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Bibliography on: Microbial Ecology

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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 14 Oct 2019 at 01:33 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: 2019-10-12

Hess AL, Benítez-Páez A, Blædel T, et al (2019)

The effect of inulin and resistant maltodextrin on weight loss during energy restriction: a randomised, placebo-controlled, double-blinded intervention.

European journal of nutrition pii:10.1007/s00394-019-02099-x [Epub ahead of print].

PURPOSE: The objective of this study was to investigate the additive effects of combining energy restriction with dietary fibres on change in body weight and gut microbiota composition.

METHODS: The study was a 12-week randomised, placebo-controlled, double-blinded, parallel intervention trial. A total of 116 overweight or obese participants were assigned randomly either to 10 g inulin plus 10 g resistant maltodextrin or to 20 g of placebo supplementation through 400 mL of milk a day, while on a - 500 kcal/day energy restricted diet.

RESULTS: Altogether, 86 participants completed the intervention. There were no significant differences in weight loss or body composition between the groups. The fibre supplement reduced systolic (5.35 ± 2.4 mmHg, p = 0.043) and diastolic (2.82 ± 1.3 mmHg, p = 0.047) blood pressure to a larger extent than placebo. Furthermore, a larger decrease in serum insulin was observed in the placebo group compared to the fibre group (- 26.0 ± 9.2 pmol/L, p = 0.006). The intake of fibre induced changes in the composition of gut microbiota resulting in higher abundances of Parabacteroides and Bifidobacteria, compared to placebo. The effects on blood pressure and glucose metabolism were mainly observed in women, and could be attributed to a higher gut microbiota diversity after intervention. Finally, the fibre group experienced a higher degree of gastrointestinal symptoms, which attenuated over time.

CONCLUSIONS: Supplementation of inulin and resistant maltodextrin did not provide an additional weight loss during an energy-restricted diet, but reduced both systolic and diastolic blood pressure. Furthermore, the fibre supplement did stimulate the growth of potentially beneficial bacteria genera.

CLINICAL TRIAL REGISTRY: The study was registered at http://www.clinicaltrials.gov , NCT03135041.

RevDate: 2019-10-11

Lin X, Gao D, Lu K, et al (2019)

Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City.

International journal of environmental research and public health, 16(20): pii:ijerph16203794.

Effects of nitrogen pollution on bacterial community shifts in river sediments remain barely understood. Here, we investigated the bacterial communities in sediments of urban and suburban rivers in a highly urbanized city, Shanghai. Sediment nitrate (NO3-) and ammonia (NH4+) were highly accumulated in urban river. Operation Taxonomic Units (OTUs), Abundance-based Coverage Estimators (ACEs) and Chao 1 estimator in urban rivers were slightly lower than those in suburban rivers, while Shannon and Simpson indices were higher in urban rivers than those in suburban rivers. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum communities, accounting for 68.5-84.9% of all communities. In particular, the relative abundances of Firmicutes and Nitrospirae were significantly higher in suburban rivers than in urban rivers, while relative abundances of Bacteroidetes, Verrucomicrobia, and Spirochaetes were significantly lower in suburban rivers than in urban rivers. NH4+ was significantly and negatively correlated with abundances of Firmicutes, Nitrospirae, and Actinobacteria. Importantly, the significant and negative effects of sediment NH4+ on bacterial richness and diversity suggested that nitrogen pollution likely contribute to the decrease in the bacterial richness and diversity. The results highlight that nitrogen enrichment could drive the shifts of bacterial abundance and diversity in the urban river sediments where are strongly influenced by human activities under the rapid urbanization stress.

RevDate: 2019-10-10

Cavaco MA, Louis St VL, Engel K, et al (2019)

Freshwater microbial community diversity in a rapidly changing high arctic watershed.

FEMS microbiology ecology pii:5585388 [Epub ahead of print].

Current models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially-driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition, (16S rRNA gene sequencing), to physicochemical parameters (e.g. dissolved oxygen, nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: 1) glacial rivers; 2) active layer thaw-fed streams and waterbodies, and; 3) Lake Hazen, into which 1) and 2) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial profiles were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that microbial communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.

RevDate: 2019-10-10

Brunel C, Beifen Y, Pouteau R, et al (2019)

Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism.

Microbial ecology pii:10.1007/s00248-019-01438-z [Epub ahead of print].

Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.

RevDate: 2019-10-10

Sodhi KK, Kumar M, Balan B, et al (2019)

Isolation and characterization of amoxicillin-resistant bacteria and amoxicillin-induced alteration in its protein profiling and RNA yield.

Archives of microbiology pii:10.1007/s00203-019-01737-6 [Epub ahead of print].

Amoxicillin-resistant bacteria were isolated using selective enrichment procedure. The morphological, biochemical and molecular characterization based on 16S rRNA gene sequencing and phylogenetic analysis of the bacterial strain WA5 confirmed that the strain belongs to the genus Stenotrophomonas. The bacteria were named as Stenotrophomonas sp. strain WA5 (MK110499). Substantial growth was seen in M9 minimal media supplemented with 5 mg L-1 of amoxicillin as a sole source of carbon and energy. RNA yield was also observed to be decreased in the presence of amoxicillin. Amoxicillin (5 mg L-1)-induced alteration is seen on bacterial protein profile and unique polypeptide bands were seen to be induced in the presence of amoxicillin, the bands were subjected to trypsin digestion, and LC-MS/MS analysis showed that the bands belong to the family of DNA-dependent RNA polymerase subunit β (rpoC). Plasmid DNA isolation indicated the presence of antibiotic-resistant genes being harboured by the plasmid.

RevDate: 2019-10-10

Baruzzo G, Patuzzi I, B Di Camillo (2019)

SPARSim Single Cell: a count data simulator for scRNA-seq data.

Bioinformatics (Oxford, England) pii:5584234 [Epub ahead of print].

MOTIVATION: Single cell RNA-seq (scRNA-seq) count data shows many differences compared to bulk RNA-seq count data, making the application of many RNA-seq preprocessing/analysis methods not straightforward or even inappropriate.For this reason, the development of new methods for handling scRNA-seq count data is currently one of the most active research field in bioinformatics. To help the development of such new methods, the availability of simulated data could play a pivotal role. However, only few scRNA-seq count data simulators are available, often showing poor or not demonstrated similarity with real data.

RESULTS: In this article we present SPARSim, a scRNA-seq count data simulator based on a Gamma-Multivariate Hypergeometric model. We demonstrate that SPARSim allows to generate count data that resemble real data in terms of count intensity, variability and sparsity, performing comparably or better than one of the most used scRNA-seq simulator, Splat. In particular, SPARSim simulated count matrices well resemble the distribution of zeros across different expression intensities observed in real count data.

AVAILABILITY: SPARSim R package is freely available at http://sysbiobig.dei.unipd.it/?q=SPARSim and at https://gitlab.com/sysbiobig/sparsim.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2019-10-09

Wepking C, Badgley B, Barrett JE, et al (2019)

Prolonged exposure to manure from livestock-administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling.

Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase. Exposure to manure from antibiotic-treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two-fold increase in ecosystem respiration of recently fixed-carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic-treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.

RevDate: 2019-10-09

Li F, Li P, Hua H, et al (2019)

Diversity, Tissue Localization, and Infection Pattern of Bacterial Symbionts of the White-Backed Planthopper, Sogatella furcifera (Hemiptera: Delphacidae).

Microbial ecology pii:10.1007/s00248-019-01433-4 [Epub ahead of print].

The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is a destructive pest of rice. Bacterial symbionts play an important role in insect hosts, especially hemipteran hosts. This study was designed to examine the bacterial symbionts of the WBPH using 16S rDNA high-throughput sequencing. A total of 63 and 177 operational taxonomic units (OTUs) were identified in females and males of three WBPH populations, respectively. These OTUs included bacteria of 75 genera from 11 phyla, where Wolbachia, Cardinium, and Asaia were the dominant genera, accounting for over 97.99% of all the symbiotic bacteria. Fluorescence in situ hybridization detected Wolbachia, Cardinium, and Asaia in the salivary glands, guts, testes, and eggs of the WBPH, indicating the potential for both horizontal and vertical transmission. Moreover, the infection pattern of the three dominant bacterial symbionts was detected in six WBPH populations. The frequencies of Wolbachia infection of females and Cardinium infection of both sexes were over 96.7%. Wolbachia infection of males ranged between 46.7 and 63.3%, which was significantly lower than that observed for females. Asaia infection of both sexes varied substantially among the populations. These results indicate that the complex host-symbiotic bacteria interaction is influenced by host sex and geographical origin and potentially by the transmission modes of the symbionts.

RevDate: 2019-10-09

Soffe R, Bernach M, Remus-Emsermann MNP, et al (2019)

Replicating Arabidopsis Model Leaf Surfaces for Phyllosphere Microbiology.

Scientific reports, 9(1):14420 pii:10.1038/s41598-019-50983-7.

Artificial surfaces are commonly used in place of leaves in phyllosphere microbiology to study microbial behaviour on plant leaf surfaces. These surfaces enable a reductionist approach to be undertaken, to enable individual environmental factors influencing microorganisms to be studied. Commonly used artificial surfaces include nutrient agar, isolated leaf cuticles, and reconstituted leaf waxes. Recently, replica surfaces mimicking the complex topography of leaf surfaces for phyllosphere microbiology studies are appearing in literature. Replica leaf surfaces have been produced in agar, epoxy, polystyrene, and polydimethylsiloxane (PDMS). However, none of these protocols are suitable for replicating fragile leaves such as of the model plant Arabidopsis thaliana. This is of importance, as A. thaliana is a model system for molecular plant genetics, molecular plant biology, and microbial ecology. To overcome this limitation, we introduce a versatile replication protocol for replicating fragile leaf surfaces into PDMS. Here we demonstrate the capacity of our replication process using optical microscopy, atomic force microscopy (AFM), and contact angle measurements to compare living and PDMS replica A. thaliana leaf surfaces. To highlight the use of our replica leaf surfaces for phyllosphere microbiology, we visualise bacteria on the replica leaf surfaces in comparison to living leaf surfaces.

RevDate: 2019-10-08

Prévoteau A, Carvajal-Arroyo JM, Ganigué R, et al (2019)

Microbial electrosynthesis from CO2: forever a promise?.

Current opinion in biotechnology, 62:48-57 pii:S0958-1669(19)30068-0 [Epub ahead of print].

Microbial electrosynthesis (MES) is an electrochemical process used to drive microbial metabolism for bio-production, such as the reduction of CO2 into industrially relevant organic products as an alternative to current fossil-fuel-derived commodities. After a decade of research on MES from CO2, figures of merit have increased significantly but are plateauing yet far from those expected to allow competitiveness for synthesis of commodity chemicals. Here we discuss the substantial technological shortcomings still associated with MES and evoke possible ways to mitigate them. It appears particularly challenging to obtain both relevant production rates (driven by high current densities) and energy conversion efficiency (i.e. low cell voltage) in microbial-compatible electrolytes. More competitive processes could arise by decoupling effective abiotic electroreductions (e.g. CO2 to CO or ethanol; H2 evolution) with subsequent fermentation processes.

