Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

Microbial communities of methane producing methanogens and consuming methanotrophs play an important role for the earths atmospheric methane budget. Despite their global significance, the functional potential of these communities is poorly understood. To investigate this, we applied the molecular technique, captured metagenomics, to identify the variability in functional diversity of microorganisms involved in the metabolism of methanein an environmentally controlled laboratory study. Nine plant-peat mesocosms dominated by the sedge Eriophorum vaginatum, with varying coverage, were collected from a temperate natural wetland is Sweden and subjected to a simulated growing season. Samples for analysis of captured metagenomes were taken from the top, bottom and root adjacent zone at the end of the experiment. In addition, over the simulated season, measured gas fluxes of carbon dioxide (CO2) and CH4, &#948;13C of emitted CH4 and the pore water concentration of dissolved methane and low molecular weight organic acids were recorded. The functional genes resulting from the captured metagenomes had a higher Shannon &#945;-diversity in the root zone when compared to the bottom and top. Sequences coding for methane metabolism were significantly more diverse in the root and bottom zones when compared to the top. However, the frequency of Acetyl-CoA decarbonylase and methane monooxygenase subunit A were significantly higher in the high emitting methane flux category when compared to the medium and low emitting mesocosms. We conclude that captured metagenomic analyses of functional genes provides a good measure of the functional potential methanogenic and methanotrophic microbial communities. This technique can be used to investigate how methanogens and methanotrophs function in peatlands and thus, contribute to the concentration of atmospheric methane.

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Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

Microbial Ecology ◽

10.1007/s00248-015-0612-9 ◽

2015 ◽

Vol 70 (3) ◽

pp. 596-611 ◽

Cited By ~ 20

Author(s):

Özgul İnceoğlu ◽

Marc Llirós ◽

Sean A. Crowe ◽

Tamara García-Armisen ◽

Cedric Morana ◽

...

Keyword(s):

Vertical Distribution ◽

Microbial Communities ◽

Meromictic Lake ◽

Functional Potential ◽

Lake Kivu

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Genetic functional potential displays minor importance in explaining spatial variability of methane fluxes within a Eriophorum vaginatum dominated Swedish peatland

10.5194/bg-2021-353 ◽

2022 ◽

Author(s):

Joel Dawson White ◽

Lena Ström ◽

Veiko Lehsten ◽

Janne Rinne ◽

Dag Ahrén

Keyword(s):

Spatial Variability ◽

Microbial Communities ◽

Growing Season ◽

Future Climate ◽

Minor Importance ◽

Type I ◽

Eriophorum Vaginatum ◽

Ch4 Emission ◽

Climate Scenarios ◽

Functional Potential

Abstract. Microbial communities of methane (CH4) producing methanogens and consuming methanotrophs play an important role for Earth's atmospheric CH4 budget. Despite their global significance, knowledge on how much they control the spatial variation in CH4 fluxes from peatlands is poorly understood. We studied variation in CH4 producing and consuming communities in a natural peatland dominated by Eriophorum vaginatum, via a metagenomics approach using custom designed hybridization-based oligonucleotide probes to focus on taxa and functions associated with methane cycling. We hypothesized that sites with different magnitudes of methane flux are occupied by structurally and functionally different microbial communities, despite the dominance of a single vascular plant species. To investigate this, nine plant-peat mesocosms dominated by the sedge Eriophorum vaginatum, with varying vegetation coverage, were collected from a temperate natural wetland and subjected to a simulated growing season. During the simulated growing season, measurements of CH4 emission, carbon dioxide (CO2) exchange and δ13C signature of emitted CH4 were made. Mesocosms 1 through 9 were classified into three categories according to the magnitude of CH4 flux. Gross primary production and ecosystem respiration followed the same pattern as CH4 fluxes, but this trend was not observed in net ecosystem exchange. We observed that genetic functional potential was of minor importance in explaining spatial variability of CH4 fluxes with only small shifts in taxonomic community and functional genes. In addition, a higher β-diversity was observed in samples with high CH4 emission. Among methanogens, Methanoregula, made up over 50 % of the community composition. This, in combination with the remaining hydrogenotrophic methanogens matched the δ13C isotopic signature of emitted CH4. However, the presence of acetoclastic and methylotrophic taxa and type I, II and Verrucomicrobia methanotrophs indicates that the microbial community holds the ability to produce and consume CH4 in multiple ways. This is important in terms of future climate scenarios, where peatlands are expected to alter in nutrient status, hydrology, and peat biochemistry. Due to the high functional potential, we expect the community to be highly adaptive to future climate scenarios.

