1
|
Dong Y, Sanford RA, Connor L, Chee-Sanford J, Wimmer BT, Iranmanesh A, Shi L, Krapac IG, Locke RA, Shao H. Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL. WATER RESEARCH 2021; 202:117431. [PMID: 34320445 DOI: 10.1016/j.watres.2021.117431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput FluidigmTM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.
Collapse
Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, USA
| | | | | | | | | | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | | | | | | |
Collapse
|
2
|
Dong Y, Sanford RA, Boyanov MI, Flynn TM, O'Loughlin EJ, Kemner KM, George S, Fouke KE, Li S, Huang D, Li S, Fouke BW. Controls on Iron Reduction and Biomineralization over Broad Environmental Conditions as Suggested by the Firmicutes Orenia metallireducens Strain Z6. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10128-10140. [PMID: 32693580 DOI: 10.1021/acs.est.0c03853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial iron reduction is a ubiquitous biogeochemical process driven by diverse microorganisms in a variety of environments. However, it is often difficult to separate the biological from the geochemical controls on bioreduction of Fe(III) oxides. Here, we investigated the primary driving factor(s) that mediate secondary iron mineral formation over a broad range of environmental conditions using a single dissimilatory iron reducer, Orenia metallireducens strain Z6. A total of 17 distinct geochemical conditions were tested with differing pH (6.5-8.5), temperature (22-50 °C), salinity (2-20% NaCl), anions (phosphate and sulfate), electron shuttle (anthraquinone-2,6-disulfonate), and Fe(III) oxide mineralogy (ferrihydrite, lepidocrocite, goethite, hematite, and magnetite). The observed rates and extent of iron reduction differed significantly with kint between 0.186 and 1.702 mmol L-1 day-1 and Fe(II) production ranging from 6.3% to 83.7% of the initial Fe(III). Using X-ray absorption and scattering techniques (EXAFS and XRD), we identified and assessed the relationship between secondary minerals and the specific environmental conditions. It was inferred that the observed bifurcation of the mineralization pathways may be mediated by differing extents of Fe(II) sorption on the remaining Fe(III) minerals. These results expand our understanding of the controls on biomineralization during microbial iron reduction and aid the development of practical applications.
Collapse
Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Maxim I Boyanov
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Samantha George
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kaitlyn E Fouke
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543, United States
| | - Shuyi Li
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
| | - Dongmei Huang
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
| | - Shuzhen Li
- School of Environmental Studies, China University of Geosciences (Wuhan), Hubei, 430074, China
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
3
|
Casar CP, Kruger BR, Flynn TM, Masterson AL, Momper LM, Osburn MR. Mineral-hosted biofilm communities in the continental deep subsurface, Deep Mine Microbial Observatory, SD, USA. GEOBIOLOGY 2020; 18:508-522. [PMID: 32216092 DOI: 10.1111/gbi.12391] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/29/2020] [Accepted: 02/27/2020] [Indexed: 06/10/2023]
Abstract
Deep subsurface biofilms are estimated to host the majority of prokaryotic life on Earth, yet fundamental aspects of their ecology remain unknown. An inherent difficulty in studying subsurface biofilms is that of sample acquisition. While samples from marine and terrestrial deep subsurface fluids have revealed abundant and diverse microbial life, limited work has described the corresponding biofilms on rock fracture and pore space surfaces. The recently established Deep Mine Microbial Observatory (DeMMO) is a long-term monitoring network at which we can explore the ecological role of biofilms in fluid-filled fractures to depths of 1.5 km. We carried out in situ cultivation experiments with single minerals representative of DeMMO host rock to explore the ecological drivers of biodiversity and biomass in biofilm communities in the continental subsurface. Coupling cell densities to thermodynamic models of putative metabolic reactions with minerals suggests a metabolic relationship between biofilms and the minerals they colonize. Our findings indicate that minerals can significantly enhance biofilm cell densities and promote selective colonization by taxa putatively capable of extracellular electron transfer. In turn, minerals can drive significant differences in biodiversity between fluid and biofilm communities. Given our findings at DeMMO, we suggest that host rock mineralogy is an important ecological driver in deep continental biospheres.
