Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India

Shekhar Nagar; Chandni Talwar; Mikael Motelica-Heino; Hans-Hermann Richnow; Mallikarjun Shakarad; Rup Lal; Ram Krishan Negi

doi:10.3389/fmicb.2022.848010

Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India

Front Microbiol. 2022 Apr 13:13:848010. doi: 10.3389/fmicb.2022.848010. eCollection 2022.

Authors

Shekhar Nagar¹, Chandni Talwar¹, Mikael Motelica-Heino², Hans-Hermann Richnow³, Mallikarjun Shakarad⁴, Rup Lal⁵, Ram Krishan Negi¹

Affiliations

¹ Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India.
² UMR 7327, Centre National de la Recherche Scientifique, Institut des Sciences de la Terre D'Orleans (ISTO), Université d'Orleans-Brgm, Orleans, France.
³ Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
⁴ Evolutionary Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India.
⁵ NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute, New Delhi, India.

Abstract

Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.

Keywords: biogeochemical cycle; evolution; hot spring; metagenomics; sulfur spring.