Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy

Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison; Thomas, Brian C.; Hess, Matthias; Tringe, Susannah G.; Banfield, Jillian F.

doi:10.1101/107789

Cited by 40 publications

(19 citation statements)

References 38 publications

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“…An in-house pipeline (Let-it-bin, https://github.com/QuentinLetourneur/Let-it-bin) was used for read trimming, assembly, and contig binning. Two of the MAGs were refined using DAS_Tool64. Completeness and contamination of the assembled MAGs were estimated with CheckM65.…”

Section: Methodsmentioning

confidence: 99%

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

et al. 2019

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Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane oxidizing archaea. Five of these MAGs represent under-sampled (e.g., Verstraetearchaeota, Methanonatronarchaeia, ANME-1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation significantly expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘ Ca . Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

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Section: Methodsmentioning

confidence: 99%

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

et al. 2019

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“…DASTool (version 1.1.0) [75] was applied to each set of binned contigs to create medium to high quality MAGs. This tool takes several different MAGs as input and identifies a consensus, non-redundant genome for each MAG, leading to higher quality genomes.…”

Section: Taxonomic Binning Of Contigs Into Metagenome Assembled Genommentioning

confidence: 99%

Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment

Buongiorno

Sipes²,

Wasmund³

et al. 2020

PLoS ONE

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Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79˚N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.

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“…The contigs from the JGI assembled data were binned using ESOM 33 , MetaBAT 34 and CONCOCT 35 and resulting bins were combined using DAS Tool (version 1.0) 36 (See Supplementary Methods). CheckM lineage_wf (v1.0.5) was run on bins generated from DAS_Tool and 577 bins showed an completeness > 50% and were characterized further 37 .…”

Section: Methodsmentioning

confidence: 99%

New Asgard archaea capable of anaerobic hydrocarbon cycling

Seitz

Dombrowski

Eme

et al. 2019

Preprint

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Large reservoirs of natural gas in the oceanic subsurface sustain a complex biosphere of 10 anaerobic microbes, including recently characterized archaeal lineages that extend the 11 potential to mediate hydrocarbon oxidation (methane and butane) beyond the 12 Methanomicrobia. Here we describe a new archaeal phylum, Helarchaeota, belonging to the 13 Asgard superphylum with the potential for hydrocarbon oxidation. We reconstructed 14Helarchaeota genomes from hydrothermal deep-sea sediment metagenomes in hydrocarbon-15 rich Guaymas Basin, and show that these encode novel methyl-CoM reductase-like enzymes 16 that are similar to those found in butane-oxidizing archaea. Based on these results as well as 17 the presence of several alkyl-CoA oxidation and Wood-Ljungdahl pathway genes in the 18 Helarchaeota genomes, we suggest that members of the Helarchaeota have the potential to 19 activate and subsequently anaerobically oxidize short-chain hydrocarbons. These findings link 20 a new phylum of Asgard archaea to the microbial utilization of hydrothermally generated 21 hydrocarbons, and extend this genomic blueprint further through the archaeal domain. 22 23 24 Short-chain alkanes, such as methane and butane, are abundant in marine sediments and play 25 an important role in carbon cycling with methane concentrations of ~1 Gt being processed 26 globally through anoxic microbial communities 1-3 . Until recently, archaeal methane cycling was 27 thought to be limited to Euryarchaeota 4 . However, additional archaeal phyla, including 28 Bathyarchaeota 5 and Verstraetarchaeota 6 , have been shown to contain proteins with homology 29 to the activating enzyme methyl-coenzyme M reductase (Mcr) and corresponding pathways for 30 methane utilization. Furthermore, new lineages within the Euryarchaeota belonging to 31 Candidatus Syntrophoarchaeum spp., have been shown to use methyl-CoM reductase-like 32 enzymes for anaerobic butane oxidation 7 . Similar to methane oxidation in many ANME-1 archaea, 33 butane oxidation in Syntrophoarchaeum is proposed to be enabled through a syntrophic 34 interaction with sulfur reducing bacteria 7 . Metagenomic reconstructions of genomes recovered 35 from deep-sea sediments from near 2000 m depth in Guaymas Basin (GB) in the Gulf of California 36 have revealed the presence of additional uncharacterized alkyl methyl-CoM reductase-like 37 enzymes in metagenome-assembled genomes within the Methanosarcinales (Gom-Arc1) 8 . GB is 38characterized by hydrothermal alterations that transform large amounts of organic carbon into 39 methane, polycyclic aromatic hydrocarbons (PAHs), low-molecular weight alkanes and organic 40 acids allowing for diverse microbial communities to thrive ( Supplementary Table 1) 8-11 . 41 Recently, genomes of novel clade of uncultured archaea, referred to as the Asgard 42 superphylum that includes the closest archaeal relatives of eukaryotes, have been recovered 43 from anoxic environments around the world [12][13][14] . Diversity surveys in anoxic marine sediments 44show that Asgar...

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Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy

Cited by 40 publications

References 38 publications

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment

New Asgard archaea capable of anaerobic hydrocarbon cycling

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