Collapse
Affiliation(s)
- Caitlin P Casar
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - Brittany R Kruger
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Andrew L Masterson
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - Lily M Momper
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - Magdalena R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| |
Collapse
|
4
|
Escudero C, Oggerin M, Amils R. The deep continental subsurface: the dark biosphere. Int Microbiol 2018; 21:3-14. [DOI: 10.1007/s10123-018-0009-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 11/28/2022]
|
5
|
Dong Y, Sanford RA, Chang YJ, McInerney MJ, Fouke BW. Hematite Reduction Buffers Acid Generation and Enhances Nutrient Uptake by a Fermentative Iron Reducing Bacterium, Orenia metallireducens Strain Z6. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:232-242. [PMID: 27943672 DOI: 10.1021/acs.est.6b04126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fermentative iron-reducing organisms have been identified in a variety of environments. Instead of coupling iron reduction to respiration, they have been consistently observed to use ferric iron minerals as an electron sink for fermentation. In the present study, a fermentative iron reducer, Orenia metallireducens strain Z6, was shown to use iron reduction to enhance fermentation not only by consuming electron equivalents, but also by generating alkalinity that effectively buffers the pH. Fermentation of glucose by this organism in the presence of a ferric oxide mineral, hematite (Fe2O3), resulted in enhanced glucose decomposition compared with fermentation in the absence of an iron source. Parallel evidence (i.e., genomic reconstruction, metabolomics, thermodynamic analyses, and calculation of electron transfer) suggested hematite reduction as a proton-consuming reaction effectively consumed acid produced by fermentation. The buffering effect of hematite was further supported by a greater extent of glucose utilization by strain Z6 in media with increasing buffer capacity. Such maintenance of a stable pH through hematite reduction for enhanced glucose fermentation complements the thermodynamic interpretation of interactions between microbial iron reduction and other biogeochemical processes. This newly discovered feature of iron reducer metabolism also has significant implications for groundwater management and contaminant remediation by providing microbially mediated buffering systems for the associated microbial and/or chemical reactions.
Collapse
Affiliation(s)
| | | | | | - Michael J McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | | |
Collapse
|
6
|
Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface. Appl Environ Microbiol 2016; 82:6440-6453. [PMID: 27565620 DOI: 10.1128/aem.02382-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 12/11/2022] Open
Abstract
A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.
Collapse
|
7
|
Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O’Loughlin EJ, Locke RA, Weber JR, Egan SM, Fouke BW. Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater. Int J Syst Evol Microbiol 2016; 66:3964-3971. [DOI: 10.1099/ijsem.0.001295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yiran Dong
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Robert A. Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Maxim I. Boyanov
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | | | - Randall A. Locke
- Illinois State Geology Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joseph R. Weber
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Sheila M. Egan
- Department of Biochemistry, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Bruce W. Fouke
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Illinois State Geology Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
| |
Collapse
|
8
|
Draft Genome Sequence of Tepidibacillus decaturensis Strain Z9, an Anaerobic, Moderately Thermophilic, and Heterotrophic Bacterium from the Deep Subsurface of the Illinois Basin, USA. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00190-16. [PMID: 27056217 PMCID: PMC4824250 DOI: 10.1128/genomea.00190-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genome of the moderately thermophilic and halotolerant bacterium Tepidibacillus decaturensis strain Z9 was sequenced. The draft genome comprises three scaffolds, for a total of 2.95 Mb. As the first sequenced genome within the genus Tepidibacillus, 2,895 protein-coding genes, 52 tRNA genes, and 3 rRNA operons were predicted.
Collapse
|
9
|
Kirk MF, Wilson BH, Marquart KA, Zeglin LH, Vinson DS, Flynn TM. Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA. Front Microbiol 2015; 6:1287. [PMID: 26635755 PMCID: PMC4649258 DOI: 10.3389/fmicb.2015.01287] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/03/2015] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4–1.1 m) coalbeds with marginal thermal maturities (0.5–0.7% Ro) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na–Cl type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L−1. Gas dryness values [C1/(C2 + C3)] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183‰. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales, an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.
Collapse
Affiliation(s)
- Matthew F Kirk
- Department of Geology, Kansas State University Manhattan KS, USA
| | - Brien H Wilson
- Department of Geology, Kansas State University Manhattan KS, USA
| | - Kyle A Marquart
- Department of Geology, Kansas State University Manhattan KS, USA
| | - Lydia H Zeglin
- Division of Biology, Kansas State University Manhattan, KS, USA
| | - David S Vinson
- Department of Geography and Earth Sciences, University of North Carolina at Charlotte Charlotte, NC, USA
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory Argonne, IL, USA
| |
Collapse
|