RevDate: 2019-10-08

Ben Maamar S, Hu J, EM Hartmann (2019)

Implications of indoor microbial ecology and evolution on antibiotic resistance.

Journal of exposure science & environmental epidemiology pii:10.1038/s41370-019-0171-0 [Epub ahead of print].

The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.

RevDate: 2019-10-08

Diaz PI, AM Valm (2019)

Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties.

Journal of dental research [Epub ahead of print].

Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.

RevDate: 2019-10-07

Le D, Nguyen P, Nguyen D, et al (2019)

Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability.

Microbial ecology pii:10.1007/s00248-019-01436-1 [Epub ahead of print].

We investigated the gut microbiota of rabbit fish larvae at three locations in Vietnam (ThuanAn-northern, QuangNam-intermediate, BinhDinh-southern sampling site) over a three-year period. In the wild, the first food for rabbit fish larvae remains unknown, while the juveniles and adults are herbivores, forming schools near the coasts, lagoons, and river mouths, and feeding mainly on filamentous algae. This is the first study on the gut microbiota of the wild fish larvae and with a large number of individuals analyzed spatially and temporally. The Clostridiales order was the most predominant in the gut, and location-by-location alpha diversity showed significant differences in Chao-1, Hill number 1, and evenness. Analysis of beta diversity indicated that the location, not year, had an effect on the composition of the microbiota. In 2014, the gut microbiota of fish from QuangNam was different from that in BinhDinh; in 2015, the gut microbiota was different for all locations; and, in 2016, the gut microbiota in ThuanAn was different from that in the other locations. There was a time-dependent trend in the north-south axis for the gut microbiota, which is considered to be tentative awaiting larger datasets. We found limited variation in the gut microbiota geographically and in time and strong indications for a core microbiome. Five and fifteen OTUs were found in 100 and 99% of the individuals, respectively. This suggests that at this life stage the gut microbiota is under strong selection due to a combination of fish-microbe and microbe-microbe interactions.

RevDate: 2019-10-07

Sebastián M, JM Gasol (2019)

Visualization is crucial for understanding microbial processes in the ocean.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 374(1786):20190083.

Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems. This article is part of a discussion meeting issue 'Single cell ecology'.

RevDate: 2019-10-04

Wang D, Tooker NB, Srinivasan V, et al (2019)

Side-stream enhanced biological phosphorus removal (S2EBPR) process improves system performance - A full-scale comparative study.

Water research, 167:115109 pii:S0043-1354(19)30883-8 [Epub ahead of print].

To address the common challenges in enhanced biological phosphorus removal (EBPR) related to stability and unfavorable influent carbon to phosphorus ratio, a side-stream EBPR (S2EBPR) process that involves a side-stream anaerobic biological sludge hydrolysis and fermentation reactor was proposed as an emerging alternative. In this study, a full-scale pilot testing was performed with side-by-side operation of a conventional anaerobic-anoxic-aerobic (A2O) process versus a S2EBPR process. A comparison of the performance, activity and microbial community between the two configurations was performed. The results demonstrated that, with the same influent wastewater characteristics, S2EBPR configuration showed improved P removal performance and stability than the conventional A2O configuration, especially when the mixers in the side-stream anaerobic reactor were operated intermittently. Mass balance analysis illustrated that both denitrification and EBPR were enhanced in S2EBPR configuration, where return activated sludge was diverted into the anaerobic zone to promote fermentation and enrichment of polyphosphate accumulating organisms (PAOs), and the influent was bypassed to the anoxic zone for enhancing denitrification. A relatively higher PAO activity and total PAO abundance were observed in S2EBPR than in A2O configuration, accompanied by a higher degree of dependence on glycolysis pathway than tricarboxylic acid cycle. No significant difference in the relative abundances of putative PAOs, including Ca. Accumulibacter and Tetrasphaera, were observed between the two configurations. However, higher microbial community diversity indices were observed in S2EBPR configuration than in conventional one. In addition, consistently lower relative abundance of known glycogen accumulating organisms (GAOs) was observed in S2EBPR system. Extended anaerobic retention time and conditions that generate continuous and more complex volatile fatty acids in the side-stream anaerobic reactor of S2EBPR process likely give more competitive advantage for PAOs over GAOs. PAOs exhibited sustained EBPR activity and delayed decay under extended anaerobic condition, likely due to their versatile metabolic pathways depending on the availability and utilization of multiple intracellular polymers. This study provided new insights into the effects of implementing side-stream EBPR configuration on microbial populations, EBPR activity profiles and resulted system performance.

RevDate: 2019-10-04

Browne PD, Kot W, Jørgensen TS, et al (2020)

The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.

Methods in molecular biology (Clifton, N.J.), 2075:253-264.

Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.

RevDate: 2019-10-04

Schultz J, Kallies R, Nunes da Rocha U, et al (2019)

Draft Genome Sequence of Brevibacillus sp. Strain LEMMJ03, Isolated from an Antarctic Volcano.

Microbiology resource announcements, 8(40): pii:8/40/e00921-19.

Here, we announce the draft genome sequence of Brevibacillus sp. strain LEMMJ03, isolated from Whalers Bay sediment (Deception Island, Antarctica). In total, 4,500 coding sequences (CDS), among those 102 coding for tRNAs and 5 for noncoding RNAs (ncRNAs), were predicted from the 4.64-Mb genome. Predicted functions were for bacteriocin and degradation of aromatic compounds.

RevDate: 2019-10-03

Li X, Garbeva P, Liu X, et al (2019)

Volatile-mediated antagonism of soil bacterial communities against fungi.

Environmental microbiology [Epub ahead of print].

Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonisation of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-03

Benucci GMN, Longley R, Zhang P, et al (2019)

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses.

PeerJ, 7:e7744 pii:7744.

Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.

RevDate: 2019-10-03

An SQ, Potnis N, Dow M, et al (2019)

Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas.

FEMS microbiology reviews pii:5580289 [Epub ahead of print].

Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.

RevDate: 2019-10-02

Brewer TE, Aronson EL, Arogyaswamy K, et al (2019)

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.

mBio, 10(5): pii:mBio.01318-19.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

RevDate: 2019-10-01

Carney RL, Labbate M, Siboni N, et al (2019)

Urban beaches are environmental hotspots for antibiotic resistance following rainfall.

Water research, 167:115081 pii:S0043-1354(19)30855-3 [Epub ahead of print].

To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.

RevDate: 2019-10-01

Mondo SJ, Jiménez DJ, Hector RE, et al (2019)

Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery.

Biotechnology for biofuels, 12:229 pii:1569.

Background: Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1).

Results: The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.

Conclusions: We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.

RevDate: 2019-10-01

Dagher DJ, de la Providencia IE, Pitre FE, et al (2019)

Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments.

Frontiers in microbiology, 10:2144.

Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.

RevDate: 2019-10-01

Schweitzer-Natan O, Ofek-Lalzar M, Sher D, et al (2019)

Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession.

Frontiers in microbiology, 10:2142.

Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.

RevDate: 2019-10-01

Shin GY, Schachterle JK, Shyntum DY, et al (2019)

Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis.

Frontiers in microbiology, 10:2075.

To successfully infect plant hosts, the collective regulation of virulence factors in a bacterial pathogen is crucial. Hfq is an RNA chaperone protein that facilitates the small RNA (sRNA) regulation of global gene expression at the post-transcriptional level. In this study, the functional role of Hfq in a broad host range phytopathogen Pantoea ananatis was determined. Inactivation of the hfq gene in P. ananatis LMG 2665T resulted in the loss of pathogenicity and motility. In addition, there was a significant reduction of quorum sensing signal molecule acyl-homoserine lactone (AHL) production and biofilm formation. Differential sRNA expression analysis between the hfq mutant and wild-type strains of P. ananatis revealed 276 sRNAs affected in their abundance by the loss of hfq at low (OD600 = 0.2) and high cell (OD600 = 0.6) densities. Further analysis identified 25 Hfq-dependent sRNAs, all showing a predicted Rho-independent terminator of transcription and mapping within intergenic regions of the P. ananatis genome. These included known sRNAs such as ArcZ, FnrS, GlmZ, RprA, RyeB, RyhB, RyhB2, Spot42, and SsrA, and 16 novel P. ananatis sRNAs. The current study demonstrated that Hfq is an important component of the collective regulation of virulence factors and sets a foundation for understanding Hfq-sRNA mediated regulation in the phytopathogen P. ananatis.

RevDate: 2019-09-30

Šimek K, D Sirova (2019)

Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems.

Journal of visualized experiments : JoVE.

Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.

RevDate: 2019-09-30

Ahmed EH, Hassan HM, El-Sherbiny NM, et al (2019)

Bacteriological Monitoring of Inanimate Surfaces and Equipment in Some Referral Hospitals in Assiut City, Egypt.

International journal of microbiology, 2019:5907507.

Hospital-acquired infections represent a serious public health problem in all countries. It is clear that monitoring of the hospital environment is an essential element in the control and a part of the policy for preventing nosocomial infections. It allows a better understanding of the microbial ecology for the purpose of conducting preventive and corrective actions. The aims of this work were to determine the percentage of bacterial contamination of environmental samples and to identify potential nosocomial pathogens isolated from environments of seven referral hospitals from 2009 to 2015. By using the swab technique, 12863 samples were collected. Qualitative and quantitative cultures were performed. The organisms were primarily identified by colony morphology, microscopy of Gram stain, and standard biochemical tests. 25.6% of total samples showed contamination (93% was monomicrobial and 7.0% was polymicrobial). The predominant species was coagulase-negative staphylococcus (CNS) (32%), followed by methicillin-resistant S. aureus (MRSA) (26%) and then K. pneumonia (10.6%). The percentage of contamination varied among the covered hospitals and according to the year of monitoring with highly statistically significant difference (p value < 0.001). Direct contact with environmental surfaces or equipment transmits the majority of nosocomial infection. Major nosocomial pathogens have been identified. Hospital managers and healthcare bodies must be aware of the reality of the concept of environmental bacterial tanks and the need for respect of biocleaning procedures and choice of biocleaning tools.

RevDate: 2019-09-28

Villegas-Plazas M, Sanabria J, H Junca (2019)

A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems.

Journal of environmental management, 251:109581 pii:S0301-4797(19)31299-X [Epub ahead of print].

Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.

RevDate: 2019-09-28

Assié A, Leisch N, Meier DV, et al (2019)

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).

The ISME journal pii:10.1038/s41396-019-0508-7 [Epub ahead of print].

Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

RevDate: 2019-09-27

Zheng P, Li Y, Wu J, et al (2019)

Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.

Advanced science (Weinheim, Baden-Wurttemberg, Germany), 6(18):1901441 pii:ADVS1275.

