scholarly journals Genome-reconstruction for eukaryotes from complex natural microbial communities

2017 ◽  
Author(s):  
Patrick T. West ◽  
Alexander J. Probst ◽  
Igor V. Grigoriev ◽  
Brian C. Thomas ◽  
Jillian F. Banfield
Keyword(s):  
Organic Carbon ◽  
Microbial Communities ◽  
Environmental Samples ◽  
Carbon Fixation ◽  
Sulfur Oxidation ◽  
Metabolic Potential ◽  
Microbial Eukaryotes ◽  
Sequence Identification ◽  
Ecosystem Studies ◽  
Almost All

AbstractMicrobial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a kmer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.

scholarly journals The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 248
Author(s):  
Changling Ding ◽  
Chao Wu ◽  
Congcong Guo ◽  
Jiang Gui ◽  
Yuqiu Wei ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Calvin Cycle ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Eastern Indian Ocean ◽  
Rrna Genes ◽  
Metabolic Potential

Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its metabolic function in the equatorial EIO. Our results show that Cyanobacterial Prochlorococcus made up the majority of the population. Interestingly, there were fewer contributions from clades SAR11 (Alphaproteobacteria) and SAR86 (Gammaproteobacteria) to microbial communities than contributions from Prochlorococcus. Based on functional gene analysis, functional genes rbcL, narB, and nasA were relatively abundant among the relevant genes. The abundance of Prochlorococcus implies its typically ecological adaptation in the local ecosystem. The microbial metabolic potential shows that in addition to the main carbon fixation pathway Calvin cycle, the rTCA cycle and the 3-HP/4-HB cycle have potential alternative carbon fixation contributions to local ecosystems. For the nitrogen cycle, the assimilatory nitrate and nitrite reduction pathway is potentially the crucial form of nitrogen utilization; unexpectedly, nitrogen fixation activity was relatively weak. This study extends our knowledge of the roles of microbes in energy and resource cycling in the EIO and provides a foundation for revealing profound biogeochemical processes driven by the microbial community in the ocean.

scholarly journals Metabolic Potential of Microbial Communities in the Hypersaline Sediments of the Bonneville Salt Flats

2021 ◽  
Author(s):  
Julia M McGonigle ◽  
Jeremiah A Bernau ◽  
Brenda B Bowen ◽  
William J Brazelton
Keyword(s):  
Microbial Communities ◽  
Metabolic Pathways ◽  
Carbon Fixation ◽  
Sulfide Oxidation ◽  
Anaerobic Respiration ◽  
Ecosystem Functions ◽  
Metabolic Potential ◽  
Shallow Subsurface ◽  
Microbial Ecosystems ◽  
Salt Flats

The Bonneville Salt Flats (BSF) appear to be entirely desolate when viewed from above, but in reality they host rich microbial communities just below the surface salt crust. In this study, we investigate the metabolic potential of the BSF microbial ecosystem. The predicted and measured metabolic activities provide new insights into the ecosystem functions of evaporite landscapes and are an important analog for potential subsurface microbial ecosystems on ancient and modern Mars. Hypersaline and evaporite systems have been investigated previously as astrobiological analogs for Mars and other salty celestial bodies. Still, these studies have generally focused on aquatic systems and cultivation-dependent approaches. Here, we present an ecosystem-level examination of metabolic pathways within the shallow subsurface of evaporites. We detected aerobic and anaerobic respiration as well as methanogenesis in BSF sediments. Metagenome-assembled genomes (MAGs) of diverse bacteria and archaea encoded a remarkable diversity of metabolic pathways, including those associated with carbon fixation, carbon monoxide oxidation, acetogenesis, methanogenesis, sulfide oxidation, denitrification, and nitrogen fixation. These results demonstrate the potential for multiple energy sources and metabolic pathways in BSF and highlight the possibility for vibrant microbial ecosystems in the shallow subsurface of evaporites.

scholarly journals Taxonomically and metabolically distinct microbial communities with depth and across a hillslope to riparian zone transect

2019 ◽  
Author(s):  
Adi Lavy ◽  
Paula B. Matheus Carnevali ◽  
Ray Keren ◽  
Markus Bill ◽  
Jiamin Wan ◽  
...  
Keyword(s):  
Stable Isotopes ◽  
Microbial Communities ◽  
Carbon Fixation ◽  
Riparian Zone ◽  
Genomic Variation ◽  
Metabolic Potential ◽  
Mancos Shale ◽  
East River ◽  
Species Overlap ◽  
Different Depths