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Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities

The Science of The Total Environment ◽

10.1016/j.scitotenv.2019.05.090 ◽

2019 ◽

Vol 681 ◽

pp. 413-423 ◽

Cited By ~ 10

Author(s):

Raj Kumar Regar ◽

Vivek Kumar Gaur ◽

Abhay Bajaj ◽

Subodh Tambat ◽

Natesan Manickam

Keyword(s):

Microbial Communities ◽

Contaminated Soils ◽

Anthropogenic Influence ◽

Microbiome Analysis ◽

Functional Potential

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Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

Open Biology ◽

10.1098/rsob.130160 ◽

2013 ◽

Vol 3 (12) ◽

pp. 130160 ◽

Cited By ~ 78

Author(s):

Simon Roux ◽

Mart Krupovic ◽

Didier Debroas ◽

Patrick Forterre ◽

François Enault

Keyword(s):

Life Cycle ◽

Microbial Communities ◽

Metabolic Pathways ◽

General Trend ◽

Computational Method ◽

Natural Ecosystems ◽

Viral Genomes ◽

Functional Potential ◽

Viral Communities ◽

Cellular Dna

Although the importance of viruses in natural ecosystems is widely acknowledged, the functional potential of viral communities is yet to be determined. Viral genomes are traditionally believed to carry only those genes that are directly pertinent to the viral life cycle, though this view was challenged by the discovery of metabolism genes in several phage genomes. Metagenomic approaches extended these analyses to a community scale, and several studies concluded that microbial and viral communities encompass similar functional potentials. However, these conclusions could originate from the presence of cellular DNA within viral metagenomes. We developed a computational method to estimate the proportion and origin of cellular sequences in a set of 67 published viromes. A quarter of the datasets were found to contain a substantial amount of sequences originating from cellular genomes. When considering only viromes with no cellular DNA detected, the functional potential of viral and microbial communities was found to be fundamentally different—a conclusion more consistent with the actual picture drawn from known viruses. Yet a significant number of cellular metabolism genes was still retrieved in these viromes, suggesting that the presence of auxiliary genes involved in various metabolic pathways within viral genomes is a general trend in the virosphere.

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The Functional Potential of Microbial Communities in Hydraulic Fracturing Source Water and Produced Water from Natural Gas Extraction Characterized by Metagenomic Sequencing

PLoS ONE ◽

10.1371/journal.pone.0107682 ◽

2014 ◽

Vol 9 (10) ◽

pp. e107682 ◽

Cited By ~ 35

Author(s):

Arvind Murali Mohan ◽

Kyle J. Bibby ◽

Daniel Lipus ◽

Richard W. Hammack ◽

Kelvin B. Gregory

Keyword(s):

Natural Gas ◽

Hydraulic Fracturing ◽

Microbial Communities ◽

Produced Water ◽

Gas Extraction ◽

Metagenomic Sequencing ◽

Source Water ◽

Functional Potential ◽

Natural Gas Extraction

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Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River

mSphere ◽

10.1128/msphere.00346-18 ◽

2018 ◽

Vol 3 (5) ◽

Cited By ~ 3

Author(s):

Aneisha M. Collins-Fairclough ◽

Rebecca Co ◽

Melessa C. Ellis ◽

Laura A. Hug

Keyword(s):

Microbial Communities ◽

Solid Waste ◽

Human Health ◽

Surface Waters ◽

Landfill Leachate ◽

Aromatic Compounds ◽

Human Health Risk ◽

Human Populations ◽

Shotgun Metagenomics ◽

Functional Potential

ABSTRACT The Riverton City dump is Jamaica’s largest solid waste disposal site, but it lacks engineered protection for leachate containment and treatment. Shotgun metagenomics was used to survey the microbial communities in the Riverton City dump leachate and in surface waters of the Duhaney River, an urban waterway abutting the dump. The community within the leachate pond was taxonomically distinct from that found in the surface waters of the Duhaney River. Higher microbial diversity was observed within the dump leachate, with members of the Bacteroidetes, Firmicutes, Gammaproteobacteria, Deltaproteobacteria, and Tenericutes being the most abundant, while the river community was dominated by Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The microbial communities exhibit similar functional potential profiles, including chemoorganoheterotrophy as the dominant metabolism, and the potential to degrade aromatic compounds. From reconstruction of metagenome-assembled genomes (MAGs), organisms within both environments are predicted to survive in the presence of multiple antibiotics, antiseptics, biocides, and metals. Strong virulence potential coincided with the most diverse multiple resistance profiles in 1 of 5 leachate MAGs and 5 of 33 river MAGs. Unexpectedly, the microbial resistance profiles were more varied and widespread in the river populations, where we had expected the chemical composition of the leachate to select and enrich for resistance characteristics. This study provides valuable insights into the total functional potential of a landfill leachate microbial community and identifies possible human health hazards within the Duhaney River and Riverton City dump, urban environments with the potential to impact human populations. IMPORTANCE Landfill leachate is a persistent contamination threat for terrestrial waters. Microbial metabolism in landfills transforms contaminants and contributes to greenhouse gas emissions. A better understanding of landfill-associated microbial communities will inform bioremediation of solid waste environments and improve pathogen monitoring. We leveraged shotgun metagenomics to investigate the microbial communities of the Riverton City dump and the adjoining Duhaney River near Kingston City, Jamaica. We identified no overlap between the microbial communities inhabiting the Riverton City dump leachate and the Duhaney River. Both communities are predicted to degrade aromatic compounds, which are ubiquitous environmental pollutants. Adversely, microbes in both environments are predicted to withstand widely used antibiotics, antiseptics, and metal contamination. The absence of evidence for microbial transfer from the leachate to the river is encouraging; however, the Duhaney River contained several organisms with predicted pathogenic lifestyles, indicating that the river represents a human health risk regardless of impact from the dump.

