed to avirulent C. difficile spores ingested increasing quantities of laxatives, more individuals experienced C. difficile blooms. Our results indicate that the likelihood of colonization is highest in the days immediately following acute disturbances, suggesting that this could be an important window during which transmission could be interrupted and the incidence of infection lowered.

RevDate: 2020-02-10

Lee JY, Haruta S, Kato S, et al (2019)

Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data.

Frontiers in microbiology, 10:3049.

Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients - basic parameters required for implementing the MIIA - are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite.

RevDate: 2020-02-10

Babaahmadifooladi M, Jacxsens L, Van de Wiele T, et al (2020)

Gap analysis of nickel bioaccessibility and bioavailability in different food matrices and its impact on the nickel exposure assessment.

Food research international (Ottawa, Ont.), 129:108866.

The metal nickel is well known to cause nickel allergy in sensitive humans by prolonged dermal contact to materials releasing (high) amounts of nickel. Oral nickel exposure via water and food intake is of potential concern. Nickel is essential to plants and animals and can be naturally found in food products or contamination may occur across the agro-food chain. This gap analysis is an evaluation of nickel as a potential food safety hazard causing a risk for human health. In the first step, the available data regarding the occurrence of nickel and its contamination in food and drinks have been collected through literature review. Subsequently, a discussion is held on the potential risks associated with this contamination. Elevated nickel concentrations were mostly found in plant-based foods, e.g. legumes and nuts in which nickel of natural origin is expected. However, it was observed that dedicated and systematic screening of foodstuffs for the presence of nickel is currently still lacking. In a next step, published studies on exposure of humans to nickel via foods and drinks were critically evaluated. Not including bioaccessibility and/or bioavailability of the metal may lead to an overestimation of the exposure of the body to nickel via food and drinks. This overestimation may be problematic when the measured nickel level in foods is high and bioaccessibility and/or bioavailability of nickel in these products is low. Therefore, this paper analyzes the outcomes of the existing dietary intake and bioaccessibility/bioavailability studies conducted for nickel. Besides, the available gaps in nickel bioaccessibility and/or bioavailability studies have been clarified in this paper. The reported bioaccessibility and bioavailability percentages for different food and drinks were found to vary between

RevDate: 2020-02-10

Vossen E, Goethals S, De Vrieze J, et al (2020)

Red and processed meat consumption within two different dietary patterns: Effect on the colon microbial community and volatile metabolites in pigs.

Food research international (Ottawa, Ont.), 129:108793.

Pigs were fed either red and processed meat or chicken meat within either a prudent or a Western dietary pattern for four weeks (2 × 2 full factorial design). The colon microbial community and volatile organic compounds were assessed (either quantified or based on their presence). Results show that Lactobacilli were characteristic for the chicken × prudent dietary pattern treatment and Paraprevotella for the red and processed meat × prudent dietary pattern treatment. Enterobacteriaceae and Desulfovibrio were characteristic for the chicken × Western dietary pattern treatment and Butyrivibrio for the red and processed meat × Western dietary pattern treatment. Campylobacter was characteristic for chicken consumption and Clostridium XIVa for red and processed meat, irrespective of the dietary pattern. Ethyl valerate and 1-methylthio-propane were observed more frequently in pigs fed red and processed meat compared to chicken meat. The prevalence of 3-methylbutanal was >80% for pigs receiving a Western dietary pattern, whereas for pigs fed a prudent dietary pattern the prevalence was <35%. The concentration of butanoic acid was significantly higher when the prudent dietary pattern was given, compared to the Western dietary pattern, but no differences for other short chain fatty acids or protein fermentation products were observed.

RevDate: 2020-02-08

Rombouts JL, Kranendonk EMM, Regueira A, et al (2020)

Selecting for lactic acid producing and utilising bacteria in anaerobic enrichment cultures.

Biotechnology and bioengineering [Epub ahead of print].

Lactic acid producing bacteria are important in many fermentations, such as the production of biobased plastics. Insight in the competitive advantage of lactic acid bacteria over other fermentative bacteria in a mixed culture enables ecology-based process design and can aid the development of sustainable and energy-efficient bioprocesses. Here we demonstrate the enrichment of lactic acid bacteria in a controlled sequencing batch bioreactor environment using a glucose based medium supplemented with peptides and B vitamins. A mineral medium enrichment operated in parallel was dominated by Ethanoligenens species and fermented glucose to acetate, butyrate and hydrogen. The complex medium enrichment was populated by Lactococcus, Lactobacillus and Megasphaera species and showed a product spectrum of acetate, ethanol, propionate, butyrate and valerate. An intermediate peak of lactate was observed, showing the simultaneous production and consumption of lactate, which is of concern for lactic acid production purposes. This study underlines that the competitive advantage for lactic acid producing bacteria primarily lies in their ability to attain a high biomass specific uptake rate of glucose, which was two times higher for the complex medium enrichment when compared to the mineral medium enrichment. The competitive advantage of lactic acid production in rich media can be explained using a resource allocation theory for microbial growth processes. This article is protected by copyright. All rights reserved.

RevDate: 2020-02-08

Kitzinger K, Marchant HK, Bristow LA, et al (2020)

Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.

Nature communications, 11(1):767 pii:10.1038/s41467-020-14542-3.

Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean.

RevDate: 2020-02-07

Fenske GJ, Ghimire S, Antony L, et al (2020)

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.

FEMS microbiology ecology pii:5729940 [Epub ahead of print].

Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contented that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

RevDate: 2020-02-07

Mariano C, Mello IS, Barros BM, et al (2020)

Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association.

Environmental science and pollution research international pii:10.1007/s11356-020-07913-2 [Epub ahead of print].

This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.

RevDate: 2020-02-06

Lee HJ, KS Whang (2020)

Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

A Gram-stain-negative bacterium, designated strain PF-30T, was isolated from floodwater of a paddy field in South Korea. Strain PF-30T was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25-40 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum pH 7.0) and at salinities of 0.5-3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30T belongs to the genus Elioraea, showing highest sequence similarity to Elioraea tepidiphila TU-7T (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae. The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain PF-30T and E. tepidiphila TU-7T yielded an ANI value of 75.1 % and DNA-DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30T was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30T represents a novel species of the genus Elioraea, for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30T (=KACC 19985T=NBRC 113984T).

RevDate: 2020-02-06

Smichi N, Messaoudi Y, Allaf K, et al (2020)

Steam explosion (SE) and instant controlled pressure drop (DIC) as thermo-hydro-mechanical pretreatment methods for bioethanol production.

Bioprocess and biosystems engineering pii:10.1007/s00449-020-02297-6 [Epub ahead of print].

Lignocellulosic biomass can be considered as one of the largest sources for the production of renewable biofuels (bioethanol). It involves an enzymatic treatment capable of ensuring the depolymerization of cellulose into fermentable sugars, followed by the production of ethanol by appropriate bacteriological fermentation. Proper destruction of the compact natural structure of the biomass would allow an interesting intensification of the operation. Among the most prominent technical approaches, the steam explosion (SE) is the most famous. However, this high pressure-high temperature process implies too high energy consumption while leading to the generation of many non-fermentable molecules. In recent years, many studies have proposed the use of the Instant Controlled Pressure-Drop (DIC) texturing pretreatment as an effective alternative to SE for ethanol production. Therefore, in this manuscript, we propose to compare and discuss the fundamental principles and experimental results of these two operations, as presented in the relevant literature.

RevDate: 2020-02-06

Snyder GT, Matsumoto R, Suzuki Y, et al (2020)

Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes.