Myasthenia gravis (MG) is a devastating acquired autoimmune disease. Emerging evidence indicates that the gut microbiome plays a key role in maintaining immune system homeostasis. This work reports that MG is characterized by decreased α-phylogenetic diversity, and significantly disturbed gut microbiome and fecal metabolome. The altered gut microbial composition is associated with fecal metabolome changes, with 38.75% of altered bacterial operational taxonomic units showing significant correlations with a range of metabolite biomarkers. Some microbes are particularly linked with MG severity. Moreover, a combination of microbial makers and their correlated metabolites enable discriminating MG from healthy controls (HCs) with 100% accuracy. To investigate whether disturbed gut mcirobiome might contribute to the onset of MG, germ-free (GF) mice are initially colonized with MG microbiota (MMb) or healthy microbiota (HMb), and then immunized in a classic mouse model of MG. The MMb mice demonstrate substantially impaired locomotion ability compared with the HMb mice. This effect could be reversed by cocolonizing GF mice with both MMb and HMb. The MMb mice also exhibit similar disturbances of fecal metabolic pathways as found in MG. Together these data demonstrate disturbances in microbiome composition and activity that are likely to be relevant to the pathogenesis of MG.

RevDate: 2019-09-27

Zhang Z, Mocanu V, Cai C, et al (2019)

Impact of Fecal Microbiota Transplantation on Obesity and Metabolic Syndrome-A Systematic Review.

Nutrients, 11(10): pii:nu11102291.

Fecal microbiota transplantation (FMT) is a gut microbial-modulation strategy that has been investigated for the treatment of a variety of human diseases, including obesity-associated metabolic disorders. This study appraises current literature and provides an overview of the effectiveness and limitations of FMT as a potential therapeutic strategy for obesity and metabolic syndrome (MS). Five electronic databases and two gray literature sources were searched up to 10 December 2018. All interventional and observational studies that contained information on the relevant population (adult patients with obesity and MS), intervention (receiving allogeneic FMT) and outcomes (metabolic parameters) were eligible. From 1096 unique citations, three randomized placebo-controlled studies (76 patients with obesity and MS, body mass index = 34.8 ± 4.1 kg/m2, fasting plasma glucose = 5.8 ± 0.7 mmol/L) were included for review. Studies reported mixed results with regards to improvement in metabolic parameters. Two studies reported improved peripheral insulin sensitivity (rate of glucose disappearance, RD) at 6 weeks in patients receiving donor FMT versus patients receiving the placebo control. In addition, one study observed lower HbA1c levels in FMT patients at 6 weeks. No differences in fasting plasma glucose, hepatic insulin sensitivity, body mass index (BMI), or cholesterol markers were observed between two groups across all included studies. While promising, the influence of FMT on long-term clinical endpoints needs to be further explored. Future studies are also required to better understand the mechanisms through which changes in gut microbial ecology and engraftment of microbiota affect metabolic outcomes for patients with obesity and MS. In addition, further research is needed to better define the optimal fecal microbial preparation, dosing, and method of delivery.

RevDate: 2019-09-26

Wang Y, Lin Z, He L, et al (2019)

Simultaneous partial nitrification, anammox and denitrification (SNAD) process for nitrogen and refractory organic compounds removal from mature landfill leachate: Performance and metagenome-based microbial ecology.

Bioresource technology, 294:122166 pii:S0960-8524(19)31396-3 [Epub ahead of print].

In this study, a simultaneous partial nitrification, Anammox and denitrification (SNAD) bioreactor was constructed for mature landfill leachate treatment, which exhibited favorable NH4+-N (98.9-99.9%), TN (90.7-94.9%) and bio-refractory organic compounds (46.2-67.7%) removal efficiencies. Stoichiometric analysis demonstrated that the synergy of ammonium-oxidizing bacteria and Anammox bacteria dominated TN removal (96.1-97.2%). NO3--N produced in Anammox could be further reduced through (partial) denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The results highlighted that humic-like and their intermediates might serve as the electron donor for these (partial) denitrifiers and DNRA bacteria to remove NO3--N, and could be effectively removed from mature landfill leachate in SNAD bioreactor. Metagenomic characterization further demonstrated that phyla Chloroflexi, Chlorobi and genera Nitrosomonas, Ignavibacterium and Aminiphilus might be responsible for such humic-like degradation. Overall, this work offers new insights into the metagenome-based bioinformatic roles for the previously understudied microorganisms in SNAD bioreactor for mature landfill leachate treatment.

RevDate: 2019-09-26

Tang HC, Sieo CC, Abdullah N, et al (2019)

Effects of supplementing freeze-dried Mitsuokella jalaludinii phytase on the growth performance and gut microbial diversity of broiler chickens.

Journal of animal physiology and animal nutrition [Epub ahead of print].

Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p < .05) and T2 diets (p < .05), demonstrating the efficiency of MJ as a supplement to low aP diet. Nevertheless, MJ did not significantly affect the microbial population and diversity in broilers' caeca, which mainly consists of members from Bacteroidetes, Firmicutes, and Proteobacteria. Regardless, significant variations in the caecal bacterial composition were observed over time, probably due to succession as the broilers aged. This is the first reported study on the effect of MJ on the microbial diversity of broiler's caeca.

RevDate: 2019-09-26

Sarkar A, Morita D, Ghosh A, et al (2019)

Altered Integrative and Conjugative Elements (ICEs) in Recent Vibrio cholerae O1 Isolated From Cholera Cases, Kolkata, India.

Frontiers in microbiology, 10:2072.

The self-transferring integrative and conjugative elements (ICEs) are large genomic segments carrying several bacterial adaptive functions including antimicrobial resistance (AMR). SXT/R391 family is one of the ICEs extensively studied in cholera-causing pathogen Vibrio cholerae. The genetic characteristics of ICE-SXT/R391 in V. cholerae are dynamic and region-specific. These ICEs in V. cholerae are strongly correlated with resistance to several antibiotics such as tetracycline, streptomycin and trimethoprim-sulfamethoxazole. We screened V. cholerae O1 strains isolated from cholera patients in Kolkata, India from 2008 to 2015 for antibiotic susceptibility and the presence of ICEs, and subsequently sequenced their conserved genes. Resistance to tetracycline, streptomycin and trimethoprim-sulfamethoxazole was detected in strains isolated during 2008-2010 and 2014-2015. The genes encoding resistance to tetracycline (tetA), trimethoprim-sulfamethoxazole (dfrA1 and sul2), streptomycin (strAB), and chloramphenicol (floR) were detected in the ICEs of these strains. There was a decrease in overall drug resistance in V. cholerae associated with the ICEs in 2011. DNA sequence analysis also showed that AMR in these strains was conferred mainly by two types of ICEs, i.e., ICETET (comprising tetA, strAB, sul2, and dfrA1) and ICEGEN (floR, strAB, sul2, and dfrA1). Based on the genetic structure, Kolkata strains of V. cholerae O1 had distinct genetic traits different from the ICEs reported in other cholera endemic regions. Transfer of AMR was confirmed by conjugation with sodium azide resistant Escherichia coli J53. In addition to the acquired resistance to streptomycin and trimethoprim-sulfamethoxazole, the conjugally transferred (CT) E. coli J53 with ICE showed higher resistance to chloramphenicol and tetracycline than the donor V. cholerae. Pulsed-field gel electrophoresis (PFGE) based clonal analysis revealed that the V. cholerae strains could be grouped based on their ICEs and AMR patterns. Our findings demonstrate the epidemiological importance of ICEs and their role in the emergence of multidrug resistance (MDR) in El Tor vibrios.

RevDate: 2019-09-26

Pires ES, Hardoim CCP, Miranda KR, et al (2019)

The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon.

Frontiers in microbiology, 10:2003.

During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.

RevDate: 2019-09-26

Riva A, Kuzyk O, Forsberg E, et al (2019)

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.

Nature communications, 10(1):4366 pii:10.1038/s41467-019-12413-0.

Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.

RevDate: 2019-09-26

Vissenaekens H, Grootaert C, Rajkovic A, et al (2019)

Cell line-dependent increase in cellular quercetin accumulation upon stress induced by valinomycin and lipopolysaccharide, but not by TNF-α.

Food research international (Ottawa, Ont.), 125:108596.

As the interface between the luminal and internal environment, the intestinal epithelium is strongly exposed to food-related, host-related and microbial stress. Furthermore, the endothelial stress response plays an important role in vascular disease development, which may be improved upon consumption of dietary bioactives such as polyphenols. The impact of the latter, however, is largely individual-dependent and effects are, in most cases, only observed under mild diseased conditions. Here, it is hypothesized that the individual's stressor levels may contribute to this variable response. To this end, the impact of the stressors (i) valinomycin (as model for cereulide, food-related microbial metabolite), (ii) TNF-α (host-related) and (iii) lipopolysaccharide (gram-negative bacterial cell related) on flavonoid accumulation was investigated in several intestinal and endothelial cell lines. Flow cytometry, confocal microscopy and an in-house developed, robust and high-throughput spectrofluorometric method, showed that quercetin accumulated in all tested cell lines in a dose-dependent manner. Upon stress induced by valinomycin and to a lesser extent by lipopolysaccharide, but not by TNF-α, an increased quercetin accumulation was observed in proliferating intestinal and endothelial cells and not in differentiated intestinal or quiescent endothelial cells. Therefore, flavonoid accumulation may be a potential cellular stress response mechanism which strongly depends on the applied stressor, flavonoid, cell line and even growth conditions. This opens perspectives for further understanding the mechanisms by which cellular stress may shape the individual's response to bioactive compounds.

RevDate: 2019-09-25

Zhang Y, Shen Z, Zhang F, et al (2019)

Taxonomy and phylogeny of Pseudovorticella littoralis sp. n. and P. alani sp. n. (Ciliophora: Peritrichia) from coastal waters of southern China.

European journal of protistology, 71:125635 pii:S0932-4739(19)30072-0 [Epub ahead of print].

The morphology, infraciliature, and silverline system of two peritrich ciliates, Pseudovorticella littoralis sp. n. and P. alani sp. n., isolated from coastal waters of southern China, were investigated based on both living and silver-stained specimens. Pseudovorticella littoralis sp. n. is characterized by the following combination of characters: cell inverted cone-shaped; contractile vacuole ventral; J-shaped macronucleus; infundibular polykinety 3 with two kinetosome rows of equal length; 19-26 silverlines from peristome to trochal band and 5-14 from trochal band to scopula. Pseudovorticella alani sp. n. is characterized by: cell inverted bell-shaped; contractile vacuole ventral; J-shaped macronucleus recurved almost forming a loop; infundibular polykinety 3 with three kinetosome rows, outer two rows longer than inner one; 48-61 silverlines between peristome and aboral trochal band, and 12-20 between aboral trochal band and scopula. The SSU rDNA sequences of both new species are reported and their genetic distances with congeners and phylogenetic relationships are investigated. Pseudovorticella and Epicarchesium cluster into two subclades with low support values. One subclade contains nearly all the available sequences of Pseudovorticella and Epicarchesium. Another one contains P. monilata and E. pectinatum. This calls on the need of a generic re-classification of Pseudovorticella and Epicarchesium based on more morphological and molecular data.

RevDate: 2019-09-25

Subirats J, Di Cesare A, Varela Della Giustina S, et al (2019)

High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance.

Water research, 167:114895 pii:S0043-1354(19)30669-4 [Epub ahead of print].

We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L-1 of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (blaTEM, blaCTX-M, blaOXA, and blaKPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (blaCTX-M, blaOXA, and blaKPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.