SummaryWatersheds are important for supplying fresh water, the quality of which depends on complex interplay involving physical, chemical and biological processes. As water percolates through the soil and underlying weathering rock en route to the river corridor, microorganisms mediate key geochemical transformations, yet the distribution and functional capacities of subsurface microbial communities remain little understood. We have studied metabolic capacities of microbial communities along a meadow to floodplain hillslope transect within the East-River watershed, Colorado, using genome resolved metagenomics and carbon and hydrogen stable isotopes. Very limited strain/species overlap was found at different depths below the ground surface and at different distances along the hillslope, possibly due to restricted hydraulic connectivity after early stages of snowmelt. Functions such as carbon fixation and selenate reduction were prevalent at multiple sites, although the lineages of organisms responsible tend to be location-specific. Based on its abundance, sulfur is significantly more important for microbial metabolism at the floodplain compared to on the hillslope. Nitrification and methylamine oxidation are likely only occurring within the floodplain, with nitrification capacity in shallow soil, and methylamine oxidation in deeper unsaturated sediment. Biogenic methane was detected in deep surface samples, but methanogenic organisms were not identified.Originality-Significance StatementIn a previous study within a hillslope to riparian zone transect of a sub-alpine watershed, the community structure was explored using ribosomal protein S3 genes, and the metabolic potential was hypothesized based on the presence of metabolism related genes. However, tying specific strains and species to metabolic functioning was not discussed as resolved genomes were not available.In the current study, we use genome-resolved metagenomics along with carbon and hydrogen stable isotopes to explore the spatial distribution of biogeochemical processes. By linking taxonomy and function, using multiple functional genes indicative of full metabolic pathways, we detect heterogeneity in the distribution of metabolic potential and the organisms involved with depth and landscape position. Thus, we infer how microbiome genomic variation impacts biogeochemical cycling across the watershed.We found very limited strain/species overlap at different depths below the surface and along the hillslope, possibly due to the restricted site to site hydraulic connectivity, and show that communities are largely distinct in their metabolic capacities. Both proximity to the river and the underlying Mancos shale apparently control species distribution and metabolic potential.Functions such as carbon fixation and selenate reduction were prevalent at multiple sites, although the lineages of organisms responsible tend to be location-specific. Arsenate detoxification was found to be prevalent in the riparian zone whereas selenate reduction was detected within weathered Mancos shale. We conclude that important ecosystem functions are strongly associated with the riparian zone, some of which may have crucial implications as to water quality and human health.

scholarly journals Diversity and Metabolic Potential of Microbial Communities in a Serpentinite-Hosted Spring at the Tablelands

2021 ◽  
Author(s):  
Emily Dart ◽  
William J. Brazelton
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Hydrogen Oxidation ◽  
Sampling Technique ◽  
16S Rrna Gene Sequencing ◽  
Direct Access ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Rrna Gene Sequencing ◽  
Community Dissimilarity

The geochemical process of serpentinization releases energy and organic carbon: two of the basic requirements needed to support life. Sites of active serpentinization in the deep subsurface provide the intriguing possibility of a non-photosynthetically-supported biosphere. However, serpentinization also creates conditions, such as high pH and limited electron acceptors, which may limit microbial growth and diversity. Gaining an understanding of the identity and metabolic potential of microbes that thrive in these environments may provide insight as to whether serpentinization is sufficient to independently support life. Tablelands Ophiolite in Gros Morne National Park, Newfoundland, Canada is a continental site of serpentinization where serpentinite springs form surface pools. These pools provide easy sampling access to subsurface fluids and may allow for sampling of the subsurface microbial community. However, identification of members of the subsurface community in these pools is complicated by both surface contamination and contamination by organisms that inhabit the transition zone where hydrogen-rich subsurface fluids meet oxygen-rich surface fluids. This study was designed to distinguish among these potential sources of microorganisms by using a sampling technique that more effectively samples subsurface fluids. Community dissimilarity comparisons using environmental 16S rRNA gene sequencing indicate that the sampling design led to more direct access to subsurface fluids. These results are supported by metagenomic analyses that show metabolic pathways consistent with non-photosynthetic carbon fixation in the samples expected to represent subsurface fluids and that show hydrogen oxidation pathways in samples associated with the surface sources. These results provide a clearer picture of the diversity and metabolic potential of microbial communities potentially inhabiting subsurface, serpentinite-hosted habitats.