Scientific reports, 10(1):1876 pii:10.1038/s41598-020-58723-y.

Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.

RevDate: 2020-02-05

Dhaulaniya AS, Balan B, Yadav A, et al (2020)

Development of an FTIR based chemometric model for the qualitative and quantitative evaluation of cane sugar as an added sugar adulterant in apple fruit juices.

Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment [Epub ahead of print].

A Fourier Transform Infrared Spectroscopy based chemometric model was evaluated for the rapid identification and estimation of cane sugar as an added sugar adulterant in apple fruit juices. For all the ninety samples, spectra were acquired in the mid-infrared range (4000 cm-1-400 cm-1). The spectral analysis provided information regarding the distinctive variable region, which lies in the range of 1200cm-1 to 900cm-1, designated as fingerprint region for the carbohydrates. A specific peak in the fingerprint region was observed at 997cm-1 in all the adulterated samples and was undetectable in pure samples. Based on different levels of cane sugar adulteration (5, 10, 15, and 20%), principal component analysis showed the clustering of samples and further helped us in compression of data by selecting wavenumbers with maximum variability based on the loading line plot. Supervised classification methods (SIMCA and LDA) were evaluated based on their classification efficiencies for a test set. Though SIMCA showed 100% classification efficiency (Raw data set), LDA was able to classify the test set with an accuracy of only 96.67% (Raw as well as Transformed data set) between pure and 5% adulterated samples. For the quantitative estimation, calibration models were developed using partial least square regression (PLS-R) and principal component regression method (PCR) methods. PLS-1st derivative showed a maximum coefficient of determination (R2) with a value of 0.991 for calibration and 0.992 for prediction. The RMSECV, RMSEP, LOD and LOQ observed for PLS-1st derivative model were 0.75% w/v, 0.61% w/v, 1.28%w/v and 3.88%w/v, respectively. The coefficient of variation as a measure of precision (repeatability) was also determined for all models, and it ranged from 0.23% to 1.83% (interday), and 0.25% to 1.43% (intraday).

RevDate: 2020-02-05

Wang F, Cale JA, N Erbilgin (2020)

Induced Defenses of a Novel Host Tree Affect the Growth and Interactions of Bark Beetle-Vectored Fungi.

Microbial ecology pii:10.1007/s00248-020-01490-0 [Epub ahead of print].

Mountain pine beetle (MPB) has recently expanded its host range to the novel jack pine forests in Alberta. Invasion success of MPB may depend on the outcome of interactions between its symbiotic fungus Grosmannia clavigera and Ophiostoma ips, a fungal associate of a potential competitor Ips pini. However, how the quality of jack pine phloem could influence interactions between the fungi is unknown. We investigated whether introduced concentrations of host nitrogen and monoterpenes affect the growth of and interaction between the fungi. Nitrogen concentrations did not affect the growth rate of either fungus. In the absence of monoterpenes, the presence of O. ips promoted G. clavigera growth. Monoterpenes either promoted or inhibited the growth of both fungi, and altered the outcome of species interactions from facilitation to no-effect. Overall, these results suggest that jack pine phloem quality and the presence of a niche-sharing fungus could influence MPB development.

RevDate: 2020-02-05

Rodriguez-Gonzalez RA, Leung CY, Chan BK, et al (2020)

Quantitative Models of Phage-Antibiotic Combination Therapy.

mSystems, 5(1): pii:5/1/e00756-19.

The spread of multidrug-resistant (MDR) bacteria is a global public health crisis. Bacteriophage therapy (or "phage therapy") constitutes a potential alternative approach to treat MDR infections. However, the effective use of phage therapy may be limited when phage-resistant bacterial mutants evolve and proliferate during treatment. Here, we develop a nonlinear population dynamics model of combination therapy that accounts for the system-level interactions between bacteria, phage, and antibiotics for in vivo application given an immune response against bacteria. We simulate the combination therapy model for two strains of Pseudomonas aeruginosa, one which is phage sensitive (and antibiotic resistant) and one which is antibiotic sensitive (and phage resistant). We find that combination therapy outperforms either phage or antibiotic alone and that therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotics, e.g., ciprofloxacin. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of innate immunity in shaping therapeutic outcomes.IMPORTANCE This work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa In doing so, the paper addresses three key questions. How robust is combination therapy to variation in the resistance profiles of pathogens? What is the role of immune responses in shaping therapeutic outcomes? What levels of phage and antibiotics are necessary for curative success? As we show, combination therapy outperforms either phage or antibiotic alone, and therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotic. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of system-level feedbacks in shaping therapeutic outcomes.

RevDate: 2020-02-05

Tkacz A, Bestion E, Bo Z, et al (2020)

Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison.

mBio, 11(1): pii:mBio.02785-19.

Plant roots influence the soil microbiota via physical interaction, secretion, and plant immunity. However, it is unclear whether the root fraction or soil is more important in determining the structure of the prokaryotic or eukaryotic community and whether this varies between plant species. Furthermore, the leaf (phyllosphere) and root microbiotas have a large overlap; however, it is unclear whether this results from colonization of the phyllosphere by the root microbiota. Soil, rhizosphere, rhizoplane, and root endosphere prokaryote-, eukaryote-, and fungus-specific microbiotas of four plant species were analyzed with high-throughput sequencing. The strengths of factors controlling microbiota structure were determined using permutational multivariate analysis of variance (PERMANOVA) statistics. The origin of the phyllosphere microbiota was investigated using a soil swap experiment. Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root itself more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. A reciprocal soil swap experiment shows that the phyllosphere is colonized from the soil in which the plant is grown.IMPORTANCE Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined, indicating conserved adaptation of microbial communities to plants. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. We observed a remarkable similarity in the structure of a plant's phyllosphere and root microbiotas and show by reciprocal soil swap experiments that both fractions are colonized from the soil in which the plant is grown. Thus, the phyllosphere is continuously colonized by the soil microbiota.

RevDate: 2020-02-05

Gionchetta G, Oliva F, Romaní AM, et al (2020)

Hydrological variations shape diversity and functional responses of streambed microbes.

The Science of the total environment, 714:136838 pii:S0048-9697(20)30348-X [Epub ahead of print].

Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.

RevDate: 2020-02-04

Pantigoso HA, Manter DK, JM Vivanco (2020)

Differential Effects of Phosphorus Fertilization on Plant Uptake and Rhizosphere Microbiome of Cultivated and Non-cultivated Potatoes.

Microbial ecology pii:10.1007/s00248-020-01486-w [Epub ahead of print].

There is evidence that shows that phosphorus (P) fertilization has a moderate effect on the rhizosphere microbial composition of cultivated crops. But how this effect is manifested on wild species of the same crop is not clear. This study compares the impact of phosphorus fertilization with rhizosphere bacterial community composition and its predicted functions, related to P-cycling genes, in both cultivated and non-cultivated potato (Solanum sp.) plants. It was found that the biomass of non-cultivated potatoes was more responsive to P fertilization as compared with cultivated plants. Differences in general bacterial community composition patterns under increasing P amendments were subtle for both potato groups. However, potato genotype significantly influenced community composition with several bacterial families being more abundant in the cultivated plants. In addition, the predicted phosphatases had lower abundances in modern cultivars compared with non-cultivated potatoes. In summary, despite higher accumulation of differentially abundant bacteria in the rhizosphere of cultivated plants, the responsiveness of these plants to increase P levels was lower than in non-cultivated plants.