RevDate: 2019-09-25

Regnery J, Parrhysius P, Schulz RS, et al (2019)

Wastewater-borne exposure of limnic fish to anticoagulant rodenticides.

Water research, 167:115090 pii:S0043-1354(19)30864-4 [Epub ahead of print].

The recent emergence of second-generation anticoagulant rodenticides (AR) in the aquatic environment emphasizes the relevance and impact of aquatic exposure pathways during rodent control. Pest control in municipal sewer systems of urban and suburban areas is thought to be an important emission pathway for AR to reach wastewater and municipal wastewater treatment plants (WWTP), respectively. To circumstantiate that AR will enter streams via effluent discharges and bioaccumulate in aquatic organisms despite very low predicted environmental emissions, we conducted a retrospective biological monitoring of fish tissue samples from different WWTP fish monitoring ponds exclusively fed by municipal effluents in Bavaria, Germany. At the same time, information about rodent control in associated sewer systems was collected by telephone survey to assess relationships between sewer baiting and rodenticide residues in fish. In addition, mussel and fish tissue samples from several Bavarian surface waters with different effluent impact were analyzed to evaluate the prevalence of anticoagulants in indigenous aquatic organisms. Hepatic AR residues were detected at 12 out of 25 WWTP sampling sites in the low μg/kg range, thereof six sites with one or more second-generation AR (i.e., brodifacoum, difenacoum, bromadiolone). 14 of 18 surveyed sites confirmed sewer baiting with AR and detected hepatic residues matched the reported active ingredients used for sewer baiting at six sites. Furthermore, second-generation AR were detected in more than 80% of fish liver samples from investigated Bavarian streams. Highest total hepatic AR concentrations in these fish were 9.1 and 8.5 μg/kg wet weight, respectively and were observed at two riverine sampling sites characterized by close proximity to upstream WWTP outfalls. No anticoagulant residues were found in fish liver samples from two lakes without known influences of effluent discharges. The findings of our study clearly show incomplete removal of anticoagulants during conventional wastewater treatment and confirm exposure of aquatic organisms via municipal effluents. Based on the demonstrated temporal and spatial coherence between sewer baiting and hepatic AR residues in effluent-exposed fish, sewer baiting in combined sewer systems contributes to the release of active ingredients into the aquatic environment.

RevDate: 2019-09-25

Wagner AO, Praeg N, P Illmer (2019)

Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment.

Current microbiology pii:10.1007/s00284-019-01772-y [Epub ahead of print].

In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.

RevDate: 2019-09-25

Keiser CN, Hammer TJ, JN Pruitt (2019)

Social spider webs harbour largely consistent bacterial communities across broad spatial scales.

Biology letters, 15(9):20190436.

Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbour microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbours compositionally distinct microbes from the more ephemeral capture webs in the desert social spider, Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harboured similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey and web samples. These data suggest that social spider webs can harbour characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.

RevDate: 2019-09-24

De Vrieze J, Verbeeck K, Pikaar I, et al (2019)

The hydrogen gas bio-based economy and the production of renewable building block chemicals, food and energy.

New biotechnology pii:S1871-6784(18)31885-5 [Epub ahead of print].

The carrying capacity of the planet is being exceeded and there is an urgent need to bring forward revolutionary approaches, particularly in terms of energy supply, carbon emissions and nitrogen inputs into the biosphere. Hydrogen gas, generated by means of renewable energy through water electrolysis, can be a platform molecule to drive the future bioeconomy and electrification in the 21st century. The potential to use hydrogen gas in microbial metabolic processes is highly versatile, and this opens a broad range of opportunities for novel biotechnological developments and applications. A first approach concerns the central role of hydrogen gas in the production of bio-based building block chemicals using the methane route, thus, bypassing the inherent low economic value of methane towards higher-value products. Secondly, hydrogen gas can serve as a key carbon-neutral source to produce third-generation proteins, i.e. microbial protein for food applications, whilst simultaneously enabling carbon capture and nutrient recovery, directly at their point of emission. Combining both approaches to deal with the intermittent nature of renewable energy sources maximises the ability for efficient use of renewable resources.

RevDate: 2019-09-24

Mahjoubi M, Aliyu H, Cappello S, et al (2019)

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.

PloS one, 14(9):e0221574 pii:PONE-D-18-36621.

Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.

RevDate: 2019-09-24

Soares-Castro P, Araújo-Rodrigues H, Godoy-Vitorino F, et al (2019)

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring.

Scientific reports, 9(1):13679 pii:10.1038/s41598-019-50139-7.

The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.

RevDate: 2019-09-24

Petersen J, Vollmers J, Ringel V, et al (2019)

A marine plasmid hitchhiking vast phylogenetic and geographic distances.

Proceedings of the National Academy of Sciences of the United States of America pii:1905878116 [Epub ahead of print].

Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.

RevDate: 2019-09-24

Messal M, Slippers B, Naidoo S, et al (2019)

Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone.

Microorganisms, 7(10): pii:microorganisms7100375.

Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal-host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal-plant and fungal-microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant-microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant-microbe interactions.

RevDate: 2019-09-24

Wang J, Sun Y, Tao D, et al (2019)

Reduction of Escherichia coli O157:H7, Listeria monocytogenes, and Naturally Present Microbe Counts on Lettuce using an Acid Mixture of Acetic and Lactic Acid.

Microorganisms, 7(10): pii:microorganisms7100373.

Lactic acid (LA) and acetic acid (AA) are independently used to disinfect fresh leaf vegetables. LA has a higher efficacy but costs more than AA. Herein, we compared the disinfection efficacy of LA, AA, and their mixture on lettuce to determine whether the cheaper acid mixture shows similar or more efficacy than LA. Quality analysis indicated that the acid mixture and individual acids did not cause additional loss of instrument color and polyphenolic content compared with that of the control; however, visible defects were observed at AA concentrations exceeding 0.8%. Analysis of Escherichia coli O157:H7, Listeria monocytogenes, and naturally present microbes (aerobic mesophilic and psychrotrophic bacteria, coliforms, molds, and yeasts) showed that the acid mixture led to the highest reduction in microbial count during storage. 16S rRNA sequencing was further employed to understand the effects of the acid mixture and individual acids on lettuce microbial ecology. During storage, the acid mixture and individual acids significantly decreased the abundance of Massilia spp. and Alkanindiges spp. but there was a marked increase in Escherichia-Shigella abundance (LA: 0.003-58.82%; AA: 0.01-55.34%; acid mixture: undetected to 50.71%; control: 0.007-33.09%), indicating that acid disinfection altered the microbial ecology to stimulate Escherichia-Shigella growth. These results enhance our understanding of the relationship between lettuce disinfection and ecological changes.

RevDate: 2019-09-23

Pietro-Souza W, de Campos Pereira F, Mello IS, et al (2019)

Mercury resistance and bioremediation mediated by endophytic fungi.

Chemosphere, 240:124874 pii:S0045-6535(19)32113-7 [Epub ahead of print].

The present study proposes the use of endophytic fungi for mercury bioremediation in in vitro and host-associated systems. We examined mercury resistance in 32 strains of endophytic fungi grown in culture medium supplemented with toxic metal concentrations. The residual mercury concentrations were quantified after mycelial growth. Aspergillus sp. A31, Curvularia geniculata P1, Lindgomycetaceae P87, and Westerdykella sp. P71 were selected and further tested for mercury bioremediation and bioaccumulation in vitro, as well as for growth promotion of Aeschynomene fluminensis and Zea mays in the presence or absence of the metal. Aspergillus sp. A31, C. geniculata P1, Lindgomycetaceae P87 and Westerdykella sp. P71 removed up to 100% of mercury from the culture medium in a species-dependent manner and they promoted A. fluminensis and Z. mays growth in substrates containing mercury or not (Dunnett's test, p < 0.05). Lindgomycetaceae P87 and C. geniculata P1 are dark septate endophytic fungi that endophytically colonize root cells of their host plants. The increase of host biomass correlated with the reduction of soil mercury concentration due to the metal bioaccumulation in host tissues and its possible volatilization. The soil mercury concentration was decreased by 7.69% and 57.14% in A. fluminensis plants inoculated with Lindgomycetaceae P87 + Aspergillus sp. A31 and Lindgomycetaceae P87, respectively (Dunnet's test, p < 0.05). The resistance mechanisms of mercury volatilization and bioaccumulation in plant tissues mediated by these endophytic fungi can contribute to bioremediation programs. The biochemical and genetic mechanisms involved in bioaccumulation and volatilization need to be elucidated in the future.

RevDate: 2019-09-23

Pikaar I, Flugen M, Lin HW, et al (2019)

Full-scale investigation of in-situ iron and alkalinity generation for efficient sulfide control.

Water research, 167:115032 pii:S0043-1354(19)30806-1 [Epub ahead of print].

Hydrogen sulfide induced corrosion of concrete sewer pipes is a major issue for wastewater utilities globally. One of the most commonly used methods to combat hydrogen sulfide is the addition of ferric chloride. While a reliable and effective method, ferric chloride is acidic causing OH&S concerns as well as alkalinity consumption in sewage. This study investigates, under full-scale field conditions, an alternative method for sulfide control by in-situ electrochemical generation of iron ions using sacrificial iron electrodes. This method concomitantly produces alkalinity through cathodic OH- generation, rather than consumption. The gaseous hydrogen sulfide concentrations at the discharge wet well of a real-life rising main (length: ∼1 km in, diameter: 150 mm) decreased from 173 ppm to 43 ppm (90 percentile of peak values), when a current of 0.86 A/m3 of sewage was applied. The 90 percentile peak H2S value was further reduced to 6.6 ppm when the applied current was increased to 1.14 A/m3 sewage. Moreover, methane generation was almost completely inhibited from 25.3 ± 1.46 mg COD/L to 0.06 ± 0.04 mg COD/L. The overall cell voltage remained constant throughout the experimental period clearly showing the stability of the process. Detailed characterization of the down-stream sewer pipe biofilm revealed the complexity of the iron chemistry as the in-situ produced iron ions undergo transformation into a variety of iron species. Overall, this study demonstrates that in-situ generation of iron and alkalinity is an effective alternative method for hydrogen sulfide control in sewers.

RevDate: 2019-09-23

Huang X, Chen W, Yan C, et al (2019)

Gypenosides improve the intestinal microbiota of non-alcoholic fatty liver in mice and alleviate its progression.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 118:109258 pii:S0753-3322(19)33015-X [Epub ahead of print].

Gypenosides (GP) are a type of traditional Chinese medicine (TCM) extracted from plants and commonly applied for treatment of metabolic diseases. This study aims to explore the effects of GP extracts on alleviating non-alcoholic fatty liver disease (NAFLD). In this experiment, C57BL/6 J mice were randomly assigned into normal diet control (ND), HFHC (high-fat and high-cholesterol) and HFHC + GP (GP) groups. Mice in HFHC group were fed HFHC diet combined with fructose drinking water for 12 weeks to induce the animal model of NAFLD, followed by ordinary drinking water until the end of the experiment. In the HFHC + GP group, mice were fed HFHC diet combined with fructose drinking water for 12 weeks, followed by GP-containing drinking water till the end. Mouse body weight was measured weekly. After animal procedures, mouse liver and serum samples were collected. It is shown that GP administration reduced body weight, enhanced the sensitivity to insulin resistance (IR) and decreased serum levels of ALT, AST and TG in NAFLD mice. In addition, GP treatment alleviated steatohepatitis, and downregulated ACC1, PPARγ, CD36, APOC3 and MTTP levels in mice fed with HFHC diet. Furthermore, GP treatment markedly improved intestinal microbiota, and reduced relative abundance ratio of Firmicutes / Bacteroidetes in the feces of NAFLD mice. Our results suggested that GP alleviated NAFLD in mice through improving intestinal microbiota.

