Data_Sheet_1_Bacterial community of sediments under the Eastern Boundary Current System shows high microdiversity and a latitudinal spatial pattern.PDF

The sediments under the Oxygen Minimum Zone of the Eastern Boundary Current System (EBCS) along Central-South Peru and North-Central Chile, known as Humboldt Sulfuretum (HS), is an organic-matter-rich benthic habitat, where bacteria process a variety of sulfur compounds under low dissolved-oxygen concentrations, and high sulfide and nitrate levels. This study addressed the structure, diversity and spatial distribution patterns of the HS bacterial community along Northern and South-Central Chile using 16S rRNA gene amplicon sequencing. The results show that during the field study period, the community was dominated by sulfur-associated bacteria. Indeed, the most abundant phylum was Desulfobacterota, while Sva0081 sedimentary group, of the family Desulfosarcinaceae (the most abundant family), which includes sulfate-reducer and H2 scavenger bacteria, was the most abundant genus. Furthermore, a spatial pattern was unveiled along the study area to which the family Desulfobulbaceae contributed the most to the spatial variance, which encompasses 42 uncharacterized amplicon sequence variants (ASVs), three assigned to Ca. Electrothrix and two to Desulfobulbus. Moreover, a very high microdiversity was found, since only 3.7% of the ASVs were shared among localities, reflecting a highly diverse and mature community.</p

Phylogenetic tree based on 16S rRNA gene sequences.

<p>Blue rectangle depicts the clade for “<i>Ca</i>. V. ishoeyi”. In bold is shown the position for “<i>Ca</i>. V. ishoeyi” into the clade, and the numbers next to the nodes indicates the <i>a posteriori</i> probability in percentage of 0 to 1. The tree was calculated using Bayesian approach with MrBayes tool.</p

Dissimilatory nitrate reduction, ammonification, and sulfur oxidation.

<p>Predicted proteins identified in the draft genome of “<i>Ca</i>. V. ishoeyi” are shown in green, identification of close homologue proteins are shown in grey, and proteins identified in other related taxa, but not in “<i>Ca</i>. V. ishoeyi”, are shown in red.</p

Microphotograph of the MDA1 macrobacteria filament which was later isolated and its whole genome amplified.

<p>Isolations were done using microcapillaries approximately 10 μm in diameter <b>(</b>Photo CE).</p

Circular representation of the draft genome of “<i>Ca</i>. V. ishoeyi”.

<p>Moving out from the innermost circle: the black circle describes the GC% content in a window = 1000 bp; the green circle represents the CDSs of the antisense DNA strand, and the red circle the CDSs of the sense DNA strand; the outermost circle shows all scaffolds, each one alternating between blue and black.</p

Genomic features of <i>“Candidatus</i> Venteria ishoeyi”, a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

<div><p>The Humboldt Sulfuretum (HS), in the productive Humboldt Eastern Boundary Current Upwelling Ecosystem, extends under the hypoxic waters of the Peru-Chile Undercurrent (<i>ca</i>. 6°S and <i>ca</i>. 36°S). Studies show that primeval sulfuretums held diverse prokaryotic life, and, while rare today, still sustain species-rich giant sulfur-oxidizing bacterial communities. We here present the genomic features of a new bacteria of the HS, “<i>Candidatus</i> Venteria ishoeyi” (“<i>Ca</i>. V. ishoeyi”) in the family <i>Thiotrichaceae</i>.Three identical filaments were micro-manipulated from reduced sediments collected off central Chile; their DNA was extracted, amplified, and sequenced by a Roche 454 GS FLX platform. Using three sequenced libraries and through <i>de novo</i> genome assembly, a draft genome of 5.7 Mbp, 495 scaffolds, and a N50 of 70 kbp, was obtained. The 16S rRNA gene phylogenetic analysis showed that “<i>Ca</i>. V. ishoeyi” is related to non-vacuolate forms presently known as <i>Beggiatoa</i> or <i>Beggiatoa</i>-like forms. The complete set of genes involved in respiratory nitrate-reduction to dinitrogen was identified in “<i>Ca</i>. V. ishoeyi”; including genes likely leading to ammonification. As expected, the sulfur-oxidation pathway reported for other sulfur-oxidizing bacteria were deduced and also, key inorganic and organic carbon acquisition related genes were identified. Unexpectedly, the genome of “<i>Ca</i>. V. ishoeyi” contained numerous CRISPR repeats and an I-F CRISPR-Cas type system gene coding array. Findings further show that, as a member of an eons-old marine ecosystem, “<i>Ca</i>. V. ishoeyi” contains the needed metabolic plasticity for life in an increasingly oxygenated and variable ocean.</p></div

Schematic representation of the dissimilatory sulfite reductase (DSR) system, identified in “<i>Ca</i> V. ishoeyi”.

<p>In yellow: <i>dsrAB</i> genes coding for sulfite reductases: in pink: <i>dsrEFH</i> genes, coding for heterohexameric protein; in black: the <i>dsrC</i> gene, coding for sulfurtransferase; in red: <i>dsrMKJOP</i> genes, coding for transmembrane electron-transporting complex; and, in blue: the <i>dsrL</i> gene, coding for intracellular sulfur oxidation protein, are shown. F1, F2, and F3 represent the frame arrangement in the sense strand DNA.</p

Main genomic features among some representative sulfur-oxidizing bacteria and the draft genome of “<i>Ca</i>. V. ishoeyi”.

<p>Main genomic features among some representative sulfur-oxidizing bacteria and the draft genome of “<i>Ca</i>. V. ishoeyi”.</p

Biosynthetic gene clusters, identified as terpene and undetermined type in “<i>Ca</i>. V. ishoeyi”.

<p><b>A. Terpene gene cluster.</b> Sphere indicates the Phytoene synthase (phythoen_synt) domain. <b>B</b>. <b>Undetermined biosynthetic gene cluster.</b> Spheres show the Acyltransferase (AT), involved in biosynthesis of Polyketide synthase (PKS) compounds, Aminotransferase (Amino), involved in biosynthesis of Polyketide synthase/nonribosomal peptide synthetases (PKS/NRPS) compounds, Adenylation (A) and Carrier Protein (CP; Thiolation) domains, from undetermined compounds (Other). Asterisks indicate domains used as a rule for gene cluster classification. Identified genes are indicated in the backbone of the gene clusters and the product list is available in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188371#pone.0188371.s007" target="_blank">S5A and S5B Table</a>.</p

Comau metagenomic reads, taxonomy annotation

Taxonomic annotation of the sequence reads obtained from a microbial mat in the Comau Fjord, Chile. The reads were classified using MG-TAXA