RevDate: 2020-02-04

Morand C, De Roos B, Garcia-Conesa MT, et al (2020)

Why interindividual variation in response to consumption of plant food bioactives matters for future personalised nutrition.

The Proceedings of the Nutrition Society pii:S0029665120000014 [Epub ahead of print].

Food phytochemicals are increasingly considered to play a key role in the cardiometabolic health effects of plant foods. However, the heterogeneity in responsiveness to their intake frequently observed in clinical trials can hinder the beneficial effects of these compounds in specific subpopulations. A range of factors, including genetic background, gut microbiota, age, sex and health status, could be involved in these interindividual variations; however, the current knowledge is limited and fragmented. The European network, European Cooperation in Science and Technology (COST)-POSITIVe, has analysed, in a systematic way, existing knowledge with the aim to better understand the factors responsible for the interindividual variation in response to the consumption of the major families of plant food bioactives, regarding their bioavailability and bioefficacy. If differences in bioavailability, likely reflecting differences in human subjects' genetics or in gut microbiota composition and functionality, are believed to underpin much of the interindividual variability, the key molecular determinants or microbial species remain to be identified. The systematic analysis of published studies conducted to assess the interindividual variation in biomarkers of cardiometabolic risk suggested some factors (such as adiposity and health status) as involved in between-subject variation. However, the contribution of these factors is not demonstrated consistently across the different compounds and biological outcomes and would deserve further investigations. The findings of the network clearly highlight that the human subjects' intervention studies published so far are not adequate to investigate the relevant determinants of the absorption/metabolism and biological responsiveness. They also emphasise the need for a new generation of intervention studies designed to capture this interindividual variation.

RevDate: 2020-02-05

Woodhams DC, Bletz MC, Becker CG, et al (2020)

Host-associated microbiomes are predicted by immune system complexity and climate.

Genome biology, 21(1):23 pii:10.1186/s13059-019-1908-8.

BACKGROUND: Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.

RESULTS: Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.

CONCLUSIONS: Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.

RevDate: 2020-02-04

Purushotham N, Jones E, Monk J, et al (2020)

Community Structure, Diversity and Potential of Endophytic Bacteria in the Primitive New Zealand Medicinal Plant Pseudowintera colorata.

Plants (Basel, Switzerland), 9(2): pii:plants9020156.

Although the importance of the plant microbiome in commercial plant health has been well established, there are limited studies in native medicinal plants. Pseudowintera colorata (horopito) is a native New Zealand medicinal plant recognized for its antimicrobial properties. Denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq analysis of P. colorata plants from ten sites across New Zealand showed that tissue type strongly influenced the diversity and richness of endophytic bacteria (PERMANOVA, P < 0.05). In addition, two OTUs belonging to the genus Pseudomonas (Greengenes ID: 646549 and 138914) were found to be present in >75% of all P. colorata leaf, stem and root samples and were identified as the members of the P. colorata "core endomicrobiome". Culture-independent analysis was complemented by the recovery of 405 endophytic bacteria from the tissues of P. colorata. Some of these cultured endophytic bacteria (n = 10) showed high antagonism against four different phytopathogenic fungi tested. The influence of endophytic bacteria on plant growth was assessed by inoculating P. colorata seedlings. The mean shoot height of seedlings treated with Bacillus sp. TP1LA1B were longer (1.83×), had higher shoot dry weight (1.8×) and produced more internodes (1.8×) compared to the control.

RevDate: 2020-02-03

Mascarenhas R, Ruziska FM, Moreira EF, et al (2019)

Integrating Computational Methods to Investigate the Macroecology of Microbiomes.

Frontiers in genetics, 10:1344.

Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.

RevDate: 2020-02-01

Trebuch LM, Oyserman BO, Janssen M, et al (2020)

Impact of hydraulic retention time on community assembly and function of photogranules for wastewater treatment.

Water research, 173:115506 pii:S0043-1354(20)30042-7 [Epub ahead of print].

Photogranules are dense, spherical agglomerates of cyanobacteria, microalgae and non-phototrophic microorganisms that have considerable advantages in terms of harvesting and nutrient removal rates for light driven wastewater treatment processes. This ecosystem is poorly understood in terms of the microbial community structure and the response of the community to changing abiotic conditions. To get a better understanding, we investigated the effect of hydraulic retention time (HRT) on photogranule formation and community assembly over a period of 148 days. Three laboratory bioreactors were inoculated with field samples from various locations in the Netherlands and operated in sequencing batch mode. The bioreactors were operated at four different HRTs (2.00, 1.00, 0.67, 0.33 days), while retaining the same solid retention time of 7 days. A microbial community with excellent settling characteristics (95-99% separation efficiency) was established within 2-5 weeks. The observed nutrient uptake rates ranged from 24 to 90 mgN L-1 day-1 and from 3.1 to 5.4 mgP L-1 day-1 depending on the applied HRT. The transition from single-cell suspension culture to floccular agglomeration to granular sludge was monitored by microscopy and 16S/18S sequencing. In particular, two important variables for driving aggregation and granulation, and for the structural integrity of photogranules were identified: 1. Extracellular polymeric substances (EPS) with high protein to polysaccharide ratio and 2. specific microorganisms. The key players were found to be the cyanobacteria Limnothrix and Cephalothrix, the colony forming photosynthetic eukaryotes within Chlamydomonadaceae, and the biofilm producing bacteria Zoogloea and Thauera. Knowing the makeup of the microbial community and the operational conditions influencing granulation and bioreactor function is crucial for successful operation of photogranular systems.

RevDate: 2020-01-31

Eichorst SA, Trojan D, Huntemann M, et al (2020)

One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil.

Microbiology resource announcements, 9(5): pii:9/5/e01087-19.

We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.

RevDate: 2020-01-31

De Maayer P, Pillay T, TA Coutinho (2020)

Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales.

BMC genomics, 21(1):100 pii:10.1186/s12864-020-6529-9.

BACKGROUND: The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized.

RESULTS: Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~ 3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria.

CONCLUSIONS: The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.

RevDate: 2020-01-30

Ahmad JI, Liu G, van der Wielen PWJJ, et al (2020)

Effects of cold recovery technology on the microbial drinking water quality in unchlorinated distribution systems.

Environmental research, 183:109175 pii:S0013-9351(20)30067-0 [Epub ahead of print].

Drinking water distribution systems (DWDSs) are used to supply hygienically safe and biologically stable water for human consumption. The potential of thermal energy recovery from drinking water has been explored recently to provide cooling for buildings. Yet, the effects of increased water temperature induced by this "cold recovery" on the water quality in DWDSs are not known. The objective of this study was to investigate the impact of cold recovery from DWDSs on the microbiological quality of drinking water. For this purpose, three pilot distribution systems were operated in parallel for 38 weeks. System 1 has an operational heat exchanger, mimicking the cold recovery system by maintaining the water temperature at 25 °C; system 2 operated with a non-operational heat exchanger and system 3 run without heat exchanger. The results showed no significant effects on drinking water quality: cell numbers and ATP concentrations remained around 3.5 × 105 cells/ml and 4 ng ATP/l, comparable observed operational taxonomic units (OTUs) (~470-490) and similar Shannon indices (7.7-8.9). In the system with cold recovery, a higher relative abundance of Pseudomonas spp. and Chryseobacterium spp. was observed in the drinking water microbial community, but only when the cold recovery induced temperature difference (ΔT) was higher than 9 °C. In the 38 weeks' old biofilm, higher ATP concentration (475 vs. 89 pg/cm2), lower diversity (observed OTUs: 88 vs. ≥200) and a different bacterial community composition (e.g. higher relative abundance of Novosphingobium spp.) were detected, which did not influence water quality. No impacts were observed for the selected opportunisitic pathogens after introducing cold recovery. It is concluded that cold recovery does not affect bacterial water quality. Further investigation for a longer period is commended to understand the dynamic responses of biofilm to the increased temperature caused by cold recovery.