RevDate: 2019-09-23

Alviz-Gazitua P, Fuentes-Alburquenque S, Rojas LA, et al (2019)

Corrigendum: The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.

Frontiers in microbiology, 10:2014.

[This corrects the article DOI: 10.3389/fmicb.2019.01499.].

RevDate: 2019-09-21

Petrin S, Patuzzi I, Di Cesare A, et al (2019)

Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms.

Environmental pollution (Barking, Essex : 1987), 255(Pt 1):113183 pii:S0269-7491(19)33234-8 [Epub ahead of print].

Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.

RevDate: 2019-09-20

Santos-Clotas E, Cabrera-Codony A, Boada E, et al (2019)

Efficient removal of siloxanes and volatile organic compounds from sewage biogas by an anoxic biotrickling filter supplemented with activated carbon.

Bioresource technology, 294:122136 pii:S0960-8524(19)31366-5 [Epub ahead of print].

The removal of siloxanes (D4 and D5) and volatile organic contaminants (hexane, toluene and limonene) typically found in sewage biogas was investigated in a lab-scale biotrickling filter (BTF) packed with lava rock under anoxic conditions. Complete removal efficiencies for toluene and limonene were recorded at all empty bed residence time (EBRT) tested. The influence of EBRT was remarkable on the abatement of D5, whose removal decreased from 37% at 14.5 min to 16% at 4 min, while the removal of D4 and hexane remained below 16%. The packing material was supplemented with 20% of activated carbon aiming at increasing the mass transfer of the most hydrophobic pollutants. This strategy supported high removal efficiencies of 43 and 45% for hexane and D5 at the lowest EBRT. CO2 and silica were identified as mineralization products along with the presence of metabolites in the trickling solution such as dimethylsilanediol, 2-carene and α-terpinene.

RevDate: 2019-09-20

Tomar SL (2019)

Oral Health Effects of Tobacco Products: Science and Regulatory Policy.

Advances in dental research, 30(1):2-3.

RevDate: 2019-09-19

Lambrecht E, Van Coillie E, Van Meervenne E, et al (2019)

Commensal E. coli rapidly transfer antibiotic resistance genes to human intestinal microbiota in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME).

International journal of food microbiology, 311:108357 pii:S0168-1605(19)30287-9 [Epub ahead of print].

Food-producing animals are indicated as a reservoir of antibiotic resistance genes and a potential vector for transmission of plasmid-encoded antibiotic resistance genes by conjugation to the human intestinal microbiota. In this study, transfer of an antibiotic resistance plasmid from a commensal E. coli originating from a broiler chicken towards the human intestinal microbiota was assessed by using a Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). This in vitro model mimics the human intestinal ecosystem and received a single dose of 109E. coli MB6212, which harbors a plasmid known to confer resistance towards several antibiotics including tetracycline, sulfamethoxazole and cefotaxime. Since the degree of stress imposed by stomach pH and bile acids vary with the consumed meal size, the effect of meal size on E. coli donor survival and on plasmid transfer towards lumen and mucosal coliforms and anaerobes was determined. The administered commensal E. coli strain survived stomach acid and bile salt stress and was able to grow in the colon environment during the timeframe of the experiment (72 h). Transfer of antibiotic resistance was observed rapidly since cultivable transconjugant coliforms and anaerobes were already detected in the lumen and mucosa after 2 h in the simulated proximal colon. The presence of the resistance plasmid in the transconjugants was confirmed by PCR. Differences in meal size and adapted digestion had neither a detectable impact on antibiotic resistance transfer, nor on the survival of the E. coli donor strain, nor on short chain fatty acid profiles. The median number of resistant indigenous coliforms in the lumen of the inoculated colon vessels was 5.00 × 105 cfu/ml [min - max: 3.47 × 104-3.70 × 108 cfu/ml], and on the mucosa 1.44 × 107 cfu/g [min-max: 4.00 × 103-4.00 × 108 cfu/g]. Exact quantification of the anaerobic transconjugants was difficult, as (intrinsic) resistant anaerobic background microbiota were present. QPCR data supported the observation of plasmid transfer in the simulated colon. Moreover, inoculation of E. coli MB6212 had no significant impact on the microbial diversity in the lumen as determined by 16 S ribosomal gene based next generation sequencing on lumen samples. This study demonstrates that a commensal, antibiotic resistant E. coli strain present in food can transfer its antibiotic resistance plasmid relatively quickly to intestinal microbiota in the M-SHIME. The spread and persistence of antibiotic resistance genes and resistant bacteria in our intestinal system is an alarming scenario which might present clinical challenges, since it implies a potential reservoir for dissemination to pathogenic bacteria.

RevDate: 2019-09-19

Contador CA, Veas-Castillo L, Tapia E, et al (2019)

Atacama Database: a platform of the microbiome of the Atacama Desert.

Antonie van Leeuwenhoek pii:10.1007/s10482-019-01328-x [Epub ahead of print].

The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl .

RevDate: 2019-09-19

Harkes P, Suleiman AKA, van den Elsen SJJ, et al (2019)

Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents.

Scientific reports, 9(1):13521 pii:10.1038/s41598-019-49854-y.

Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.

RevDate: 2019-09-19

Zwart MP, Ali G, Strien EAV, et al (2019)

Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing.

Viruses, 11(9): pii:v11090872.

Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.

RevDate: 2019-09-18

Tiwari UP, Singh AK, R Jha (2019)

Fermentation characteristics of resistant starch, arabinoxylan, and β-glucan and their effects on the gut microbial ecology of pigs: A review.

Animal nutrition (Zhongguo xu mu shou yi xue hui), 5(3):217-226.

Dietary fibers (DF) contain an abundant amount of energy, although the mammalian genome does not encode most of the enzymes required to degrade them. However, a mutual dependence is developed between the host and symbiotic microbes, which has the potential to extract the energy present in these DF. Dietary fibers escape digestion in the foregut and are fermented in the hindgut, producing short-chain fatty acids (SCFA) that alter the microbial ecology in the gastrointestinal tract (GIT) of pigs. Most of the carbohydrates are fermented in the proximal part, allowing protein fermentation in the distal part, resulting in colonic diseases. The structures of resistant starch (RS), arabinoxylan (AX), and β-glucan (βG) are complex; hence, makes their way into the hindgut where these are fermented and provide energy substrates for the colonic epithelial cells. Different microbes have different preferences of binding to different substrates. The RS, AX and βG act as a unique substrate for the microbes and modify the relative composition of the gut microbial community. The granule dimension and surface area of each substrate are different, which influences the penetration capacity of microbes. Arabinose and xylan are 2 different hemicelluloses, but arabinose is substituted on the xylan backbone and occurs in the form of AX. Fermentation of xylan produces butyrate primarily in the small intestine, whereas arabinose produces butyrate in the large intestine. Types of RS and forms of βG also exert beneficial effects by producing different metabolites and modulating the intestinal microbiota. Therefore, it is important to have information of different types of RS, AX and βG and their roles in microbial modulation to get the optimum benefits of fiber fermentation in the gut. This review provides relevant information on the similarities and differences that exist in the way RS, AX, and βG are fermented, and their positive and negative effects on SCFA production and gut microbial ecology of pigs. These insights will help nutritionists to develop dietary strategies that can modulate specific SCFA production and promote beneficial microbiota in the GIT of swine.

RevDate: 2019-09-18

Connor R, Brister R, Buchmann JP, et al (2019)

NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.

Genes, 10(9): pii:genes10090714.

A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.

RevDate: 2019-09-18

de Los Santos Villalobos S, Robles RI, Parra Cota FI, et al (2019)

Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico.

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

Strain TE3T, an endophytic plant growth promoting bacterium, was isolated from wheat (Triticumturgidum subsp. durum) sampled in the Yaqui Valley, Mexico. Biochemical, phenotypic and genotypic approaches were used to clarify the taxonomic affiliation of this strain. Based on analysis of its full-length 16S rRNA gene, strain TE3T was assigned to the genus Bacillus (similarity ≥98.7 %). This finding was supported by morphological and metabolic characteristics, such as rod shape, strictly aerobic metabolism, spore formation, Gram-positive staining, catalase-positive activity, reduction of nitrate to nitrite, starch and casein hydrolysis, growth in presence of lysozyme and 2 % NaCl, citrate utilization, growth pH from 6.0 to 8.0, and acid and indole production from glucose and tryptophan, respectively. The whole-genome phylogenetic relationship showed that TE3T formed an individual clade with Bacillus tequilensis KCTC 13622T, distant from that generated by all Bacillus subtilis subspecies. The maximum values for average nucleotide identity and in silico DNA-DNA hybridization were 93.85 and 54.30 %, respectively, related to Bacillus subtilissubsp. inaquosorum KCTC 13429T. Analysis of its fatty acid content showed the ability of strain TE3T to bio-synthetize fatty acids that are not present in closely related Bacillus species, such as C12 : 0, C12 : 0 2OH, C12 : 0 3OH, C17 : 0, iso-C17 : 0 3OH and C18 : 1ω9c. These results provide evidence that strain TE3T is a novel species of the genus Bacillus, for which the name Bacilluscabrialesii sp. nov. is proposed. The type strain of Bacilluscabrialesii is TE3T (CM-CNRG TB54T=CCStamb A1T).

RevDate: 2019-09-16

Koga Y, Ohtsu T, Kimura K, et al (2019)

Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota.

BMJ open gastroenterology, 6(1):e000314 pii:bmjgast-2019-000314.

Objective: To describe probiotics including a Lactobacillus gasseri strain LG21 used for the upper gastrointestinal tract, which are considered to act through improvement of indigenous microbiota inhabiting there.

Background and design: Because the early definition of probiotics emphasized their effects on improving the intestinal microbial ecology, their effects on the intestinal tract and its immunity have been considered common general benefits associated with probiotics. This conclusion was also based on a body of successful clinical trials whose endpoints were the prevention or treatment of intestinal diseases. In contrast to intestinal microbiota, our understanding of the role of gastric microbiota in human health and physiology remains poor, as the bacterial load in the stomach is considered too small to exert a significant effect due to the highly acidic environment of the human stomach. Therefore, the intervention using probiotics in the stomach is still limited at present.Results:In this article using representative 38 quoted articles, we first describe the gastric microbiota, as the indigenous microbiota in the stomach is thought to be significantly involved in the pathophysiology of this organ, since probiotics exert their beneficial effects through improving the resident microbiota. We then review the present status and future prospects of probiotics for the treatment of upper gastrointestinal diseases by quoting representative published articles, including our basic and clinical data.

