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Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

He S, Malfatti SA, McFarland JW, Anderson FE, Pati A, Huntemann M, Tremblay J, Glavina del Rio T, Waldrop MP, Windham-Myers L, Tringe SG - MBio (2015)

Bottom Line: Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches.We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem.These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.

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Diversity of mcrA genes and abundance of methanogens. (a) Phylogenetic tree of mcrA, including all sequences recovered from metagenome assemblies with lengths of >150 amino acids. Wetland sequences are labeled with colors indicative of different sample sites, and their fold coverage in metagenomes is indicated in the parentheses. The accession numbers of reference sequences are in brackets. (b) Relative abundance of methanogens in the total community estimated by mcr genes.
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fig5: Diversity of mcrA genes and abundance of methanogens. (a) Phylogenetic tree of mcrA, including all sequences recovered from metagenome assemblies with lengths of >150 amino acids. Wetland sequences are labeled with colors indicative of different sample sites, and their fold coverage in metagenomes is indicated in the parentheses. The accession numbers of reference sequences are in brackets. (b) Relative abundance of methanogens in the total community estimated by mcr genes.

Mentions: The genes encoding methyl coenzyme M reductase (MCR), which catalyzes the terminal step in methanogenesis, are functional markers of methanogenesis, and the gene for its subunit A, mcrA, is often used as a methanogen phylogenetic marker. We performed phylogenetic analysis using metagenome mcrA sequences from the assembled part, presumably derived from abundant methanogen populations in this wetland (Fig. 5a). All analyzed metagenome mcrA sequences were affiliated with Methanomicrobiales, Methanobacteriales, and Methanosarcinales, spanning three out of the six major orders of known methanogens. The Methanoregulaceae family within Methanomicrobiales harbors more than half of metagenome mcrA sequences, some of which have high coverage (e.g., >50×). Particularly, an mcrA gene closely affiliated with Methanoregula boonei 6A8 has a very high coverage (i.e., 186×), which allowed the recovery of a near-complete genome of the methanogen containing it (data not shown). This genome has only the hydrogenotrophic methanogenesis pathway and lacks the methylotrophic pathway and the hdrDE genes needed for growing on acetate, confirming it as a hydrogenotrophic specialist. As members of Methanomicrobiales and Methanobacteriales are mostly hydrogenotrophic (23–25), their abundant presence suggests the importance of hydrogenotrophic methanogenesis in this wetland.


Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

He S, Malfatti SA, McFarland JW, Anderson FE, Pati A, Huntemann M, Tremblay J, Glavina del Rio T, Waldrop MP, Windham-Myers L, Tringe SG - MBio (2015)

Diversity of mcrA genes and abundance of methanogens. (a) Phylogenetic tree of mcrA, including all sequences recovered from metagenome assemblies with lengths of >150 amino acids. Wetland sequences are labeled with colors indicative of different sample sites, and their fold coverage in metagenomes is indicated in the parentheses. The accession numbers of reference sequences are in brackets. (b) Relative abundance of methanogens in the total community estimated by mcr genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4442139&req=5

fig5: Diversity of mcrA genes and abundance of methanogens. (a) Phylogenetic tree of mcrA, including all sequences recovered from metagenome assemblies with lengths of >150 amino acids. Wetland sequences are labeled with colors indicative of different sample sites, and their fold coverage in metagenomes is indicated in the parentheses. The accession numbers of reference sequences are in brackets. (b) Relative abundance of methanogens in the total community estimated by mcr genes.
Mentions: The genes encoding methyl coenzyme M reductase (MCR), which catalyzes the terminal step in methanogenesis, are functional markers of methanogenesis, and the gene for its subunit A, mcrA, is often used as a methanogen phylogenetic marker. We performed phylogenetic analysis using metagenome mcrA sequences from the assembled part, presumably derived from abundant methanogen populations in this wetland (Fig. 5a). All analyzed metagenome mcrA sequences were affiliated with Methanomicrobiales, Methanobacteriales, and Methanosarcinales, spanning three out of the six major orders of known methanogens. The Methanoregulaceae family within Methanomicrobiales harbors more than half of metagenome mcrA sequences, some of which have high coverage (e.g., >50×). Particularly, an mcrA gene closely affiliated with Methanoregula boonei 6A8 has a very high coverage (i.e., 186×), which allowed the recovery of a near-complete genome of the methanogen containing it (data not shown). This genome has only the hydrogenotrophic methanogenesis pathway and lacks the methylotrophic pathway and the hdrDE genes needed for growing on acetate, confirming it as a hydrogenotrophic specialist. As members of Methanomicrobiales and Methanobacteriales are mostly hydrogenotrophic (23–25), their abundant presence suggests the importance of hydrogenotrophic methanogenesis in this wetland.

Bottom Line: Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches.We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem.These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.

Show MeSH