RevDate: 2020-01-30

Harkes P, van Steenbrugge JJM, van den Elsen SJJ, et al (2019)

Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management.

Frontiers in plant science, 10:1697.

Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.

RevDate: 2020-01-30

Eberl C, Ring D, Münch PC, et al (2019)

Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities.

Frontiers in microbiology, 10:2999.

The Oligo-Mouse-Microbiota (OMM12) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al., 2016). To date, the OMM12 model has been established in several germ-free mouse facilities world-wide and is employed to address a growing variety of research questions related to infection biology, mucosal immunology, microbial ecology and host-microbiome metabolic cross-talk. The OMM12 consists of 12 sequenced and publically available strains isolated from mice, representing five bacterial phyla that are naturally abundant in the murine gastrointestinal tract (Lagkouvardos et al., 2016). Under germ-free conditions, the OMM12 colonizes mice stably over multiple generations. Here, we investigated whether stably colonized OMM12 mouse lines could be reproducibly established in different animal facilities. Germ-free C57Bl/6J mice were inoculated with a frozen mixture of the OMM12 strains. Within 2 weeks after application, the OMM12 community reached the same stable composition in all facilities, as determined by fecal microbiome analysis. We show that a second application of the OMM12 strains after 72 h leads to a more stable community composition than a single application. The availability of such protocols for reliable de novo generation of gnotobiotic rodents will certainly contribute to increasing experimental reproducibility in biomedical research.

RevDate: 2020-01-30

Rath S, Rud T, Pieper DH, et al (2019)

Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia.

Frontiers in microbiology, 10:2966.

Human gut bacteria metabolize dietary components such as choline and carnitine to trimethylamine (TMA) that is subsequently oxidized to trimethylamine-N-oxide (TMAO) by hepatic enzymes. Increased plasma levels of TMAO are associated with the development of cardiovascular and renal disease. In this study, we applied gene-targeted assays in order to quantify (qPCR) and characterize (MiSeq) bacterial genes encoding enzymes responsible for TMA production, namely choline-TMA lyase (CutC), carnitine oxygenase (CntA) and betaine reductase (GrdH) in 89 fecal samples derived from various mammals spanning three dietary groups (carnivores, omnivores and herbivores) and four host orders (Carnivora, Primates, Artiodactyla and Perissodactyla). All samples contained potential TMA-producing bacteria, however, at low abundances (<1.2% of total community). The cutC gene was more abundant in omnivores and carnivores compared with herbivores. CntA was almost absent from herbivores and grdH showed lowest average abundance of all three genes. Bacteria harboring cutC and grdH displayed high diversities where sequence types affiliated with various taxa within Firmicutes dominated, whereas cntA comprised sequences primarily linked to Escherichia. Composition of TMA-forming communities was strongly influenced by diet and host taxonomy and despite their high correlation, both factors contributed uniquely to community structure. Furthermore, Random Forest (RF) models could differentiate between groups at high accuracies. This study gives a comprehensive overview of potential TMA-producing bacteria in the mammalian gut demonstrating that both diet and host taxonomy govern their abundance and composition. It highlights the role of functional redundancy sustaining potential TMA formation in distinct gut environments.

RevDate: 2020-01-30

Rahi P, P Vaishampayan (2019)

Editorial: MALDI-TOF MS Application in Microbial Ecology Studies.

Frontiers in microbiology, 10:2954.

RevDate: 2020-01-30

Van Gestel NC, Ducklow HW, E Bååth (2020)

Comparing temperature sensitivity of bacterial growth in Antarctic marine water and soil.

Global change biology [Epub ahead of print].

The western Antarctic Peninsula is an extreme low temperature environment that is warming rapidly due to global change. Little is known, however, about the temperature sensitivity of growth of microbial communities in Antarctic soils and in the surrounding oceanic waters. This is the first study that directly compares temperature adaptation of adjacent marine and terrestrial bacteria in a polar environment. The bacterial communities in the ocean were adapted to lower temperatures than those from nearby soil, with cardinal temperatures for growth in the ocean being the lowest so far reported for microbial communities. This was reflected in lower minimum (Tmin) and optimum temperatures (Topt) for growth in water (-17°C and +20°C, respectively) than in soil (-11°C and +27°C), with lower sensitivity to changes in temperature (Q10 ; 0-10°C interval) in Antarctic water (2.7) than in soil (3.9). This is likely due to the more stable low temperature conditions of Antarctic waters than soils, and the fact that maximum in situ temperatures in water are lower than in soils, at least in summer. Importantly, the thermally stable environment of Antarctic marine water makes it feasible to create a single temperature response curve for bacterial communities. This would thus allow for calculations of temperature-corrected growth rates, and thereby quantifying the influence of factors other than temperature on observed growth rates, as well as predicting the effects of future temperature increases on Antarctic marine bacteria.

RevDate: 2020-01-30

Zhang Z, Liu W, Shao S, et al (2020)

Diverse Genomic Backgrounds Vs. Highly Conserved Symbiotic Genes in Sesbania-Nodulating Bacteria: Shaping of the Rhizobial Community by Host and Soil Properties.

Microbial ecology pii:10.1007/s00248-020-01489-7 [Epub ahead of print].

Aiming at investigating the overall diversity, biogeography, and symbiosis gene evolutionary history of the Sesbania cannabina-nodulating rhizobia in China, a total of 874 rhizobial isolates originating from the root nodules of this plant grown at different sites were characterized and compared with those of some reference strains. All of the S. cannabina-nodulating rhizobia were classified into 16 (geno) species, including seven novel genospecies in the genera Ensifer, Rhizobium, Neorhizobium, and Agrobacterium, with Ensifer sesbaniae and Neorhizobium huautlense as the dominant and universal species. Ten of these species were found to nodulate other leguminous hosts or to lack nodulating abilities and were defined as symbiovar sesbania. Biogeographic patterns were observed, for which pH, TN, AK, and AP were the main determinants. The effects of pH were opposite to those of TN and AK, while AP presented effects independently of TN, AK, and pH. Symbiotic genes of these rhizobia showed a common origin, but nodA evolved faster than nifH. Point mutation is the main driving force in the evolution of both nodA and nifH, and lateral transfer of symbiotic genes might play an important role in the formation of diverse S. cannabina-nodulating rhizobial species. S. cannabina only nodulates with Sesbania rhizobia, demonstrating its severe selection on rhizobial symbiosis genes. Soil pH and physiochemical characteristics could affect rhizobial survival and competitive nodulation. This study provides insight into the community shifts and evolution of rhizobia in relation to their host and soil environments.

RevDate: 2020-01-30

Ghannam RB, Schaerer LG, Butler TM, et al (2020)

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities.

mSphere, 5(1): pii:5/1/e00481-19.