Conclusions: Probiotics have been demonstrated to suppress Helicobacter pylori in the stomach, and are also expected to improve functional dyspepsia through the correction of dysbiotic gastric microbiota.

RevDate: 2019-09-16

Cruz H, Law YY, Guest JS, et al (2019)

Mainstream Ammonium Recovery to Advance Sustainable Urban Wastewater Management.

Environmental science & technology [Epub ahead of print].

Throughout the 20th century, the prevailing approach toward nitrogen management in municipal wastewater treatment was to remove ammonium by transforming it into dinitrogen (N2) using biological processes such as conventional activated sludge. While this has been a very successful strategy for safeguarding human health and protecting aquatic ecosystems, the conversion of ammonium into its elemental form is incompatible with the developing circular economy of the 21st century. Equally important, the activated sludge process and other emerging ammonium removal pathways have several environmental and technological limitations. Here, we assess that the theoretical energy embedded in ammonium in domestic wastewater represents roughly 38-48% of the embedded chemical energy available in the whole of the discharged bodily waste. The current routes for ammonium removal not only neglect the energy embedded in ammonium, but they can also produce N2O, a very strong greenhouse gas, with such emissions comprising the equivalent of 14-26% of the overall carbon footprint of wastewater treatment plants. N2O emissions often exceed the carbon emissions related to the electricity consumption for the process requirements of WWTPs. Considering these limitations, there is a need to develop alternative ammonium management approaches that center around recovery of ammonium from domestic wastewater rather than deal with its "destruction" into elemental dinitrogen. Current ammonium recovery techniques are applicable only at orders of magnitude above domestic wastewater strength, and so new techniques based on physicochemical adsorption are of particular interest. A new pathway is proposed that allows for mainstream ammonium recovery from wastewater based on physicochemical adsorption through development of polymer-based adsorbents. Provided adequate adsorbents corresponding to characteristics outlined in this paper are designed and brought to industrial production, this adsorption-based approach opens perspectives for mainstream continuous adsorption coupled with side-stream recovery of ammonium with minimal chemical requirements. This proposed pathway can bring forward an effective resource-oriented approach to upgrade the fate of ammonium in urban water management without generating hidden externalized environmental costs.

RevDate: 2019-09-14

Wichmann S, Z Ardern (2019)

Optimality in the standard genetic code is robust with respect to comparison code sets.

Bio Systems, 185:104023 pii:S0303-2647(19)30180-7 [Epub ahead of print].

The genetic code and its evolution have been studied by many different approaches. One approach is to compare the properties of the standard genetic code (SGC) to theoretical alternative codes in order to determine how optimal it is and from this infer whether or not it is likely that it has undergone a selective evolutionary process. Many different properties have been studied in this way in the literature. Less focus has been put on the alternative code sets which are used as a comparison to the standard code. Each implicitly represents an evolutionary hypothesis and the sets used differ greatly across the literature. Here we determine the influence of the comparison set on the results of the optimality calculation by using codes based upon different sub-structures of the SGC. With these results we can generalize the results to different evolutionary hypotheses. We find that the SGC's optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses. Our results provide important information for any future studies on the evolution of the standard genetic code. We also studied properties of the SGC concerning overlapping genes, which have recently been found to be more widespread than often believed. Although our results are not conclusive yet we find additional intriguing structures in the SGC that need explanation.

RevDate: 2019-09-13

Duysburgh C, Van den Abbeele P, Krishnan K, et al (2019)

A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro.

International journal of pharmaceutics: X, 1:100021 pii:100021.

A standardized in vitro simulation of the human gastrointestinal tract (M-SHIME®) was used to assess the effect of repeated daily administration of a synbiotic formulation, containing five spore-forming Bacillus strains and a prebiotic fiber blend, on the microbial activity and composition of three simulated human subjects. Firstly, while confirming recent findings, deeper phylogenetic insight was obtained in the resident M-SHIME® microbiota, demonstrating that the model maintains a diverse and representative, colon region-specific luminal and mucosal microbial community. Supplementation of the synbiotic concept increased microbial diversity in the distal colon areas, whereas specific enhancement of Bacillaceae levels was observed in the ascending colon suggesting a successful engraftment of the Bacillus spores, which probably resulted in a stimulatory effect on, among others, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Tannerellaceae and Faecalibacterium prausnitzii contributing directly or indirectly to stimulation of acetate, propionate and butyrate production. When compared with a previous study investigating the Bacillus strains, the generated data suggest a synergistic effect on the intestinal microbiota for the synbiotic formulation. Given the fact that the probiotic strains have been shown to impact post-prandial metabolic endotoxemia in human individuals, it might be interesting to further investigate the efficacy of the synbiotic concept in protecting against obesity-related disorders.

RevDate: 2019-09-13

Lee HJ, Shin SY, KS Whang (2019)

Paenibacillus pinistramenti sp. nov., isolated from pine litter.

Antonie van Leeuwenhoek pii:10.1007/s10482-019-01325-0 [Epub ahead of print].

A Gram-stain-positive bacterium, designated strain ASL46T, was isolated from litter layer of a pine forest located in Anmyondo, Korea. Strain ASL46T was found to be an aerobic, motile, endospore-forming rod which can grow at 20-45 °C (optimum, 37 °C), at pH 6.0-11.0 (optimum, pH 7.0) and at salinities of 0-2% (w/v) NaCl (optimum, 1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ASL46T belongs to the genus Paenibacillus, showing highest sequence similarity to P. yonginensis DCY84T (98.3%), P. physcomitrella XBT (97.4%) and P. faecis CIP 101062T (96.6%). The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain ASL46T and P. physcomitrella XBT and P. yonginensis DCY84T yielded ANI values of 84.6 and 84.5% and DNA-DNA relatedness of 11.7 ± 0.7 and 10.9 ± 0.2%, respectively. The DNA G+C content of the genomic DNA of strain ASL46T was 52.1 mol%. The predominant isoprenoid quinone was identified as menaquinone-7 and the major cellular fatty acids were determined to be anteiso-C15:0, C16:0 and iso-C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified phospholipid and an unidentified glycolipid. The whole-cell sugar was found to be ribose and cell wall peptidoglycan contained meso-diaminopimelic acid. On the basis of phylogenetic analyses, and phenotypic and chemotaxonomic characteristics, strain ASL46T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus pinistramenti sp. nov. is proposed. The type strain is ASL46T (= KACC 18701T = NBRC 111876T).

RevDate: 2019-09-13

Pereira-Flores E, Glöckner FO, A Fernandez-Guerra (2019)

Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data.

BMC bioinformatics, 20(1):453 pii:10.1186/s12859-019-3031-y.

BACKGROUND: Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms' characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms' ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms' ecological strategies as well as the environmental conditions they inhabit.

RESULTS: Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers.

CONCLUSION: We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms' ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools .

RevDate: 2019-09-12

Sekhohola-Dlamini L, M Tekere (2019)

Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing.

Biodegradation pii:10.1007/s10532-019-09890-x [Epub ahead of print].

Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.

RevDate: 2019-09-12

Wang L, Han M, Li X, et al (2019)

Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems.

Microbial ecology pii:10.1007/s00248-019-01439-y [Epub ahead of print].

This data-intensive study investigated the delicate balance of niche and neutrality underlying microbial communities in freshwater ecosystems through comprehensive application of high-throughput sequencing, species abundance distribution (SAD), and the neutral community model (NCM), combined with species diversity and phylogenetic measures, which unite the traditional and microbial ecology. On the genus level, 45.10% and 41.18% of the water samples could be explained by the log-normal and Volkov model respectively, among which 31.37% could fit both models. Meanwhile, 55.56% of the sediment samples could be depicted by the log-normal model, and Volkov-fitted samples comprised only 13.33%. Besides, operational taxonomic units (OTUs) from water samples fit Sloan's neutral model significantly better than those in sediment. Therefore, it was concluded that deterministic processes played a great role in both water and sediment ecosystems, whereas neutrality was much more involved in water assemblages than in non-fluidic sediment ecosystems. Secondly, log-normal fitted samples had lower phylogenetic species variability (PSV) than Volkov-fitted ones, indicating that niche-based communities were more phylogenetically clustered than neutrally assembled counterparts. Additionally, further testing showed that the relative richness of rare species was vital to SAD modeling, either niche-based or neutral, and communities containing fewer rare species were more easily captured by theoretical SAD models.

RevDate: 2019-09-12

Makarchuk S, Braz VC, Araújo NAM, et al (2019)

Enhanced propagation of motile bacteria on surfaces due to forward scattering.

Nature communications, 10(1):4110 pii:10.1038/s41467-019-12010-1.

How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell's propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells' motion. Here, we show that micro-obstacles influence the propagation of peritrichously flagellated bacteria on a flat surface in a non-monotonic way. Instead of hindering it, an optimal, relatively low obstacle density can significantly enhance cells' propagation on surfaces due to individual forward-scattering events. This finding provides insight on the emerging dynamics of chiral active matter in complex environments and inspires possible routes to control microbial ecology in natural habitats.

RevDate: 2019-09-11

Durán-Viseras A, Andrei AS, Ghai R, et al (2019)

New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea.

Frontiers in microbiology, 10:1928.

Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15BT and F9-27T) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525T, Halonotius aquaticus F13-13T and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15BT = CECT 9688T = CCM 8954T) and Halonotius roseus sp. nov. (type strain F9-27T = CECT 9745T = CCM 8956T) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B12) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide "expensive" commodities (i.e., vitamin B12) to the halophilic microbial communities at large.

RevDate: 2019-09-11

Bates KA, Shelton JMG, Mercier VL, et al (2019)

Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome.

Frontiers in microbiology, 10:1834.

The emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome can influence disease outcome for several host-pathogen systems, yet little is known of its role in Bsal infection. In addition, many experimental in-vivo amphibian disease studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterized the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt, Lissotriton vulgaris and the great-crested newt, Triturus cristatus. We show that captivity led to significant losses in bacterial and fungal diversity of amphibian skin, which may be indicative of a decline in microbe-mediated protection. We further demonstrate that in both L. vulgaris and T. cristatus, Bsal infection was associated with changes in the composition of skin bacterial communities with possible negative consequences to host health. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.

RevDate: 2019-09-11

Callejas C, Fernández A, Passeggi M, et al (2019)

Microbiota adaptation after an alkaline pH perturbation in a full-scale UASB anaerobic reactor treating dairy wastewater.

Bioprocess and biosystems engineering pii:10.1007/s00449-019-02198-3 [Epub ahead of print].

The aim of this study was to understand how the microbial community adapted to changes, including a pH perturbation, occurring during the start-up and operation processes in a full-scale methanogenic UASB reactor designed to treat dairy wastewater. The reactor performance, prokaryotic community, and lipid degradation capacity were monitored over a 9-month period. The methanogenic community was studied by mcrA/mrtA gene copy-number quantification and methanogenic activity tests. A diverse prokaryotic community characterized the seeding sludge as assessed by sequencing the V4 region of the 16S rRNA gene. As the feeding began, the bacterial community was dominated by Firmicutes, Synergistetes, and Proteobacteria phyla. After an accidental pH increase that affected the microbial community structure, a sharp increase in the relative abundance of Clostridia and a decrease in the mcrA/mrtA gene copy number and methanogenic activity were observed. After a recovery period, the microbial population regained diversity and methanogenic activity. Alkaline shocks are likely to happen in dairy wastewater treatment because of the caustic soda usage. In this work, the plasticity of the prokaryotic community was key to surviving changes to the external environment and supporting biogas production in the reactor.

