Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

Gies, Esther A.; Konwar, Kishori M.; Beatty, J. Thomas; Hallam, Steven J.

doi:10.1128/aem.01774-14

Cited by 97 publications

(116 citation statements)

References 62 publications

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“…PhylopythiaS, Metawatt and ESOM produced bins that were significantly larger than the methods based on homology alone (BLASTN and BLASTP), as would be expected for these more generalized, nucleotide frequency-based methods (Supplementary Figure S1). Similar results were obtained through binning of the Sakinaw Lake metagenome, although the bins were somewhat less distinct, possibly because of increased abundance and diversity of JS1 lineages present in this environment (Gies et al, 2014), including at least two prominent, distinct JS1 lineages in the monimolimnion based on previous 16S rRNA gene clone libraries (data not shown). After manual filtering based on contig coverage statistics, the PhylopythiaS bins were selected for further analysis because they were larger and had fewer duplicated SCMs than bins made by Metawatt and ESOM for the TA biofilm (Supplementary Figure S1) and the Sakinaw Lake metagenomes (data not shown).…”

Section: Resultssupporting

confidence: 69%

“…Caldatribacterium', 'Atribacteria' members from the JS1-1 and JS1-2 lineages found in Sakinaw Lake and the TA-degrading bioreactor ('Ca. Atricorium thermopropionicum'; Nobu et al, 2015b) lack such sugar fermentation pathways but appear to have the capacity to catabolize organic acids such as acetate (Gies et al, 2014) or propionate (Figure 4a). Previous studies have proposed that this lineage may oxidize acetate through syntrophy or sulfate reduction based on observation of WoodLjungdahl pathway genes and acetate uptake in marine enrichment cultures, respectively (Webster et al, 2011;Gies et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

“…Atricorium thermopropionicum'; Nobu et al, 2015b) lack such sugar fermentation pathways but appear to have the capacity to catabolize organic acids such as acetate (Gies et al, 2014) or propionate (Figure 4a). Previous studies have proposed that this lineage may oxidize acetate through syntrophy or sulfate reduction based on observation of WoodLjungdahl pathway genes and acetate uptake in marine enrichment cultures, respectively (Webster et al, 2011;Gies et al, 2014). In network analysis of Sakinaw Lake microbial communities, 'Atribacteria' co-occurred with H 2 -and formate-scavenging methanogens and putative propionate-metabolizing Cloacimonetes, also suggesting involvement in syntrophic degradation of propionate (Gies et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

“…Previous studies have proposed that this lineage may oxidize acetate through syntrophy or sulfate reduction based on observation of WoodLjungdahl pathway genes and acetate uptake in marine enrichment cultures, respectively (Webster et al, 2011;Gies et al, 2014). In network analysis of Sakinaw Lake microbial communities, 'Atribacteria' co-occurred with H 2 -and formate-scavenging methanogens and putative propionate-metabolizing Cloacimonetes, also suggesting involvement in syntrophic degradation of propionate (Gies et al, 2014). Further supporting a role in propionate catabolism, metatranscriptomics of the TA-degrading community revealed the expression of 'Ca.…”

Section: Resultsmentioning

confidence: 99%

“…It has been estimated that there may be ⩾ 100 candidate phyla in the domain Bacteria (Baker and Dick, 2013;Kantor et al, 2013;Yarza et al, 2014), significantly outnumbering phyla with cultivated representatives. Although candidate phyla are typically of low abundance, that is, part of the 'rare biosphere' (Sogin et al, 2006;Elshahed et al, 2008), they are prominent members of microbial communities in several different environments (Harris et al, 2004;Chouari et al, 2005;Vick et al, 2010;Peura et al, 2012;Cole et al, 2013;Farag et al, 2014;Gies et al, 2014;Parkes et al, 2014) and may have important ecological roles (Sekiguchi, 2006;Yamada et al, 2011). SAG sequencing and metagenomics have yielded partial, nearly-complete or complete genomes for close to 20 candidate bacterial phyla (Glöckner et al, 2010;Siegl et al, 2011;Youssef et al, 2011;Takami et al, 2012;Wrighton et al, 2012;Dodsworth et al, 2013;Kantor et al, 2013;McLean et al, 2013;Rinke et al, 2013;Kamke et al, 2014;Wrighton et al, 2014), as well as several major uncultivated lineages of Archaea (Elkins et al, 2008;Baker et al, 2010;Ghai et al, 2011;Nunoura et al, 2011;Narasingarao et al, 2012;Kozubal et al, 2013;Rinke et al, 2013;Youssef et al, 2015), opening a genomic window to a much better understanding of this so-called 'microbial dark matter' …”

Section: Introductionmentioning

confidence: 99%

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Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

et al. 2015

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The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species-to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.

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Section: Resultssupporting

confidence: 69%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

et al. 2015

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A Guide to Gene‐Centric Analysis Using TreeSAPP

Morgan-Lang

Hallam

2023

Current Protocols

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Gene-centric analysis is commonly used to chart the structure, function, and activity of microbial communities in natural and engineered environments. A common approach is to create custom ad hoc reference marker gene sets, but these come with the typical disadvantages of inaccuracy and limited utility beyond assigning query sequences taxonomic labels. The Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software package standardizes analysis of phylogenetic and functional marker genes and improves predictive performance using a classification algorithm that leverages information-rich reference packages consisting of a multiple sequence alignment, a profile hidden Markov model, taxonomic lineage information, and a phylogenetic tree. Here, we provide a set of protocols that link the various analysis modules in TreeSAPP into a coherent process that both informs and directs the user experience. This workflow, initiated from a collection of candidate reference sequences, progresses through construction and refinement of a reference package to marker identification and normalized relative abundance calculations for homologous sequences in metagenomic and metatranscriptomic datasets. The alpha subunit of methyl-coenzyme M reductase (McrA) involved in biological methane cycling is presented as a use case given its dual role as a phylogenetic and functional marker gene driving an ecologically relevant process. These protocols fill several gaps in prior TreeSAPP documentation and provide best practices for reference package construction and refinement, including manual curation steps from trusted sources in support of reproducible gene-centric analysis.

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Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

et al. 2017

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About half of the global methane (CH ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.

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Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

Cited by 97 publications

References 62 publications

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

A Guide to Gene‐Centric Analysis Using TreeSAPP

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

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