We conducted a global characterization of the microbial communities of shipping ports to serve as a novel system to investigate microbial biogeography. The community structures of port microbes from marine and freshwater habitats house relatively similar phyla, despite spanning large spatial scales. As part of this project, we collected 1,218 surface water samples from 604 locations across eight countries and three continents to catalogue a total of 20 shipping ports distributed across the East and West Coast of the United States, Europe, and Asia to represent the largest study of port-associated microbial communities to date. Here, we demonstrated the utility of machine learning to leverage this robust system to characterize microbial biogeography by identifying trends in biodiversity across broad spatial scales. We found that for geographic locations sharing similar environmental conditions, subpopulations from the dominant phyla of these habitats (Actinobacteria, Bacteroidetes, Cyanobacteria, and Proteobacteria) can be used to differentiate 20 geographic locations distributed globally. These results suggest that despite the overwhelming diversity within microbial communities, members of the most abundant and ubiquitous microbial groups in the system can be used to differentiate a geospatial location across global spatial scales. Our study provides insight into how microbes are dispersed spatially and robust methods whereby we can interrogate microbial biogeography.IMPORTANCE Microbes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment. Here, we display how supervised machine learning approaches can be useful to understand microbial biodiversity and biogeography using microbes from globally distributed shipping ports. Our findings indicate that the members of globally dominant phyla are important for differentiating locations, which reduces the reliance on rare taxa to probe geography. Further, this study displays how global biogeographic patterning of aquatic microbial communities (and other systems) can be assessed through populations of the highly abundant and ubiquitous taxa that dominant the system.

RevDate: 2020-01-30

Bartelme RP, Custer JM, Dupont CL, et al (2020)

Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation.

mSphere, 5(1): pii:5/1/e00024-20.

The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here, we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted cells extracted from soil into one of two custom-designed defined growth media that differed by 100-fold in the concentration of amino acids and organic carbon. Across the two media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobium spp.) and representatives of five of the top 10 most abundant Actinobacteria phylotypes, including Nocardioides spp., Mycobacterium spp., and several other phylogenetically divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and that the concentration of substrates in culture medium influences the culturability of specific microbial lineages.IMPORTANCE Isolating environmental microbes and studying their physiology under controlled conditions are essential aspects of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities-the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.

RevDate: 2020-01-29

Yuan S, F Meng (2020)

Ecological insights into the underlying evolutionary patterns of biofilm formation from biological wastewater treatment systems: Red or Black Queen Hypothesis?.

Biotechnology and bioengineering [Epub ahead of print].

Interspecies interactions and phylogenetic distances were studied to reveal the underlying evolutionary adaptations of biofilms sourced from wastewater treatment processes. Based on 380 pairwise cocultures of 40 strains from two microbial aggregates (surface-attached and mobile aggregates (flocs)) at two substrate concentrations (LB broth and 0.1x LB broth), interspecies interactions were explored using biofilm classification schemes. There was a strong source-dependence of biofilm development formed by the mono-cultures, i.e., a higher biofilm formation potential for strains from attached aggregates than for those from sludge flocs at both substrate concentrations. Interestingly, the results showed that total biofilm reduction was dominant in the dual-species biofilm sourced from flocs in both LB broth (67.37%) and 0.1x LB broth (64.21%), indicating high interspecific competition in mobile aggregates and the independence of substrate concentrations. However, biofilm reduction was higher (33.68%) than induction (19.37%) for the biofilms formed by surface-attached aggregates in LB broth, while the opposite trend was apparent in 0.1x LB broth, suggesting the occurrence of indeterministic processes for biofilm formation and important roles of substrate concentrations. In addition, the more closely related phylogenetic relationships of cocultures from mobile aggregates was consistent with higher competition compared with those from surface-attached aggregates. Overall, the underlying evolutionary patterns of biofilms formed from mobile aggregates consistently followed the essence of the 'Red Queen Hypothesis', while biofilms developed from surface-attached aggregates were not deterministic. This study advanced our understanding of biofilm-related treatment processes using the principles of microbial ecology. This article is protected by copyright. All rights reserved.

RevDate: 2020-01-29

Lennon JT (2020)

Microbial Life Deep Underfoot.

mBio, 11(1): pii:mBio.03201-19.

Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored. Brewer et al. (mBio 10:e01318-19, 2019, https://doi.org/10.1128/mBio.01318-19) documented consistent shifts in the composition and genomic attributes of microbial communities as a function of depth in 20 soil pits that spanned a range of ecosystems across North America. The unique microorganisms found in deep soils appear to be adapted to conditions of low energy based on the recovery of genes that code for traits such as internal resource storage, mixotrophy, and dormancy.

RevDate: 2020-01-28

Zhu B, Wang Z, Kanaparthi D, et al (2020)

Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments.

Microbial ecology pii:10.1007/s00248-020-01482-0 [Epub ahead of print].

Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 106-3.2 × 107 gene copies g-1 soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.

RevDate: 2020-01-28
CmpDate: 2020-01-28

Remizovschi A, Carpa R, Forray FL, et al (2020)

Mud volcanoes and the presence of PAHs.

Scientific reports, 10(1):1253 pii:10.1038/s41598-020-58282-2.

A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well - an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by GC-MS and δ13C analyses. Subsequently, this study highlighted both the occurrence and distribution of putative PAH-degrading bacterial OTUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.

RevDate: 2020-01-28

Kalita M, Małek W, TA Coutinho (2020)

Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus.

Systematic and applied microbiology pii:S0723-2020(20)30004-7 [Epub ahead of print].

In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89T and Bradyrhizobium valentinum LmjM3T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89T, Bradyrhizobium valentinum LmjM3T and Bradyrhizobium retamae Ro19T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.

RevDate: 2020-01-27

Cramer N, Fischer S, Hedtfeld S, et al (2020)

Intraclonal competitive fitness of longitudinal cystic fibrosis Pseudomonas aeruginosa airway isolates in liquid cultures.

Environmental microbiology [Epub ahead of print].

The metabolically versatile Pseudomonas aeruginosa inhabits biotic and abiotic environments including the niche of cystic fibrosis (CF) airways. This study investigated how the adaptation to CF lungs affects the within-clone fitness of P. aeruginosa to grow and persist in liquid cultures in the presence of the clonal ancestors. Longitudinal clonal P. aeruginosa isolates that had been collected from 12 CF donors since the onset of colonization for up to 30 years were subjected to within-clone competition experiments. The relative quantities of individual strains were determined by marker-free amplicon sequencing of multiplex PCR products of strain-specific nucleotide sequence variants, a novel method that is generally applicable to studies in evolutionary genetics and microbial ecology with real-world strain collections. For ten of the twelve examined patient courses, P. aeruginosa isolates of the first years of colonization grew faster in the presence of their clonal progeny than alone. Single growth of individual strains showed no temporal trend with colonization time, but in co-culture the early isolates out-competed their clonal progeny. Irrespective of the genetic make-up of the clone and its genomic microevolution in CF lungs the early isolates expressed fitness traits to win the within-clone competition that were absent in their progeny. This article is protected by copyright. All rights reserved.

RevDate: 2020-01-27

Xu H, Wang X, Feng W, et al (2020)

The gut microbiota and its interactions with cardiovascular disease.

Microbial biotechnology [Epub ahead of print].

The intestine is colonized by a considerable community of microorganisms that cohabits within the host and plays a critical role in maintaining host homeostasis. Recently, accumulating evidence has revealed that the gut microbial ecology plays a pivotal role in the occurrence and development of cardiovascular disease (CVD). Moreover, the effects of imbalances in microbe-host interactions on homeostasis can lead to the progression of CVD. Alterations in the composition of gut flora and disruptions in gut microbial metabolism are implicated in the pathogenesis of CVD. Furthermore, the gut microbiota functions like an endocrine organ that produces bioactive metabolites, including trimethylamine/trimethylamine N-oxide, short-chain fatty acids and bile acids, which are also involved in host health and disease via numerous pathways. Thus, the gut microbiota and its metabolic pathways have attracted growing attention as a therapeutic target for CVD treatment. The fundamental purpose of this review was to summarize recent studies that have illustrated the complex interactions between the gut microbiota, their metabolites and the development of common CVD, as well as the effects of gut dysbiosis on CVD risk factors. Moreover, we systematically discuss the normal physiology of gut microbiota and potential therapeutic strategies targeting gut microbiota to prevent and treat CVD.