RevDate: 2019-09-11

Lamei S, Stephan JG, Nilson B, et al (2019)

Feeding Honeybee Colonies with Honeybee-Specific Lactic Acid Bacteria (Hbs-LAB) Does Not Affect Colony-Level Hbs-LAB Composition or Paenibacillus larvae Spore Levels, Although American Foulbrood Affected Colonies Harbor a More Diverse Hbs-LAB Community.

Microbial ecology pii:10.1007/s00248-019-01434-3 [Epub ahead of print].

The main current methods for controlling American Foulbrood (AFB) in honeybees, caused by the bacterial pathogen Paenibacillus larvae, are enforced incineration or prophylactic antibiotic treatment, neither of which is fully satisfactory. This has led to an increased interest in the natural relationships between the pathogenic and mutualistic microorganisms of the honeybee microbiome, in particular, the antagonistic effects of Honeybee-Specific Lactic Acid Bacteria (hbs-LAB) against P. larvae. We investigated whether supplemental administration of these bacteria affected P. larvae infection at colony level over an entire flowering season. Over the season, the supplements affected neither colony-level hbs-LAB composition nor naturally subclinical or clinical P. larvae spore levels. The composition of hbs-LAB in colonies was, however, more diverse in apiaries with a history of clinical AFB, although this was also unrelated to P. larvae spore levels. During the experiments, we also showed that qPCR could detect a wider range of hbs-LAB, with higher specificity and sensitivity than mass spectrometry. Honeybee colonies are complex super-organisms where social immune defenses, natural homeostatic mechanisms, and microbiome diversity and function play a major role in disease resistance. This means that observations made at the individual bee level cannot be simply extrapolated to infer similar effects at colony level. Although individual laboratory larval assays have clearly demonstrated the antagonistic effects of hbs-LAB on P. larvae infection, the results from the experiments presented here indicate that direct conversion of such practice to colony-level administration of live hbs-LAB is not effective.

RevDate: 2019-09-11

Bridier A, Le Grandois P, Moreau MH, et al (2019)

Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.

Scientific reports, 9(1):12947 pii:10.1038/s41598-019-49464-8.

To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.

RevDate: 2019-09-11

Zhang CJ, Pan J, Duan CH, et al (2019)

Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes.

mSystems, 4(5): pii:4/5/e00442-19.

Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.

RevDate: 2019-09-11

Dumolin C, Aerts M, Verheyde B, et al (2019)

Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.

mSystems, 4(5): pii:4/5/e00437-19.

The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDEIMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.

RevDate: 2019-09-11

Rubbens P, Schmidt ML, Props R, et al (2019)

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry.

mSystems, 4(5): pii:4/5/e00093-19.

High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R2 = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA bacteria could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels. Selected operational taxonomic units (OTUs) ranged from low to high relative abundance and were mostly lake system specific (89.5% to 99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5% to 33.3%), suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of system-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships.IMPORTANCE A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production.

RevDate: 2019-09-10

Blackwell N, Perkins W, Palumbo-Roe B, et al (2019)

Seasonal blooms of neutrophilic Betaproteobacterial Fe(II) oxidizers and Chlorobi in iron-rich coal mine drainage sediments.

FEMS microbiology ecology pii:5561438 [Epub ahead of print].

Waters draining from flooded and abandoned coal mines in the South Wales Coalfield (SWC), are substantial sources of pollution to the environment characterized by circumneutral pH and elevated dissolved iron concentrations (>1 mg L-1). The discharged Fe precipitates to form Fe(III) (oxyhydr)oxides which sustain microbial communities. However, while several studies have investigated the geochemistry of mine drainage in the SWC, less is known about the microbial ecology of the sites presenting a gap in our understanding of biogeochemical cycling and pollutant turnover. This study investigated the biogeochemistry of the Ynysarwed mine adit in the SWC. Samples were collected from nine locations within sediment at the mine entrance from the upper and lower layers three times over one year for geochemical and bacterial 16S rRNA gene sequence analysis. During winter, members of the Betaproteobacteria bloomed in relative abundance (>40%) including the microaerophilic Fe(II)-oxidizing genus Gallionella. A concomitant decrease in Chlorobi-associated bacteria occurred, although by summer the community composition resembled that observed in the previous autumn. Here, we provide the first insights into the microbial ecology and seasonal dynamics of bacterial communities of Fe(III)-rich deposits in the SWC and demonstrate that neutrophilic Fe(II)-oxidizing bacteria are important and dynamic members of these communities.

RevDate: 2019-09-09

Chen S, AL Smith (2019)

Performance and microbial ecology of methane-driven microbial fuel cells at temperatures ranging from 25 to 5 °C.

Water research, 166:115036 pii:S0043-1354(19)30810-3 [Epub ahead of print].

The effluent of mainstream anaerobic processes is saturated with dissolved methane, representing a lost energy source and potent greenhouse gas emission if left unmanaged. This study investigated the impact of operational temperature on methane-driven microbial fuel cells (MFCs) designed for continuous operation to mitigate dissolved methane emissions in anaerobic effluents. Two bench-scale, single-chamber MFCs were operated sequentially at 25, 20, 15, 10 and 5 °C. Voltage production from both MFCs ranged from approximately 0.463 to 0.512 V over 1 kΩ resistance at temperatures ≥15 °C, but abruptly dropped as temperature decreased to 10 and 5 °C, averaging just 0.156 and 0.190 V for the replicate systems. Dissolved methane removal efficiency remained relatively stable across all operational temperatures, ranging from 53.0% to 63.6%. High-throughput sequencing of 16S rRNA genes and reverse transcription quantitative polymerase chain reaction indicated distinct distribution of methanotrophs (e.g., Methylomonas) and exoelectrogens (e.g., Geobacter) on the cathode and anode, respectively. Spearman's rank correlation suggested that an indirect interaction between methanotrophs and exoelectrogens via fermentative bacteria (e.g., Acetobacterium) may play a role in system function. Notably, diversity of the anode microbial community was positively correlated with both voltage production and Coulombic efficiency, suggesting overall diversity, as opposed to abundance or activity of exoelectrogens, was the primary factor governing performance at varying temperatures.

RevDate: 2019-09-09

Ramamurthy T, Mutreja A, Weill FX, et al (2019)

Corrigendum: Revisiting the Global Epidemiology of Cholera in Conjunction With the Genomics of Vibrio cholerae.

Frontiers in public health, 7:237.

[This corrects the article DOI: 10.3389/fpubh.2019.00203.].

RevDate: 2019-09-08

Hsu RH, Clark RL, Tan JW, et al (2019)

Microbial Interaction Network Inference in Microfluidic Droplets.

Cell systems pii:S2405-4712(19)30231-5 [Epub ahead of print].

Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantification of community members across environments and replicates. To this end, we developed Microbial Interaction Network Inference in microdroplets (MINI-Drop). Fluorescence microscopy coupled to computer vision techniques were used to rapidly determine the absolute abundance of each strain in hundreds to thousands of droplets per condition. We showed that MINI-Drop could accurately infer pairwise and higher-order interactions in synthetic consortia. We developed a stochastic model of community assembly to provide insight into the heterogeneity in community states across droplets. Finally, we elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium. In sum, we demonstrated a robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets.

RevDate: 2019-09-08

Calatayud M, Koren O, MC Collado (2019)

Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring.

Trends in endocrinology and metabolism: TEM pii:S1043-2760(19)30156-0 [Epub ahead of print].

Maternal nutritional, metabolic, and physiological states, as well as exposure to various environmental factors during conception, gestation, and lactation, have a fundamental role in the health programming of the offspring. Therefore, alterations affecting the maternal microbiota might indirectly influence fetal development. In addition, such alterations could be transmitted to the progeny at different stages of infant development (e.g., preconception, prenatal, or postnatal), thereby favoring the development of an altered microbiota in the neonate. Microbial changes of this kind have been linked to an increased risk of non-communicable diseases (NCDs), including obesity and metabolic syndrome, allergy-related problems, and diabetes. In this review, we summarize the relevance of the maternal microbiota to fetal-neonatal health programming, with a focus on maternal nutritional and metabolic states.

RevDate: 2019-09-07

Expósito JR, Coello AJ, Barreno E, et al (2019)

Endogenous NO Is Involved in Dissimilar Responses to Rehydration and Pb(NO3)2 in Ramalina farinacea Thalli and Its Isolated Phycobionts.

Microbial ecology pii:10.1007/s00248-019-01427-2 [Epub ahead of print].

Lichens undergo desiccation/rehydration cycles and are permeable to heavy metals, which induce free radicals. Nitrogen monoxide (NO) regulates important cellular functions, but the research on lichen NO is still very scarce. In Ramalina farinacea thalli, NO seems to be involved in the peroxidative damage caused by air pollution, antioxidant defence and regulation of lipid peroxidation and photosynthesis. Our hypothesis is that NO also has a critical role during the rehydration and in the responses to lead of its isolated phycobionts (Trebouxia sp. TR9 and Trebouxia jamesii). Therefore, we studied the intracellular reactive oxygen species (ROS) production, lipid peroxidation and chlorophyll autofluorescence during rehydration of thalli and isolated microalgae in the presence of a NO scavenger and Pb(NO3)2. During rehydration, NO scavenging modulates free radical release and chlorophyll autofluorescence but not lipid peroxidation in both thalli and phycobionts. Pb(NO3)2 reduced free radical release (hormetic effect) both in the whole thallus and in microalgae. However, only in TR9, the ROS production, chlorophyll autofluorescence and lipid peroxidation were dependent on NO. In conclusion, Pb hormetic effect seems to depend on NO solely in TR9, while is doubtful for T. jamesii and the whole thalli.

RevDate: 2019-09-06

Jaswal R, Pathak A, A Chauhan (2019)

Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils.

Microorganisms, 7(9): pii:microorganisms7090324.

Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the "core" microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired "core" microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired "core" bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.

RevDate: 2019-09-05

Griffero L, Alcántara-Durán J, Alonso C, et al (2019)

Basin-scale monitoring and risk assessment of emerging contaminants in South American Atlantic coastal lagoons.

The Science of the total environment, 697:134058 pii:S0048-9697(19)34035-5 [Epub ahead of print].

Emerging contaminants (ECs) such as pharmaceuticals, personal care products, drugs of abuse and polar pesticides are under particular attention due to their high consumption, frequent detection in the environment and reported ecotoxicological risk. This study investigates the occurrence and distribution of multiclass of ECs in surface waters at basin scale of two Atlantic coastal lagoons of Uruguay, South America. For this purpose, a target screening approach covering up to 362 compounds was employed using nanoflow liquid chromatography - high resolution mass spectrometry (nanoLC/HRMS). 56 compounds were identified including five banned pesticides in the European Union: atrazine, carbendazim, chlorpyrifos ethyl, diazinon, and ethion. Pharmaceuticals, hormones and drugs of abuse showed maximum detection frequencies and concentrations downstream cities. The highest occurrence of pesticides was found in lagoons and streams with neighboring agricultural activity. ECs were also found in coastal sea. Environmental risk assessment revealed that the hormones 17α-ethinylestradiol and 17-β-estradiol showed the highest risk to aquatic organisms in these basins. This study represents the first basin- scale monitoring of ECs in superficial waters encompassing streams, lagoons, and coastal seas in Uruguay, South America.

