Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Luis E Valentin-Alvarado; Sirine C Fakra; Alexander J Probst; Jonathan R Giska; Alexander L Jaffe; Luke M Oltrogge; Jacob West-Roberts; Joel Rowland; Michael Manga; David F Savage; Chris Greening; Brett J Baker; Jillian F Banfield

doi:10.1186/s40168-023-01704-w

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Microbiome. 2024 Jan 26;12(1):15. doi: 10.1186/s40168-023-01704-w.

Authors

Luis E Valentin-Alvarado^{1

2}, Sirine C Fakra³, Alexander J Probst^{4

5}, Jonathan R Giska^{4

6}, Alexander L Jaffe¹, Luke M Oltrogge^{7

8}, Jacob West-Roberts⁹, Joel Rowland^{4

10}, Michael Manga^{4

11}, David F Savage^{2

7

8}, Chris Greening¹², Brett J Baker^{13

14}, Jillian F Banfield^{15

16

17

18

19}

Affiliations

¹ Graduate Group in Microbiology, University of California, Berkeley, CA, USA.
² Innovative Genomics Institute, University of California, Berkeley, CA, USA.
³ Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁴ Earth and Planetary Science, University of California, Berkeley, CA, USA.
⁵ Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry,, University of Duisburg-Essen, Essen, Essen, Germany.
⁶ Cleaner Air Oregon Program, Oregon Department of Environmental Quality, Portland, USA.
⁷ Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
⁸ Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA.
⁹ Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
¹⁰ Earth and Env. Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
¹¹ University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany.
¹² Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.
¹³ Department of Integrative Biology, University of Texas, Austin, USA.
¹⁴ Department of Marine Science, University of Texas, Austin, USA.
¹⁵ Innovative Genomics Institute, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
¹⁶ Earth and Planetary Science, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
¹⁷ Environmental Science, Policy and Management, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
¹⁸ Department of Marine Science, University of Texas, Austin, USA. jbanfield@berkeley.edu.
¹⁹ Energy Geoscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jbanfield@berkeley.edu.

Abstract

Background: Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.

Results: Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L_2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems.

Conclusions: Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.

Keywords: Candidate phyla radiation; Groundwater microbiome; Synchrotron-based spectromicroscopy.

Publication types

Video-Audio Media

MeSH terms

Bacteria / genetics
Bacteria / metabolism
Biofilms
Ecosystem*
Groundwater* / microbiology
Hydrogen / metabolism
Oxidation-Reduction
Phylogeny
Sulfides / metabolism
Sulfur / metabolism

Substances

Sulfides
Sulfur
Hydrogen

Abstract

Publication types

MeSH terms

Substances

Grants and funding