Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

Iverson, Vaughn; Morris, Robert M.; Frazar, Christian D.; Berthiaume, Chris T.; Morales, Rhonda; Armbrust, E. Virginia

doi:10.1126/science.1212665

Cited by 419 publications

(458 citation statements)

References 64 publications

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“…Little is known about the physiology or metabolism of the enigmatic MGII archaea (Euryarchaeota) despite their moderate abundance in both surface and deep marine waters (Pernthaler et al, 2002;DeLong et al, 2006;MartinCuadrado et al, 2008). The recent reconstruction of a MGII genome from surface seawater metagenomic data suggested a photo-heterotrophic lifestyle focused on degradation of protein and lipids (Iverson et al, 2012). The MGII OTUs that are enriched in GB plumes share only 86-87% 16S rRNA gene sequence identity with the population described by Iverson et al (2012), and we found no evidence for proteorhodopsin genes in our metagenomic or metatranscriptomic data sets, thus the GB MGII populations may be quite distinct from their surface water relatives.…”

Section: Discussioncontrasting

confidence: 37%

“…The recent reconstruction of a MGII genome from surface seawater metagenomic data suggested a photo-heterotrophic lifestyle focused on degradation of protein and lipids (Iverson et al, 2012). The MGII OTUs that are enriched in GB plumes share only 86-87% 16S rRNA gene sequence identity with the population described by Iverson et al (2012), and we found no evidence for proteorhodopsin genes in our metagenomic or metatranscriptomic data sets, thus the GB MGII populations may be quite distinct from their surface water relatives. However, if the heterotrophic characteristics of surface MGII groups do indeed extend to deep-sea MGII populations such as those in our data sets, the plume enhancement observed here may signal a heterotrophic response to enhanced primary production in the plume.…”

Section: Discussioncontrasting

confidence: 37%

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The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

et al. 2012

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Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3-4 times) and microbially mediated manganese oxidation rates (15-125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10-20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California.

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Section: Discussioncontrasting

confidence: 37%

Section: Discussioncontrasting

confidence: 37%

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

et al. 2012

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“…Reference sequences from each OTU were also compared with a marine 16S rRNA sequence custom database according to Biers et al, 2009 using Smith-Waterman pairwise alignments (Smith and Waterman, 1981) and requiring sequence overlaps of X80%. HTCC2255 sequences were identified based on an alignment with the full-length 16S rRNA sequence available in the HTCC2255 metagenomic assembly of Iverson et al, 2012 because only a partial sequence was assembled in the genome of the original HTCC2255 culture. If possible, sequences were assigned to species level taxa with X97% identity across the overlap.…”

Section: Dmsp-carbon Calculationsmentioning

confidence: 99%

Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

et al. 2015

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The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.

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“…This is in large part due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional sequencing (Amann et al 1995). While shotgun sequencing and assembly of environmental samples is possible, assembly into complete genomes is generally only feasible for simple microbial communities (Tyson et al 2004;Venter et al 2004;Hess et al 2011;Iverson et al 2012). Moreover, these assemblies are actually consensus genomes derived from closely related species or strains, which makes many interesting analyses of genomes and populations impossible.…”

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confidence: 99%

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

Fitzsimons

Novotny

et al. 2013

Genome Res.

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The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.

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Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

Cited by 419 publications

References 64 publications

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

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