scholarly journals Analysis of Microbial Gene Transcripts in Environmental Samples†

2005 ◽  
Vol 71 (7) ◽  
pp. 4121-4126 ◽  
Author(s):  
Rachel S. Poretsky ◽  
Nasreen Bano ◽  
Alison Buchan ◽  
Gary LeCleir ◽  
Jutta Kleikemper ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Communities ◽  
Environmental Samples ◽  
Sulfur Oxidation ◽  
Subtractive Hybridization ◽  
Functional Genes ◽  
New Approach ◽  
Total Rna ◽  
Gene Transcripts ◽  
Taxonomic Groups

ABSTRACT We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which ∼80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly α- and γ-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.

Soil organic carbon and microbial communities respond to vineyard management

2015 ◽  
Vol 31 (4) ◽  
pp. 528-533 ◽  
Author(s):  
F. Zehetner ◽  
I. Djukic ◽  
R. Hofmann ◽  
L. Kühnen ◽  
G. Rampazzo-Todorovic ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Microbial Communities ◽  
Vineyard Management

scholarly journals Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Marie-Anne Cambon-Bonavita ◽  
Johanne Aubé ◽  
Valérie Cueff-Gauchard ◽  
Julie Reveillaud
Keyword(s):  
Hydrothermal Vents ◽  
Carbon Fixation ◽  
Iron Sulfide ◽  
Hydrogen Oxidation ◽  
Niche Partitioning ◽  
Sulfur Oxidation ◽  
Single Copy ◽  
Trophic Levels ◽  
Rimicaris Exoculata ◽  
Close Relatives

Abstract Background Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris–microbe associations. Results Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences. Conclusion These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents.

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals Soil organic carbon dynamics following afforestation in the Loess Plateau of China

2013 ◽  
Vol 10 (7) ◽  
pp. 11181-11211 ◽  
Author(s):  
N. Lu ◽  
J. Liski ◽  
R. Y. Chang ◽  
A. Akujärvi ◽  
X. Wu ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Loess Plateau ◽  
Carbon Fixation ◽  
Temporal Dynamics ◽  
Climatic Factors ◽  
Early Stage ◽  
Arable Land ◽  
The Loess Plateau ◽  
Successional Stage

Abstract. Soil organic carbon (SOC) is the largest terrestrial carbon pool and sensitive to land use and cover change; its dynamics is critical for carbon cycling in terrestrial ecosystems and the atmosphere. In this study, we combined a modeling approach and field measurements to examine the temporal dynamics of SOC following afforestation of former arable land at six sites under different climatic conditions in the Loess Plateau during 1980–2010. The results showed that the measured mean SOC increased to levels higher than before afforestation when taking the last measurements (i.e., at age 25 to 30 yr), although it decreased in the first few years at the wetter sites. The accumulation rates of SOC were 1.58 to 6.22% yr–1 in the upper 20 cm and 1.62 to 5.15% yr–1 in the upper 40 cm of soil. The simulations reproduced the basic characteristics of measured SOC dynamics, suggesting that litter input and climatic factors (temperature and precipitation) were the major causes for SOC dynamics and the differences among the sites. They explained 88–96, 48–86 and 57–74% of the variations in annual SOC changes at the soil depths of 0–20, 0–40, and 0–100 cm, respectively. Notably, the simulated SOC decreased during the first few years at all the sites, although the magnitudes of decreases were small at the drier sites. This suggested that the modeling may be advantageous in capturing SOC changes at finer time scale. The discrepancy between the simulation and measurement was a result of uncertainties in model structure, data input, and sampling design. Our findings indicated that afforestation promoted soil carbon sequestration at the study sites, which is favorable for further restoration of the vegetation and environment. Afforestation activities should decrease soil disturbances to reduce carbon release in the early stage. The long-term strategy for carbon fixation capability of the plantations should also consider the climate and site conditions, species adaptability, and successional stage of recovery.

scholarly journals The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

2015 ◽  
Vol 12 (21) ◽  
pp. 18103-18150 ◽  
Author(s):  
L. Purkamo ◽  
M. Bomberg ◽  
R. Kietäväinen ◽  
H. Salavirta ◽  
M. Nyyssönen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Keystone Species ◽  
Carbon Assimilation ◽  
Sugar Metabolism ◽  
Archaeal Community ◽  
Amino Sugar ◽  
Amplicon Sequencing ◽  
Fracture Zones ◽  
Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

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