Abstract
The Humboldt Sulfuretum (HS), in the productive Humboldt Eastern Boundary Current Upwelling Ecosystem, extends under the hypoxic waters of the Peru-Chile Undercurrent (ca. 6°S and ca. 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, “Candidatus Venteria ishoeyi” (“Ca. V. ishoeyi”) in the family Thiotrichaceae.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 de novo 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 “Ca. V. ishoeyi” is related to non-vacuolate forms presently known as Beggiatoa or Beggiatoa-like forms. The complete set of genes involved in respiratory nitrate-reduction to dinitrogen was identified in “Ca. 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 “Ca. 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, “Ca. V. ishoeyi” contains the needed metabolic plasticity for life in an increasingly oxygenated and variable ocean.
Highlights
The oxygen-deficient waters of the Peru-Chile Undercurrent, between central Peru and central Chile, the Humboldt Sulfuretum (HS), a sulfur compound- and macro, megabacteria-rich biotope has been described [1,2,3,4,5]
While the term sulfuretum stems from stagnant fresh-water systems [6], recent study suggest that this type of benthic habitat and its typical biological complements, i.e., a highly diverse community of big filamentous and spherical non-photosynthetic sulfur-oxidizing bacteria [5], and small Archaea, might have been the only or the dominant types of life in primeval ocean bottoms when free oxygen was lacking or scarce [5, 7]
Sediments were sampled from the 8.2 m R/L “Otilia” motor-whale boat with an in-house built mono-coring device equipped with a 1 m long, 5 cm in diameter sampling Plexiglas tube
Summary
The oxygen-deficient waters of the Peru-Chile Undercurrent, between central Peru (ca. 6 ̊S) and central Chile (ca. 36 ̊S), the Humboldt Sulfuretum (HS), a sulfur compound- and macro-, megabacteria-rich biotope has been described [1,2,3,4,5]. The megabacteria in turn, are defined as having a diameter greater than around 10 μm, most generally exhibiting a vacuolar system, and lengths that can reach several hundred to several thousands, and even millimeters This classification of large filamentous bacteria, while ecologically useful, probably reflects their adaptation and evolution to an ocean evolving from fully or mostly anoxic to fully or mostly oxic [2]. While the term sulfuretum stems from stagnant fresh-water systems [6], recent study suggest that this type of benthic habitat and its typical biological complements, i.e., a highly diverse community of big filamentous and spherical non-photosynthetic sulfur-oxidizing bacteria [5], and small Archaea, might have been the only or the dominant types of life in primeval ocean bottoms when free oxygen was lacking or scarce [5, 7]. The recently described early occupation of new substrate created by a submarine volcanic eruption, of the closely related Thiotrichaceae “Ca. Thiolava veneris”, could be interpreted as evidence of biotic linkages between present sulfur bacteria and primeval benthic ecosystems [13]
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