RevDate: 2020-01-26

Chen YT, Zeng Y, Wang HZ, et al (2020)

Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats.

Microbial ecology pii:10.1007/s00248-020-01485-x [Epub ahead of print].

Propionate is one of the major intermediates in anaerobic digestion of organic waste to CO2 and CH4. In methanogenic environments, propionate is degraded through a mutualistic interaction between symbiotic propionate oxidizers and methanogens. Although temperature heavily influences the microbial ecology and performance of methanogenic processes, its effect on syntrophic interaction during propionate degradation remains poorly understood. In this study, metagenomics and metatranscriptomics were employed to compare mesophilic and thermophilic propionate degradation communities. Mesophilic propionate degradation involved multiple syntrophic organisms (Syntrophobacter, Smithella, and Syntrophomonas), pathways, interactions, and preference toward formate-based electron transfer to methanogenic partners (i.e., Methanoculleus). In thermophilic propionate degradation, one syntrophic organism predominated (Pelotomaculum), interspecies H2 transfer played a major role, and phylogenetically and metabolically diverse H2-oxidizing methanogens were present (i.e., Methanoculleus, Methanothermobacter, and Methanomassiliicoccus). This study showed that microbial interactions, metabolic pathways, and niche diversity are distinct between mesophilic and thermophilic microbial communities responsible for syntrophic propionate degradation.

RevDate: 2020-01-26

Tivey TR, Parkinson JE, Mandelare PE, et al (2020)

N-Linked Surface Glycan Biosynthesis, Composition, Inhibition, and Function in Cnidarian-Dinoflagellate Symbiosis.

Microbial ecology pii:10.1007/s00248-020-01487-9 [Epub ahead of print].

The success of symbioses between cnidarian hosts (e.g., corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum.

RevDate: 2020-01-24

Lepoutre A, Faassen EJ, Zweers AJ, et al (2020)

How the Neurotoxin β-N-Methylamino-l-Alanine Accumulates in Bivalves: Distribution of the Different Accumulation Fractions among Organs.

Toxins, 12(2): pii:toxins12020061.

The environmental neurotoxin β-methylamino-l-alanine (BMAA) may represent a risk for human health. BMAA accumulates in freshwater and marine organisms consumed by humans. However, few data are available about the kinetics of BMAA accumulation and detoxification in exposed organisms, as well as the organ distribution and the fractions in which BMAA is present in tissues (free, soluble bound or precipitated bound cellular fractions). Here, we exposed the bivalve mussel Dreissena polymorpha to 7.5 µg of dissolved BMAA/mussel/3 days for 21 days, followed by 21 days of depuration in clear water. At 1, 3, 8, 14 and 21 days of exposure and depuration, the hemolymph and organs (digestive gland, the gills, the mantle, the gonad and muscles/foot) were sampled. Total BMAA as well as free BMAA, soluble bound and precipitated bound BMAA were quantified by tandem mass spectrometry. Free and soluble bound BMAA spread throughout all tissues from the first day of exposure to the last day of depuration, without a specific target organ. However, precipitated bound BMAA was detected only in muscles and foot from the last day of exposure to day 8 of depuration, at a lower concentration compared to free and soluble bound BMAA. In soft tissues (digestive gland, gonad, gills, mantle and muscles/foot), BMAA mostly accumulated as a free molecule and in the soluble bound fraction, with variations occurring between the two fractions among tissues and over time. The results suggest that the assessment of bivalve contamination by BMAA may require the quantification of total BMAA in whole individuals when possible.

RevDate: 2020-01-26

Qu EB, Omelon CR, Oren A, et al (2019)

Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts.

Frontiers in microbiology, 10:2952.

Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa, mostly oxygenic photosynthesizers, were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.

RevDate: 2020-01-26

Hao X, Zhu YG, Nybroe O, et al (2019)

The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin.

Frontiers in microbiology, 10:2951.

Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.

RevDate: 2020-01-28

Lu B, Shen Z, Zhang Q, et al (2020)

Morphology and molecular analyses of four epibiotic peritrichs on crustacean and polychaete hosts, including descriptions of two new species (Ciliophora, Peritrichia).

European journal of protistology, 73:125670 pii:S0932-4739(19)30107-5 [Epub ahead of print].

Four epibiotic sessilid peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalisMöbius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.

RevDate: 2020-01-27

Probst AJ, P Vaishampayan (2020)

Are we There Yet? Understanding Interplanetary Microbial Hitchhikers using Molecular Methods.

Current issues in molecular biology, 38:33-52.

Since the early time of space travel, planetary bodies undergoing chemical or biological evolution have been of particular interest for life detection missions. NASA's and ESA's Planetary Protection offices ensure responsible exploration of the solar system and aim at avoiding inadvertent contamination of celestial bodies with biomolecules or even living organisms. Life forms that have the potential to colonize foreign planetary bodies could be a threat to the integrity of science objectives of life detection missions. While standard requirements for assessing the cleanliness of spacecraft are still based on cultivation approaches, several molecular methods have been applied in the past to elucidate the full breadth of (micro)organisms that can be found on spacecraft and in cleanrooms, where the hardware is assembled. Here, we review molecular assays that have been applied in Planetary Protection research and list their significant advantages and disadvantages. By providing a comprehensive summary of the latest molecular methods yet to be applied in this research area, this article will not only aid in designing technological roadmaps for future Planetary Protection endeavors but also help other disciplines in environmental microbiology that deal with low biomass samples.

RevDate: 2020-01-22

Moens F, Duysburgh C, van den Abbeele P, et al (2019)

Lactobacillus rhamnosus GG and Saccharomyces cerevisiae boulardii exert synergistic antipathogenic activity in vitro against enterotoxigenic Escherichia coli.

Beneficial microbes, 10(8):923-935.

Short-term colonic in vitro batch incubations were performed to elucidate the possible synergistic effects of Lactobacillus rhamnosus GG (CNCM-I-4798) and Saccharomyces cerevisiae boulardii (CNCM-I-1079) (associated in Smebiocta/Smectaflora Protect®) on the colonic microbial fermentation process, as well as their antipathogenic activity against enterotoxigenic Escherichia coli (LMG2092) (ETEC). These incubations adequately simulate the native microbiota and environmental conditions of the proximal colon of both adult and toddler donors, including the colonic mucosal layer. Results indicated that both strains were capable of growing together without showing antagonistic effects. Co-cultivation of both strains resulted in increased butyrate (stimulated by L. rhamnosus GG), propionate (stimulated by S. boulardii), and ethanol (produced by S. boulardii) production compared to the control incubations, revealing the additive effect of both strains. After inoculation of ETEC under simulated dysbiotic conditions, a 40 and 46% reduction in the concentration of ETEC was observed upon addition of both strains during the experiments with the adult and toddler donor, respectively. Furthermore, ETEC toxin levels decreased upon S. boulardii inoculation, probably due to proteolytic activity of this strain, with a synergistic effect being observed upon co-cultivation of L. rhamnosus GG and S. boulardii resulting in a reduction of 57 and 46% for the adult and toddler donor, respectively. Altogether, the results suggest that both probiotics together may help microbiota functionality, in both adults and toddlers and under healthy or impaired conditions, which could be of great interest when the colonic microbiota is dysbiotic and therefore sensitive to pathogenic invasion such as during antibiotic treatment.

