Metabolic connectivity graph showing community distribution of protein family clusters.

<p>Cohesive populations are shown as similarly colored nodes and vectors according to numbers of shared features, based on unsupervised protein family clustering of 12 habitat-specific genomes.</p

Phylogenetic distribution of protein BLAST matches for assembled population genomes and unclassified scaffolds.

<p>Taxonomic distribution of non-self matches versus the Genbank nr database were calculated using the DarkHorse algorithm at a filter threshold setting of 0.05, including only alignments covering at least 70% of both query and target sequences with an e-value of 1e-5 or better.</p

Consensus population genome properties.

§<p>Marker gene detection details are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061692#pone.0061692.s006" target="_blank">Table S6</a>.</p>*<p>Parenthetical values indicate cases where locally elevated depth of coverage suggests that assembly software may have compressed multiple 16S gene copies into a single locus.</p

Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem

<div><p>Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative <i>de novo</i> assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.</p></div

Relative abundance of microbial population groups.

<p>Colors correspond to taxonmically related microbial populations, including both assembled genome sequences and non-genomic scaffolds containing less abundant variant sequences. Percentage calculations include total number of assembled nucleotides in reads associated with each group, normalized for the group's average genome size. Percentage of unclassified sequences was calculated using an estimated genome size of 3 MB, the approximate abundance-weighted average for all other groups. Known viral and plasmid sequences, representing approximately 0.2% of assembled nucleotides, have been excluded from these calculations.</p

Phylogenetic distribution of archaeal 16S rRNA gene sequences in assembled scaffolds and population genomes.

<p>Names in bold indicate new 16S rRNA sequences identified in this study. Boxed names indicate sequences contained within Lake Tyrrell-specific population genomes. Asterisks indicate isolated individual sequences found on small scaffolds that were not associated with any assembled population genome.</p

Length-weighted %G+C nucleotide composition of unassembled reads, assembled scaffolds, and composite population genomes.

<p>Genomes were constructed by targeted assembly of scaffolds with a uniform signature of phylogenetic binning properties, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061692#s2" target="_blank">Materials and Methods</a>. Genome names, percent G+C, and other general properties of assembled genomes are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061692#pone-0061692-t001" target="_blank">Table 1</a>.</p

Population-unique protein family clusters.

<p>Population-unique protein family clusters.</p

Vertically distinct microbial communities in the Mariana and Kermadec trenches

<div><p>Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under <i>in situ</i> hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the <i>Marinimicrobia</i>, <i>Rhodobacteraceae</i>, <i>Rhodospirilliceae</i>, and <i>Aquibacter</i>, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the <i>Gammaproteobacteria</i> whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.</p></div

Comau metagenomic reads, functional annotation

Functional annotation of the metagenomic sequences of a microbial mat from the Comau Fjord, Chile. The annotation was done using CAMERA, with the RAMMCAP pipelin