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Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

PLoS ONE ◽

10.1371/journal.pone.0112609 ◽

2014 ◽

Vol 9 (11) ◽

pp. e112609 ◽

Cited By ~ 57

Author(s):

Xiangzhen Li ◽

Junpeng Rui ◽

Jingbo Xiong ◽

Jiabao Li ◽

Zhili He ◽

...

Keyword(s):

Microbial Communities ◽

Soil Microbial Communities ◽

Maize Rhizosphere ◽

Soil Microbial ◽

Functional Potential

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Living to the high extreme: unraveling the composition, structure, and functional insights of bacterial communities thriving in the arsenic-rich Salar de Huasco – Altiplanic ecosystem.

10.1101/2021.04.13.439755 ◽

2021 ◽

Author(s):

Juan Castro-Severyn ◽

Coral Pardo-Esté ◽

Katterinne N. Mendez ◽

Jonathan Fortt ◽

Sebastián Márquez ◽

...

Keyword(s):

Microbial Communities ◽

Extreme Environments ◽

Taxonomic Diversity ◽

Functional Categories ◽

Bacterial Composition ◽

Functional Potential ◽

Metabolic Versatility ◽

Composition Structure ◽

Metagenomic Approach

Microbial communities inhabiting extreme environments like Salar de Huasco (SH) are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements like arsenic (As). Hence, we aimed to uncover the role of arsenic in shaping bacterial composition, structure, and functional potential in five different sites in this Altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of arsenic (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses showed broadly convergent patterns, contrasting with their great taxonomic variability. Arsenic-related metabolism is different among the five communities, as well as other functional categories like those related to the CH4 and S cycles. Particularly, we found that the distribution and abundance of As-related genes increase, following along the As concentration gradient. Approximately 75% of the detected genes for As-metabolism belong to expulsion mechanisms, being arsJ and arsP pumps related to sites with higher As concentrations and present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality MAGs (Metagenome Assembled Genomes) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1) and Gemmatimonadota (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of the highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with a great metabolic versatility, which needs further study.

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Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth

npj Biofilms and Microbiomes ◽

10.1038/s41522-020-00162-8 ◽

2020 ◽

Vol 6 (1) ◽

Author(s):

Conor Feehily ◽

David Crosby ◽

Calum J. Walsh ◽

Elaine M. Lawton ◽

Shane Higgins ◽

...

Keyword(s):

Preterm Birth ◽

High Risk ◽

Microbial Communities ◽

Full Term ◽

Vaginal Microbiota ◽

Metagenomic Sequencing ◽

Lactobacillus Crispatus ◽

Functional Potential ◽

Shotgun Metagenomic Sequencing ◽

Gene Functions

AbstractAn association between the vaginal microbiota and preterm birth (PTB) has been reported in several research studies. Population shifts from high proportions of lactobacilli to mixed species communities, as seen with bacterial vaginosis, have been linked to a twofold increased risk of PTB. Despite the increasing number of studies using next-generation sequencing technologies, primarily involving 16S rRNA-based approaches, to investigate the vaginal microbiota during pregnancy, no distinct microbial signature has been associated with PTB. Shotgun metagenomic sequencing offers a powerful tool to reveal community structures and their gene functions at a far greater resolution than amplicon sequencing. In this study, we employ shotgun metagenomic sequencing to compare the vaginal microbiota of women at high risk of preterm birth (n = 35) vs. a low-risk control group (n = 14). Although microbial diversity and richness did not differ between groups, there were significant differences in terms of individual species. In particular, Lactobacillus crispatus was associated with samples from a full-term pregnancy, whereas one community state-type was associated with samples from preterm pregnancies. Furthermore, by predicting gene functions, the functional potential of the preterm microbiota was different from that of full-term equivalent. Taken together, we observed a discrete structural and functional difference in the microbial composition of the vagina in women who deliver preterm. Importance: with an estimated 15 million cases annually, spontaneous preterm birth (PTB) is the leading cause of death in infants under the age of five years. The ability to accurately identify pregnancies at risk of spontaneous PTB is therefore of utmost importance. However, no single cause is attributable. Microbial infection is a known risk factor, yet the role of vaginal microbes is poorly understood. Using high-resolution DNA-sequencing techniques, we investigate the microbial communities present in the vaginal tracts of women deemed high risk for PTB. We confirm that Lactobacillus crispatus is strongly linked to full-term pregnancies, whereas other microbial communities associate with PTB. Importantly, we show that the specific functions of the microbes present in PTB samples differs from FTB samples, highlighting the power of our sequencing approach. This information enables us to begin understanding the specific microbial traits that may be influencing PTB, beyond the presence or absence of microbial taxa.

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