1
|
Voutsinos MY, West-Roberts JA, Sachdeva R, Moreau JW, Banfield JF. Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes. BMC Biol 2024; 22:41. [PMID: 38369453 PMCID: PMC10875860 DOI: 10.1186/s12915-024-01841-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. RESULTS Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. CONCLUSIONS Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.
Collapse
Affiliation(s)
- Marcos Y Voutsinos
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacob A West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Rohan Sachdeva
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Jillian F Banfield
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
2
|
Miller AZ, Jiménez-Morillo NT, Coutinho ML, Gazquez F, Palma V, Sauro F, Pereira MF, Rull F, Toulkeridis T, Caldeira AT, Forti P, Calaforra JM. Organic geochemistry and mineralogy suggest anthropogenic impact in speleothem chemistry from volcanic show caves of the Galapagos. iScience 2022; 25:104556. [PMID: 35789844 PMCID: PMC9250005 DOI: 10.1016/j.isci.2022.104556] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/09/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The network of lava tubes is one of the most unexploited natural wonders of the Galapagos Islands. Here, we provide the first morphological, mineralogical, and biogeochemical assessment of speleothems from volcanic caves of the Galapagos to understand their structure, composition, and origin, as well as to identify organic molecules preserved in speleothems. Mineralogical analyses revealed that moonmilk and coralloid speleothems from Bellavista and Royal Palm Caves were composed of calcite, opal-A, and minor amounts of clay minerals. Extracellular polymeric substances, fossilized bacteria, silica microspheres, and cell imprints on siliceous minerals evidenced microbe-mineral interactions and biologically-mediated silica precipitation. Alternating depositional layers between siliceous and carbonate minerals and the detection of biomarkers of surface vegetation and anthropogenic stressors indicated environmental and anthropogenic changes (agriculture, human waste, and cave visits) on these unique underground resources. Stable isotope analysis and Py-GC/MS were key to robustly identify biomarkers, allowing for implementation of future protection policies. Speleothems from lava tubes of Galapagos are archives of anthropogenic stressors Moonmilk and coralloids are composed of calcite, opal-A, and clay minerals Microbe-mineral interactions promote mineral dissolution and precipitation Biomarkers of surface vegetation and anthropogenic impacts detected by Py-GC/MS
Collapse
Affiliation(s)
- Ana Z. Miller
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Seville, Spain
- HERCULES Laboratory, University of Évora, Évora, Portugal
- Corresponding author
| | - Nicasio T. Jiménez-Morillo
- MED—Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Évora, Portugal
| | | | - Fernando Gazquez
- Department of Biology and Geology, University of Almería, Almería, Spain
- Andalusian Centre for the Monitoring and Assessment of Global Change (CAESCG), University of Almería, Almería, Spain
| | - Vera Palma
- HERCULES Laboratory, University of Évora, Évora, Portugal
| | - Francesco Sauro
- Department of Earth Sciences and Environmental Geology, University of Bologna, Bologna, Italy
| | | | - Fernando Rull
- CSIC-CAB Associated Unit ERICA, Department of Condensed Matter Physics, Mineralogy and Crystallography, University of Valladolid, Boecillo, Spain
| | | | | | - Paolo Forti
- Department of Earth Sciences and Environmental Geology, University of Bologna, Bologna, Italy
| | - José M. Calaforra
- Department of Biology and Geology, University of Almería, Almería, Spain
- Andalusian Centre for the Monitoring and Assessment of Global Change (CAESCG), University of Almería, Almería, Spain
| |
Collapse
|
3
|
Napieralski SA, Fang Y, Marcon V, Forsythe B, Brantley SL, Xu H, Roden EE. Microbial chemolithotrophic oxidation of pyrite in a subsurface shale weathering environment: Geologic considerations and potential mechanisms. GEOBIOLOGY 2022; 20:271-291. [PMID: 34633148 DOI: 10.1111/gbi.12474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.
Collapse
Affiliation(s)
| | - Yihang Fang
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Virginia Marcon
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brandon Forsythe
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
| | - Susan L Brantley
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Huifang Xu
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|