RevDate: 2020-01-22

Mina D, Pereira JA, Lino-Neto T, et al (2020)

Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect.

Microbial ecology pii:10.1007/s00248-020-01488-8 [Epub ahead of print].

Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall, Proteobacteria, Actinobacteria and Firmicutes were the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.

RevDate: 2020-01-22

Carini P, Delgado-Baquerizo M, Hinckley ES, et al (2020)

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities.

mBio, 11(1): pii:mBio.02776-19.

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

RevDate: 2020-01-29

Vandekerckhove TGL, Props R, Carvajal-Arroyo JM, et al (2020)

Adaptation and characterization of thermophilic anammox in bioreactors.

Water research, 172:115462 pii:S0043-1354(19)31239-4 [Epub ahead of print].

Anammox, the oxidation of ammonium with nitrite, is a key microbial process in the nitrogen cycle. Under mesophilic conditions (below 40 °C), it is widely implemented to remove nitrogen from wastewaters lacking organic carbon. Despite evidence of the presence of anammox bacteria in high-temperature environments, reports on the cultivation of thermophilic anammox bacteria are limited to a short-term experiment of 2 weeks. This study showcases the adaptation of a mesophilic inoculum to thermophilic conditions, and its characterization. First, an attached growth technology was chosen to obtain the process. In an anoxic fixed-bed biofilm bioreactor (FBBR), a slow linear temperature increase from 38 to over 48 °C (0.05-0.07 °C d-1) was imposed to the community over 220 days, after which the reactor was operated at 48 °C for over 200 days. Maximum total nitrogen removal rates reached up to 0.62 g N L-1 d-1. Given this promising performance, a suspended growth system was tested. The obtained enrichment culture served as inoculum for membrane bioreactors (MBR) operated at 50 °C, reaching a maximum total nitrogen removal rate of 1.7 g N L-1 d-1 after 35 days. The biomass in the MBR had a maximum specific anammox activity of 1.1 ± 0.1 g NH4+-N g-1 VSS d-1, and the growth rate was estimated at 0.075-0.19 d-1. The thermophilic cultures displayed nitrogen stoichiometry ratios typical for mesophilic anammox: 0.93-1.42 g NO2--Nremoved g-1 NH4+-Nremoved and 0.16-0.35 g NO3--Nproduced g-1 NH4+-Nremoved. Amplicon and Sanger sequencing of the 16S rRNA genes revealed a disappearance of the original "Ca. Brocadia" and "Ca. Jettenia" taxa, yielding Planctomycetes members with only 94-95% similarity to "Ca. Brocadia anammoxidans" and "Ca. B. caroliniensis", accounting for 45% of the bacterial FBBR community. The long-term operation of thermophilic anammox reactors and snapshot views on the nitrogen stoichiometry, kinetics and microbial community open up the development path of thermophilic partial nitritation/anammox. A first economic assessment highlighted that treatment of sludge reject water from thermophilic anaerobic digestion of sewage sludge may become attractive.

RevDate: 2020-01-20

Gontijo MTP, Silva JS, Vidigal PMP, et al (2020)

Phylogenetic distribution of the bacteriocin repertoire of lactic acid bacteria species associated with artisanal cheese.

Food research international (Ottawa, Ont.), 128:108783.

The microbiota contributes to artisanal cheese bioprotection and biopreservation through inter and intraspecific competition. This work aimed to investigate the phylogenetic distribution of the repertoire of bacteriocin structural genes of model lactic acid bacteria (LAB) in order to investigate its respective role in the artisanal cheeses microenvironment. A phylogenetic analysis of the rRNA 16S gene from 445 model strains of LAB was conducted using bayesian inference and the repertoire of bacteriocin genes was predicted from these strains by BAGEL software. Bacterial strains were clustered in five monophyletic clades (A, B, C, D and E) with high posterior probability values (PP > 0.99). One bacteriocin structural gene was predicted for 88.5% of the analyzed strains. The majority of the species encoded different classes of bacteriocins. Greater diversity of bacteriocin genes was found for strains included in clade A, comprising Lactococcus lactis, Streptococcus agalactiae, Streptococcus thermophilus, Streptococcus macedonicus, Enterococcus faecalis and Enterococcus faecium. In addition, Lactococcus lactis presented higher diversity of bacteriocin classes, encoding glycocins, lanthipeptides, sactipeptides, cyclic and linear azole-containing peptides, included in bacteriocins class I, besides class II and III. The results suggest that the distribution of bacteriocin structural genes is related to the phylogenetic clades of LAB species, with a higher frequency in some specific clades. Information comprised in this study contributes to comprehend the bacterial competition mechanisms in the artisanal cheese microenvironment.

RevDate: 2020-01-19

Liu H, Gao H, Wu M, et al (2020)

Distribution Characteristics of Bacterial Communities and Hydrocarbon Degradation Dynamics During the Remediation of Petroleum-Contaminated Soil by Enhancing Moisture Content.

Microbial ecology pii:10.1007/s00248-019-01476-7 [Epub ahead of print].

Microorganisms are the driver of petroleum hydrocarbon degradation in soil micro-ecological systems. However, the distribution characteristics of microbial communities and hydrocarbon degradation dynamics during the remediation of petroleum-contaminated soil by enhancing moisture content are not clear. In this study, polymerase chain reaction and high-throughput sequencing of soil microbial DNA were applied to investigate the compositions of microorganisms and alpha diversity in the oil-polluted soil, and the hydrocarbon removal also being analyzed using ultrasonic extraction and gravimetric method in a laboratory simulated ex-situ experiment. Results showed the distribution of petroleum hydrocarbon degrading microorganisms in the petroleum-contaminated loessal soil mainly was Proteobacteria phylum (96.26%)-Gamma-proteobacteria class (90.03%)-Pseudomonadales order (89.98%)-Pseudomonadaceae family (89.96%)-Pseudomonas sp. (87.22%). After 15% moisture content treatment, Actinobacteria, Proteobacteria, and Firmicutes still were the predominant phyla, but their relative abundances changed greatly. Also Bacillus sp. and Promicromonospora sp. became the predominant genera. Maintaining 15% moisture content increased the relative abundance of Firmicutes phylum and Bacillus sp. As the moisture-treated time increases, the uniformity and the richness of the soil bacterial community were decreased and increased respectively; the relative abundance of Pseudomonas sp. increased. Petroleum hydrocarbon degradation by enhancing soil moisture accorded with the pseudo-first-order reaction kinetic model (correlation coefficient of 0.81; half-life of 56 weeks). The richness of Firmicutes phylum and Bacillus sp. may be a main reason for promoting the removal of 18% petroleum hydrocarbons responded to 15% moisture treatment. Our results provided some beneficial microbiological information of oil-contaminated soil and will promote the exploration of remediation by changing soil moisture content for increasing petroleum hydrocarbon degradation efficiency.

RevDate: 2020-01-28

Mongui A, Lozano GL, Handelsman J, et al (2020)

Design and validation of a transposon that promotes expression of genes in episomal DNA.

Journal of biotechnology, 310:1-5 pii:S0168-1656(20)30008-0 [Epub ahead of print].

Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.

