Bacteria of the Humboldt sulfuretum comply with unifying macroecological principles

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 IF 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.

Local and global chemical shaping of bacterial communities by redox potential

“…The 15 field-based studies of sediments are approximately evenly divided between those with positive and negative correlations. The datasets with positive correlations include some for marine (Jorgensen et al, 2012;Gallardo et al, 2016), coastal/estuarine (Lanzén et al, 2021) (Fig. 4), freshwater (Han et al, 2019;Cai et al, 2019;Zhang et al, 2021b), and hypersaline (Boyd et al, 2017) sediments.…”

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

“…6°S) and central Chile ( ca . 36°S), the Humboldt Sulfuretum (HS), a sulfur compound- and macro-, megabacteria-rich biotope has been described [ 1 – 5 ]. Of varying morphology, the diameter of the filamentous macrobacteria typically range from ca.…”

“…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 ]. Paleontological, geological, and geochemical evidence from this habitat and its biota have been reported from the Archaean and Proterozoic Eons [ 8 – 10 ], and from late Miocene (Tertiary), Italian mudstone beds [ 11 ].…”

“…We here present the new filamentous sulfur-oxidizing bacteria “ Candidatus Venteria ishoeyi” (“ Ca . V. ishoeyi”), member of the highly diversified microbial community from the HS [ 5 ].…”

Substratum‐Associated Microbiota

“…Microbiologistshave long argued about the structuring mechanisms for microbial communities Gallardo et al (2016). examined benthic bacteria, and found high levels of species richness.Their data suggest that old bacterial communities, such as the ones from the Humboldt Sulfuretum, comply with macroecologically-derived principles Danovaro, Molari et al (2016).…”