RevDate: 2019-09-05

Field HR, Whitaker AH, Henson JA, et al (2019)

Sorption of copper and phosphate to diverse biogenic iron (oxyhydr)oxide deposits.

The Science of the total environment, 697:134111 pii:S0048-9697(19)34088-4 [Epub ahead of print].

Iron (Fe) transformations partially control the biogeochemical cycling of biologically and environmentally important elements, such as carbon (C), nitrogen (N), phosphorus (P), and trace metals. In marine and freshwater environments, iron oxidizing bacteria commonly promote the oxidation of ferrous iron (Fe(II)) at circumneutral oxic-anoxic interfaces, resulting in the formation of mineral-organic composites known as biogenic Fe(III) (oxyhydr)oxides (BIOS). Previous studies have examined the microbial ecology, composition, morphology, and sorption reactivity of BIOS. However, a broad survey of BIOS properties and sorption reactivity is lacking. To further explore these relationships, this study utilized X-ray absorption spectroscopy (XAS) to characterize the Fe mineral species, acid digestions and elemental analysis to determine composition, Brunauer-Emmett-Teller (BET) analysis to measure specific surface area, and copper (Cu) and phosphorus (P) adsorption experiments at concentrations designed to measure maximum sorption to evaluate reactivity of BIOS samples collected in lakes and streams of the North Carolina Piedmont. Sample composition varied widely, with Fe and C content ranging from 6.3 to 34% and 3.4-13%, respectively. XAS spectra were best fit with 42-100% poorly crystalline Fe (oxyhydr)oxides, with the remainder composed of crystalline Fe minerals and organic complexes. On a sorbent mass basis, Cu and P sorption varied by a factor of two and 15, respectively. Regression analyses reveal interrelationships between physicochemical properties, and suggest that differences in P binding are driven by sorption to Fe(III) (oxyhydr)oxide surfaces. In total, results suggest that the physical and chemical characteristics of organic and Fe(III) (oxyhydr)oxide phases in BIOS interplay to control the sorption of solutes, and thus influence nutrient and contaminant cycling in soil and natural waters.

RevDate: 2019-09-05

Hernández-Del Amo E, Ramió-Pujol S, Gich F, et al (2019)

Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW.

Microbial ecology pii:10.1007/s00248-019-01425-4 [Epub ahead of print].

In constructed wetlands (CW), denitrification usually accounts for > 60% of nitrogen removal and is supposedly affected by wetland management practices, such as dredging (and plant removal). These practices cause an impact in sediment properties and microbial communities living therein. We have quantified the effects of a sediment dredging event on dissimilatory nitrite reduction by analysing the structure and activities of the microbial community before and after the event. Potential rates for nitrate reduction to ammonia and denitrification were in accordance with changes in the physicochemical conditions. Denitrification was the predominant pathway for nitrite removal (> 60%) and eventually led to the complete removal of nitrate. On the contrary, dissimilatory nitrite reduction to ammonia (DNRA) increased from 5 to 18% after the dredging event. Both actual activities and abundances of 16S rRNA, nirK and nirS significantly decreased after sediment dredging. However, genetic potential for denitrification (qnirS + qnirK/q16S rRNA) remained unchanged. Analyses of the 16S rRNA gene sequences revealed the importance of vegetation in shaping microbial community structures, selecting specific phylotypes potentially contributing to the nitrogen cycle. Overall, we confirmed that sediment dredging and vegetation removal exerted a measurable effect on the microbial community, but not on potential nitrite + nitrate removal rates. According to redundancy analysis, nitrate concentration and pH were the main variables affecting sediment microbial communities in the Empuriabrava CWs. Our results highlight a high recovery of the functionality of an ecosystem service after a severe intervention and point to metabolic redundancy of denitrifiers. We are confident these results will be taken into account in future management strategies in CWs.

RevDate: 2019-09-04

Arias-Borrego A, Callejón-Leblic B, Calatayud M, et al (2019)

Insights into cancer and neurodegenerative diseases through selenoproteins and the connection with gut microbiota - current analytical methodologies.

Expert review of proteomics [Epub ahead of print].

Introduction: Selenium plays many key roles in health especially in connection with cancer and neurodegenerative diseases, among others. However, it needs to be appreciated that the essentiality or toxicity action of selenium depends on both, a narrow range of concentration and the chemical specie involved. In this context, human selenoproteins are essential biomolecules against these disorders, mainly due to its antioxidant action. To this end, analytical methodologies may allow identifying and quantifying individual selenospecies in human biofluids and tissues. Areas covered: This review explores the role of selenoproteins in medicine, with special emphasis in cancer and neurodegenerative diseases, considering the possible link with gut microbiota, and analytical techniques and procedures recently developed for the absolute quantification of selenoproteins and selenometabolites in human biofluids and tissues. Expert opinion: The beneficial role of selenium in human health has been extensively studied and reviewed. However, several challenges remain unsolved as discussed in this article: (i) speciation of selenium (especially selenoproteins) in cancer and neurodegenerative disease patients; (ii) supplementation of selenium in humans using functional foods and nutraceuticals; (iii) the link between selenium and selenoproteins expression and the gut microbiota and (iv) analytical methods and pitfalls for the absolute quantification of selenoproteins and selenometabolites.

RevDate: 2019-09-04

Veach AM, LH Zeglin (2019)

Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet.

Microbial ecology pii:10.1007/s00248-019-01432-5 [Epub ahead of print].

A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment ("Altered" precipitation history with extended dry periods, versus the "Ambient" field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respiration through variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative of survival) through drying/re-wet. Altered soils also had a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequences of soil microbial changes resulting from extended drought conditions.

RevDate: 2019-09-04

Ehsani E, Dumolin C, Arends JBA, et al (2019)

Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria.

Applied microbiology and biotechnology pii:10.1007/s00253-019-10082-z [Epub ahead of print].

While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.

RevDate: 2019-09-04

Keshvardoust P, Huron VAA, Clemson M, et al (2019)

Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria.

NPJ biofilms and microbiomes, 5:22 pii:95.

Despite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.

RevDate: 2019-09-05

Godoy-Vitorino F (2019)

Human microbial ecology and the rising new medicine.

Annals of translational medicine, 7(14):342.

The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.

RevDate: 2019-08-30

Overholt WA, Schwing P, Raz KM, et al (2019)

The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills.

Environmental microbiology [Epub ahead of print].

The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in >700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Further, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after two years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies. This article is protected by copyright. All rights reserved.

RevDate: 2019-08-30

Zhang L, Shen Z, Fang W, et al (2019)

Composition of bacterial communities in municipal wastewater treatment plant.

The Science of the total environment, 689:1181-1191.

Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.

RevDate: 2019-08-30

Xu M, Stedtfeld RD, Wang F, et al (2019)

Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history.

The Science of the total environment, 689:1172-1180.

Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.

RevDate: 2019-08-29

Elghandour MMY, Khusro A, Adegbeye MJ, et al (2019)

Dynamic role of single-celled fungi in ruminal microbial ecology and activities.

Journal of applied microbiology [Epub ahead of print].

In ruminants, high fermentation capacity is necessary to develop more efficient ruminant production systems. Greater level of production depends on the ability of the microbial ecosystem to convert organic matter into precursors of milk and meat. This has led to increased interest by animal nutritionists, biochemists and microbiologists in evaluating different strategies to manipulate the rumen biota to improve animal performance, production efficiency and animal health. One of such strategies is the use of natural feed additives such as single-celled fungi yeast. The main objectives of using yeasts as natural additives in ruminant diets include; a) to prevent rumen microflora disorders, b) to improve and sustain higher production of milk and meat, c) to reduce rumen acidosis and bloat which adversely affect animal health and performance, d) to decrease the risk of ruminant-associated human pathogens, e) to reduce the excretion of nitrogenous-based compounds, carbon dioxide and methane. Yeast, a natural feed additive, has the potential to enhance feed degradation by increasing the concentration of volatile fatty acids during fermentation processes. In addition, microbial growth in the rumen is enhanced in the presence of yeast leading to the delivery of a greater amount of microbial protein to the duodenum and high nitrogen retention. Single-celled fungi yeast has demonstrated its ability to increase fiber digestibility and lower fecal output of organic matter due to improved digestion of organic matter, which subsequently improves animal productivity. Yeast also has the ability to alter the fermentation process in the rumen in a way that reduces methane formation. Furthermore, yeast inclusion in ruminant diets has been reported to decrease toxins absorption such as mycotoxins and promote epithelial cell integrity. This review article provides information on the impact of single-celled fungi yeast as a feed supplement on ruminal microbiota and its function to improve the health and productive longevity of ruminants. This article is protected by copyright. All rights reserved.

RevDate: 2019-08-29

Erni-Cassola G, Wright RJ, Gibson MI, et al (2019)

Early Colonization of Weathered Polyethylene by Distinct Bacteria in Marine Coastal Seawater.

Microbial ecology pii:10.1007/s00248-019-01424-5 [Epub ahead of print].

Plastic debris in aquatic environments is rapidly colonized by a diverse community of microorganisms, often referred to as the "Plastisphere." Given that common plastics are derived from fossil fuels, one would expect that Plastispheres should be enriched with obligate hydrocarbon-degrading bacteria (OHCB). So far, though, different polymer types do not seem to exert a strong effect on determining the composition of the Plastisphere, and putative biodegrading bacteria are only found as rare taxa within these biofilms. Here, we show through 16S rRNA gene sequencing that the enrichment of a prominent OHCB member on weathered and non-weathered polyethylene only occurred at early stages of colonization (i.e., after 2 days of incubation in coastal marine water; 5.8% and 3.7% of relative abundance, respectively, vs. 0.6% on glass controls). As biofilms matured, these bacteria decreased in relative abundance on all materials (< 0.3% after 9 days). Apart from OHCB, weathered polyethylene strongly enriched for other distinct organisms during early stages of colonization, such as a specific member of the Roseobacter group and a member of the genus Aestuariibacter (median 26.9% and 1.8% of the community, respectively), possibly as a consequence of the availability of short-oxidized chains generated from weathering. Our results demonstrate that Plastispheres can vary in accordance with the weathering state of the material and that very early colonizing communities are enriched with taxa that can potentially degrade hydrocarbons. Given the lack of persistent enrichment and overall community convergence between materials over time, common non-hydrolysable polymers might not serve as an important source of carbon for mature Plastispheres once the labile substrates generated from weathering have been depleted.

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RJR Experience and Expertise

Researcher

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.

Educator

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.

Administrator

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.

Technologist

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.

Publisher

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.

Speaker

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.

Facilitator

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.

Designer

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.

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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,

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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

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