RevDate: 2020-01-29

Giri S, Shitut S, C Kost (2020)

Harnessing ecological and evolutionary principles to guide the design of microbial production consortia.

Current opinion in biotechnology, 62:228-238 pii:S0958-1669(19)30150-8 [Epub ahead of print].

Bacteria are widely used for commercially producing biomolecules. However, attempts to rationally design production strains and optimize cultivation conditions are frequently counteracted by the emergence of mutants with reduced production characteristics that decrease overall process yield. The reason why these mutants arise is likely because of a mismatch between the ecological conditions under which bacteria evolved in nature and the situation they experience in an industrial setting. Thus, there is a great potential for improving biotechnological production processes by implementing eco-evolutionary knowledge. However, this is often limited by a lack of effective communication between process engineers and microbial ecologists/evolutionary biologists. Here, we highlight recent findings in the field of microbial ecology and evolution and suggest implementation of this knowledge can significantly enhance microbial bioproduction.

RevDate: 2020-01-18

Krishnamoorthy S, Coetzee V, Kruger J, et al (2020)

Dysbiosis Signatures of Fecal Microbiota in South African Infants with Respiratory, Gastrointestinal, and Other Diseases.

The Journal of pediatrics pii:S0022-3476(19)31610-5 [Epub ahead of print].

OBJECTIVE: To determine the association between the fecal microbiota diversity of the infants with different disease conditions, and vitamin A supplementation, antibiotic, and deworming therapies.

STUDY DESIGN: In this case-control study, the bacterial community variations and the potential pathogens were identified through 16S ribosomal RNA gene-based amplicon sequencing and quantitative insights into microbial ecology pipeline in fecal samples. The participants were South African infants (mean age, 16 ± 8 months; 17 male and 17 female) hospitalized and diagnosed with gastrointestinal, respiratory, and other diseases.

RESULTS: The top phyla of the infants with respiratory disease were Proteobacteria, followed by Firmicutes, which were equally abundant in gastrointestinal disease. A significant difference in Shannon (alpha) diversity index (95% CI, 2.6-4.4; P = .008), among the microbiota of the fecal samples categorized by disease conditions, was observed. In beta diversity analysis of fecal microbiota, remarkable variations were found within the groups of deworming therapy (95% CI, 0.40-0.90; P = .033), disease conditions (95% CI, 0.44-0.86; P < .012) through unweighted and antibiotic therapy (95% CI, 0.20-0.75; P = .007), vitamin A intake (95% CI, 0.10-0.80; P < .033) and disease conditions (95% CI, 0.10-0.79; P = .006) through weighted UniFrac distances. The candidate pathogen associated with the disease groups were identified through analysis of the composition of microbiomes analysis.

CONCLUSIONS: This study provides preliminary evidence for the fecal microbiome-derived dysbiosis signature and pathobiome concept that may be observed in young children during illness.

RevDate: 2020-01-28

Feng J, Wang C, Lei J, et al (2020)

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community.

Microbiome, 8(1):3.

BACKGROUND: It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% of the world's SOC storage, will cause positive feedback that accelerates climate warming. We have previously shown that short-term warming (1.5 years) stimulates rapid, microbe-mediated decomposition of tundra soil carbon without affecting the composition of the soil microbial community (based on the depth of 42684 sequence reads of 16S rRNA gene amplicons per 3 g of soil sample).

RESULTS: We show that longer-term (5 years) experimental winter warming at the same site altered microbial communities (p < 0.040). Thaw depth correlated the strongest with community assembly and interaction networks, implying that warming-accelerated tundra thaw fundamentally restructured the microbial communities. Both carbon decomposition and methanogenesis genes increased in relative abundance under warming, and their functional structures strongly correlated (R2 > 0.725, p < 0.001) with ecosystem respiration or CH4 flux.

CONCLUSIONS: Our results demonstrate that microbial responses associated with carbon cycling could lead to positive feedbacks that accelerate SOC decomposition in tundra regions, which is alarming because SOC loss is unlikely to subside owing to changes in microbial community composition. Video Abstract.

RevDate: 2020-01-17

Li Z, Y Van de Peer (2020)

"Winter Is Coming": How did Polyploid Plants Survive?.

Molecular plant, 13(1):4-5.

RevDate: 2020-01-17

Lee JC, KS Whang (2020)

Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5-1.9 µm, and was able to grow at 10-37 °C (optimum, 28-30 °C), at pH 4.5-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2-92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2-83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn-Gly2-d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae, for which the name Segeticoccusrhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccusrhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

RevDate: 2020-01-17

Guhr A, S Kircher (2020)

Drought-Induced Stress Priming in Two Distinct Filamentous Saprotrophic Fungi.

Microbial ecology pii:10.1007/s00248-019-01481-w [Epub ahead of print].

Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is "stress priming," the ability to cope with a severe stress ("triggering") by retaining information from a previous mild stress event ("priming"). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.

RevDate: 2020-01-17

Korotetskiy IS, Joubert M, Magabotha SM, et al (2020)

Complete Genome Sequence of Collection Strain Acinetobacter baumannii ATCC BAA-1790, Used as a Model To Study the Antibiotic Resistance Reversion Induced by Iodine-Containing Complexes.

Microbiology resource announcements, 9(3): pii:9/3/e01467-19.

The strain Acinetobacter baumannii ATCC BAA-1790 was sequenced as a model for nosocomial multidrug-resistant infections. Long-read PacBio sequencing revealed a circular chromosome of 3,963,235 bp with two horizontally transferred genomic islands and a 67,023-bp plasmid. Multiple antibiotic resistance genes and genome methylation patterns were identified.

RevDate: 2020-01-17

Purkamo L, Kietäväinen R, Nuppunen-Puputti M, et al (2020)

Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context.

Life (Basel, Switzerland), 10(1): pii:life10010002.

The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.

RevDate: 2020-01-24

Guégan M, Tran Van V, Martin E, et al (2020)

Who is eating fructose within the Aedes albopictus gut microbiota?.

Environmental microbiology [Epub ahead of print].

The Asian tiger mosquito Aedes albopictus is a major public health concern because of its invasive success and its ability to transmit pathogens. Given the low availability of treatments against mosquito-borne diseases, vector control remains the most suitable strategy. The methods used thus far are becoming less effective, but recent strategies have emerged from the study of mosquito-associated microorganisms. Although the role of the microbiota in insect biology does not require further proof, much remains to be deciphered in mosquitoes, especially the contribution of the microbiota to host nutrient metabolism. Mosquitoes feed on plant nectar, composed of mostly fructose. We used stable isotope probing to identify bacteria and fungi assimilating fructose within the gut of Ae. albopictus. Mosquitoes were fed a 13 C-labelled fructose solution for 24 h. Differences in the active microbial community according to the sex of mosquitoes were highlighted. The bacterium Lelliottia and the fungi Cladosporium and Aspergillus dominated the active microbiota in males, whereas the bacterium Ampullimonas and the yeast Cyberlindnera were the most active in females. This study is the first to investigate trophic interactions between Ae. albopictus and its microbiota, thus underscoring the importance of the microbial component in nectar feeding in mosquitoes.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

Order from Amazon

This book covers the ecological activities of microbes in the biosphere with an emphasis on microbial interactions within their environments and communities In thirteen concise and timely chapters, Microbial Ecology presents a broad overview of this rapidly growing field, explaining the basic principles in an easy-to-follow manner. Using an integrative approach, it comprehensively covers traditional issues in ecology as well as cutting-edge content at the intersection of ecology, microbiology,

963 Red Tail Lane
Bellingham, WA 98226


E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )