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Sun R, Li Q. Exogenous additive ferric sulfate regulates sulfur-oxidizing bacteria in cow manure composting to promote carbon fixation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:32212-32224. [PMID: 38649605 DOI: 10.1007/s11356-024-33417-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Enhancing carbon fixation in the composting process was of great significance in the era of massive generation of organic solid waste. In this study, the experimental results showed that the contents of dissolved organic matter (DOM) in the experimental group (CT) were 37.58% higher than those in the control group (CK). The CO2 emission peaked on day 5, and the value of CK was 1.34 times that of CT. Significant differences were observed between the contents of sulfur fractions in CT and CK. This phenomenon may be due to the suppression of sulfur-reducing gene expression in CT. On day 51 of composting, the abundance of sulfur-oxidizing bacteria (SOB) Rhodobacter (5.33%), Rhodovulum (14.76%), and Thioclava (23.83%) in CT was higher than that in CK. In summary, the composting fermentation regulated by Fe2(SO4)3 increased the sulfate content, enhanced the expression of sulfur-oxidizing genes and SOB, and ultimately promoted carbon sequestration during composting.
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Affiliation(s)
- Ru Sun
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
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2
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Song M, Warr O, Telling J, Sherwood Lollar B. Hydrogeological controls on microbial activity and habitability in the Precambrian continental crust. GEOBIOLOGY 2024; 22:e12592. [PMID: 38445449 DOI: 10.1111/gbi.12592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/21/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Earth's deep continental subsurface is a prime setting to study the limits of life's relationship with environmental conditions and habitability. In Precambrian crystalline rocks worldwide, deep ancient groundwaters in fracture networks are typically oligotrophic, highly saline, and locally inhabited by low-biomass communities in which chemolithotrophic microorganisms may dominate. Periodic opening of new fractures can lead to penetration of surface water and/or migration of fracture fluids, both of which may trigger changes in subsurface microbial composition and activity. These hydrogeological processes and their impacts on subsurface communities may play a significant role in global cycles of key elements in the crust. However, to date, considerable uncertainty remains on how subsurface microbial communities may respond to these changes in hydrogeochemical conditions. To address this uncertainty, the biogeochemistry of Thompson mine (Manitoba, Canada) was investigated. Compositional and isotopic analyses of fracture waters collected here at ~1 km below land surface revealed different extents of mixing between subsurface brine and (paleo)meteoric waters. To investigate the effects this mixing may have had on microbial communities, the Most Probable Number technique was applied to test community response for a total of 13 different metabolisms. The results showed that all fracture waters were dominated by viable heterotrophic microorganisms which can utilize organic materials associated with aerobic/facultative anaerobic processes, sulfate reduction, or fermentation. Where mixing between subsurface brines and (paleo)meteoric waters occurs, the communities demonstrate higher cell densities and increased viable functional potentials, compared to the most saline sample. This study therefore highlights the connection between hydrogeologic heterogeneity and the heterogeneity of subsurface ecosystems in the crystalline rocks, and suggests that hydrogeology can have a considerable impact on the scope and scale of subsurface microbial communities on Earth and potentially beyond.
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Affiliation(s)
- Min Song
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Oliver Warr
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Jon Telling
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
- Institut de Physique du Globe de Paris (IPGP), Université Paris Cité, Paris, France
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3
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Gusmão ACB, Peres FV, Paula FS, Pellizari VH, Kolm HE, Signori CN. Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean. Int Microbiol 2023; 26:1041-1051. [PMID: 37093322 DOI: 10.1007/s10123-023-00358-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.
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Affiliation(s)
- Ana Carolina Bercini Gusmão
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil.
| | - Francielli Vilela Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Hedda Elisabeth Kolm
- Department of Oceanography, Center for Marine Studies, Federal University of Paraná, Pontal do Paraná, Brazil
| | - Camila Negrão Signori
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
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4
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Lazar CS, Schwab VF, Ueberschaar N, Pohnert G, Trumbore S, Küsel K. Microbial degradation and assimilation of veratric acid in oxic and anoxic groundwaters. Front Microbiol 2023; 14:1252498. [PMID: 37901809 PMCID: PMC10602745 DOI: 10.3389/fmicb.2023.1252498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, University of Quebec at Montreal (UQAM), Montreal, QC, Canada
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Valérie F. Schwab
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Susan Trumbore
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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5
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Zhong S, Zhou S, Liu S, Wang J, Dang C, Chen Q, Hu J, Yang S, Deng C, Li W, Liu J, Borthwick AGL, Ni J. May microbial ecological baseline exist in continental groundwater? MICROBIOME 2023; 11:152. [PMID: 37468948 PMCID: PMC10355068 DOI: 10.1186/s40168-023-01572-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/13/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Microbes constitute almost the entire biological community in subsurface groundwater and play an important role in ecological evolution and global biogeochemical cycles. Ecological baseline as a fundamental reference with less human interference has been investigated in surface ecosystems such as soils, rivers, and ocean, but the existence of groundwater microbial ecological baseline (GMEB) is still an open question so far. RESULTS Based on high-throughput sequencing information derived from national monitoring of 733 newly constructed wells, we find that bacterial communities in pristine groundwater exhibit a significant lateral diversity gradient and gradually approach the topsoil microbial latitudinal diversity gradient with decreasing burial depth of phreatic water. Among 74 phyla dominated by Proteobacteria in groundwater, Patescibacteria act as keystone taxa that harmonize microbes in shallower aquifers and accelerate decline in bacterial diversity with increasing well-depth. Decreasing habitat niche breadth with increasing well-depth suggests a general change in the relationship among key microbes from closer cooperation in shallow to stronger competition in deep groundwater. Unlike surface-water microbes, microbial communities in pristine groundwater are predominantly shaped by deterministic processes, potentially associated with nutrient sequestration under dark and anoxic environments in aquifers. CONCLUSIONS By unveiling the biogeographic patterns and mechanisms controlling the community assembly of microbes in pristine groundwater throughout China, we firstly confirm the existence of GMEB in shallower aquifers and propose Groundwater Microbial Community Index (GMCI) to evaluate anthropogenic impact, which highlights the importance of GMEB in groundwater water security and health diagnosis. Video Abstract.
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Affiliation(s)
- Sining Zhong
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shungui Zhou
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chenyuan Dang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Jinyun Hu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chunfang Deng
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Wenpeng Li
- Center for Groundwater Monitoring, China Institute of Geo-environmental Monitoring, Beijing, 100081, People's Republic of China
| | - Juan Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Alistair G L Borthwick
- School of Engineering, Computing and Mathematics, University of Plymouth, Drake Circus, Plymouth, PL8 4AA, UK
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China.
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China.
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6
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Lopez-Fernandez M, Westmeijer G, Turner S, Broman E, Ståhle M, Bertilsson S, Dopson M. Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield. NPJ Biofilms Microbiomes 2023; 9:41. [PMID: 37349512 DOI: 10.1038/s41522-023-00408-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was designed to investigate biofilm formation under in situ conditions in two groundwaters of contrasting age and geochemistry at the Äspö Hard Rock Laboratory, Sweden. Metatranscriptomes showed Thiobacillus, Sideroxydans, and Desulforegula to be abundant and together accounted for 31% of the transcripts in the biofilm communities. Differential expression analysis highlighted Thiobacillus to have a principal role in biofilm formation in these oligotrophic groundwaters by being involved in relevant processes such as the formation of extracellular matrix, quorum sensing, and cell motility. The findings revealed an active biofilm community with sulfur cycling as a prominent mode of energy conservation in the deep biosphere.
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Affiliation(s)
- Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden.
- Department of Microbiology, Faculty of Sciences, University of Granada, Avenida Fuentenueva s/n, 18071, Granada, Spain.
| | - George Westmeijer
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden
| | - Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20 A, 106 91, Stockholm, Sweden
| | - Magnus Ståhle
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Box 7050, SE75007, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 392 31, Kalmar, Sweden
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7
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Kim HS, Park K, Jo HY, Kwon MJ. Weathering extents and anthropogenic influences shape the soil bacterial community along a subsurface zonation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162570. [PMID: 36889395 DOI: 10.1016/j.scitotenv.2023.162570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Subsurface environments are composed of various active soil layers with dynamic biogeochemical interactions. We investigated soil bacterial community composition and geochemical properties along a vertical soil profile, which was categorized into surface, unsaturated, groundwater fluctuated, and saturated zones, in a testbed site formerly used as farmland for several decades. We hypothesized that weathering extent and anthropogenic inputs influence changes in the community structure and assembly processes and have distinct contributions along the subsurface zonation. Elemental distribution in each zone was strongly affected by the extent of chemical weathering. A 16S rRNA gene analysis indicated that bacterial richness (alpha diversity) was highest in the surface zone, and also higher in the fluctuated zone, than in unsaturated and saturated zones due to the effects of high organic matter, high nutrient levels, and/or aerobic conditions. Redundancy analysis showed that major elements (P, Na), a trace element (Pb), NO3, and the weathering extent were key driving forces shaping bacterial community composition along the subsurface zonation. Assembly processes were governed by specific ecological niches, such as homogeneous selection, in the unsaturated, fluctuated, and saturated zones, while in the surface zone, they were dominated by dispersal limitation. These findings together suggest that the vertical variation in soil bacterial community assembly is zone-specific and shaped by the relative influences of deterministic vs. stochastic processes. Our results provide novel insights into the relationships between bacterial communities, environmental factors, and anthropogenic influences (e.g., fertilization, groundwater, soil contamination), and into the roles of specific ecological niches and subsurface biogeochemical processes in these relationships.
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Affiliation(s)
- Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Kanghyun Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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8
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Yue XL, Xu L, Cui L, Fu GY, Xu XW. Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean. Mar Genomics 2023; 70:101045. [PMID: 37245381 DOI: 10.1016/j.margen.2023.101045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.
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Affiliation(s)
- Xiao-Lan Yue
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China; Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Ge-Yi Fu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.
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9
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Gios E, Mosley OE, Weaver L, Close M, Daughney C, Handley KM. Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles. ISME COMMUNICATIONS 2023; 3:13. [PMID: 36808147 PMCID: PMC9938205 DOI: 10.1038/s43705-023-00223-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/16/2023]
Abstract
Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford, UK
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Murray Close
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Chris Daughney
- GNS Science, Lower Hutt, New Zealand
- NIWA, National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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10
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Arce-Rodríguez A, Libby E, Castellón E, Avendaño R, Cambronero JC, Vargas M, Pieper DH, Bertilsson S, Chavarría M, Puente-Sánchez F. Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river. ENVIRONMENTAL MICROBIOME 2023; 18:6. [PMID: 36658604 PMCID: PMC9854191 DOI: 10.1186/s40793-023-00464-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Río Celeste ("Sky-Blue River") is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study indicated that this color is not caused by dissolved chemical species, but by formation of light-scattering aluminosilicate particles at the mixing point of two colorless streams, the acidic Quebrada Agria and the neutral Río Buenavista. RESULTS We now present microbiological information on Río Celeste and its two tributaries, as well as a more detailed characterization of the particles that occur at the mixing point. Our results overturn the previous belief that the light scattering particles are formed by the aggregation of smaller particles coming from Río Buenavista, and rather point to chemical formation of hydroxyaluminosilicate colloids when Quebrada Agria is partially neutralized by Río Buenavista, which also contributes silica to the reaction. The process is mediated by the activities of different microorganisms in both streams. In Quebrada Agria, sulfur-oxidizing bacteria generate an acidic environment, which in turn cause dissolution and mobilization of aluminum and other metals. In Río Buenavista, the growth of diatoms transforms dissolved silicon into colloidal biogenic forms which may facilitate particle precipitation. CONCLUSIONS We show how the sky-blue color of Río Celeste arises from the tight interaction between chemical and biological processes, in what constitutes a textbook example of emergent behavior in environmental microbiology.
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Affiliation(s)
- Alejandro Arce-Rodríguez
- Institute of Microbiology, Technical University of Braunschweig, 38106, Brunswick, Germany
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Eduardo Libby
- Escuela de Química, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Erick Castellón
- Escuela de Química, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Centro de Investigación en Ciencia e Ingeniería de Materiales (CICIMA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Juan Carlos Cambronero
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Maribel Vargas
- Centro de Investigaciones en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Stefan Bertilsson
- Deparment of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms Väg 9, 756 51, Uppsala, Sweden
| | - Max Chavarría
- Escuela de Química, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Fernando Puente-Sánchez
- Deparment of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms Väg 9, 756 51, Uppsala, Sweden.
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11
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Soares A, Edwards A, An D, Bagnoud A, Bradley J, Barnhart E, Bomberg M, Budwill K, Caffrey SM, Fields M, Gralnick J, Kadnikov V, Momper L, Osburn M, Mu A, Moreau JW, Moser D, Purkamo L, Rassner SM, Sheik CS, Sherwood Lollar B, Toner BM, Voordouw G, Wouters K, Mitchell AC. A global perspective on bacterial diversity in the terrestrial deep subsurface. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001172. [PMID: 36748549 PMCID: PMC9993121 DOI: 10.1099/mic.0.001172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/07/2022] [Indexed: 01/19/2023]
Abstract
While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.
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Affiliation(s)
- A. Soares
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
- Present address: Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Campus Essen - Environmental Microbiology and Biotechnology, Universitätsstr. 5, 45141 Essen, Germany
| | - A. Edwards
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - D. An
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - A. Bagnoud
- Institut de Génie Thermique (IGT), Haute École d'Ingénierie et de Gestion du Canton de Vaud (HEIG-VD), Yverdon-les-Bains, Switzerland
| | - J. Bradley
- School of Geography, Queen Mary University of London, London, UK
| | - E. Barnhart
- U.S. Geological Survey (USGS), USA, Reston, VA, USA
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
| | - M. Bomberg
- VTT Technical Research Centre of Finland, Finland
| | | | | | - M. Fields
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
- Department of Microbiology & Immunology, MSU, Bozeman, MT, USA
| | - J. Gralnick
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
| | - V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Russia
| | - L. Momper
- Department of Earth, Atmospheric and Planetary Sciences (DEAPS), The Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - M. Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - A. Mu
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - J. W. Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, Australia
| | - D. Moser
- Division of Hydrologic Sciences, Desert Research Institute (DRI), Las Vegas, NV, USA
| | - L. Purkamo
- VTT Technical Research Centre of Finland, Finland
- School of Earth and Environmental Sciences (SEES), University of St. Andrews, St. Andrews, UK
- Geological Survey of Finland (GTK), Finland
| | - S. M. Rassner
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - C. S. Sheik
- Large Lakes Observatory, University of Minnesota, Duluth, MN, USA
| | | | - B. M. Toner
- Department of Soil, Water & Climate, University of Minnesota, Minneapolis/Saint Paul, MN, USA
| | - G. Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - K. Wouters
- Institute for Environment, Health and Safety (EHS), Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - A. C. Mitchell
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
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12
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Mandal S, Bose H, Ramesh K, Sahu RP, Saha A, Sar P, Kazy SK. Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India. Front Microbiol 2022; 13:1018940. [PMID: 36504802 PMCID: PMC9731672 DOI: 10.3389/fmicb.2022.1018940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679-2,908 mbs) are incubated (180 days) with CO2 (+H2) or HCO3 - as the sole C source. Estimation of total protein, ATP, utilization of NO3 - and SO4 2- and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO2 (+H2) over HCO3 -. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335-2,908 mbs) with both CO2 and HCO3 -. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO2 (+H2) and HCO3 -. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO2 (+H2) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO3 -. H2 oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO2 fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO2, CH4 and H2 concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO3 -, SO4 2- , Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH4 and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H2 utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H2 metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO2 capture and conversion to useful products.
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Affiliation(s)
- Sunanda Mandal
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Kheerthana Ramesh
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India
| | - Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Sufia Khannam Kazy
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India,*Correspondence: Sufia Khannam Kazy,
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13
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Pedron R, Esposito A, Cozza W, Paolazzi M, Cristofolini M, Segata N, Jousson O. Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures. Front Microbiol 2022; 13:946460. [PMID: 36274724 PMCID: PMC9581249 DOI: 10.3389/fmicb.2022.946460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/12/2022] [Indexed: 11/26/2022] Open
Abstract
The microbiome of water springs is gaining increasing interest, especially in water intended for human consumption. However, the knowledge about large-scale patterns in water springs microbiome is still incomplete. The presence of bacteria in water sources used for human consumption is a major concern for health authorities; nonetheless, the standard microbiological quality checks are focused only on pathogenic species and total microbial load. Using 16S rRNA high throughput sequencing, we characterized the microbiome from 38 water springs in Trentino (Northern Italy) for 2 consecutive years in order to gain precious insights on the microbiome composition of these unexplored yet hardly exploited environments. The microbiological studies were integrated with standard measurements of physico-chemical parameters performed by the Provincial Office for Environmental Monitoring in order to highlight some of the dynamics influencing the microbial communities of these waters. We found that alpha diversity showed consistent patterns of variation overtime, and showed a strong positive correlation with the water nitrate concentration and negatively with fixed residue, electrical conductivity, and calcium concentration. Surprisingly, alpha diversity did not show any significant correlation with neither pH nor temperature. We found that despite their remarkable stability, different water springs display different coefficients of variation in alpha diversity, and that springs used for similar purposes showed similar microbiomes. Furthermore, the springs could be grouped according to the number of shared species into three major groups: low, mid, and high number of shared taxa, and those three groups of springs were consistent with the spring usage. Species belonging to the phyla Planctomycetes and Verrucomicrobia were prevalent and at relatively high abundance in springs classified as low number of shared species, whereas the phylum Lentisphaerae and the Candidate Phyla radiation were prevalent at higher abundance in the mineral and potable springs. The present study constitutes an example for standard water spring monitoring integrated with microbial community composition on a regional scale, and provides information which could be useful in the design and application of future water management policies in Trentino.
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Affiliation(s)
- Renato Pedron
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Alfonso Esposito
- International Centre for Genetic Engineering and Biotechnology – ICGEB, Trieste, Italy
| | - William Cozza
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Massimo Paolazzi
- Agenzia provinciale per la protezione dell'ambiente – APPA, Trento, Italy
| | | | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Olivier Jousson
- Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
- *Correspondence: Olivier Jousson,
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14
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Duhamel S, Hamilton CW, Pálsson S, Björnsdóttir SH. Microbial Response to Increased Temperatures Within a Lava-Induced Hydrothermal System in Iceland: An Analogue for the Habitability of Volcanic Terrains on Mars. ASTROBIOLOGY 2022; 22:1176-1198. [PMID: 35920884 DOI: 10.1089/ast.2021.0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fossil hydrothermal systems on Mars are important exploration targets because they may have once been habitable and could still preserve evidence of microbial life. We investigated microbial communities within an active lava-induced hydrothermal system associated with the 2014-2015 eruption of Holuhraun in Iceland as a Mars analogue. In 2016, the microbial composition in the lava-heated water differed substantially from that of the glacial river and spring water sources that fed into the system. Several taxonomic and metabolic groups were confined to the water emerging from the lava and some showed the highest sequence similarities to subsurface ecosystems, including to the predicted thermophilic and deeply branching Candidatus Acetothermum autotrophicum. Measurements show that the communities were affected by temperature and other environmental factors. In particular, comparing glacial river water incubated in situ (5.7°C, control) with glacial water incubated within a lava-heated stream (17.5°C, warm) showed that microbial abundance, richness, and diversity increased in the warm treatment compared with the control, with the predicted major metabolism shifting from lithotrophy toward organotrophy and possibly phototrophy. In addition, thermophilic bacteria isolated from the lava-heated water and a nearby acidic hydrothermal system included the known endospore-formers Geobacillus stearothermophilus and Paenibacillus cisolokensis as well as a potentially novel taxon within the order Hyphomicrobiales. Similar lava-water interactions on Mars could therefore have generated habitable environments for microbial communities.
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Affiliation(s)
- Solange Duhamel
- Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
- Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
| | | | - Snæbjörn Pálsson
- Department of Biology, University of Iceland, Reykjavík, Iceland
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15
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Geological activity shapes the microbiome in deep-subsurface aquifers by advection. Proc Natl Acad Sci U S A 2022; 119:e2113985119. [PMID: 35696589 PMCID: PMC9231496 DOI: 10.1073/pnas.2113985119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sheltered from radiation and asteroid strikes in Earth’s early history and home to a significant portion of today’s prokaryotic biomass, the deep subsurface could hold keys to understanding the early and continuing evolution of life. However, the processes that shape the distribution of subsurface microbial communities remain poorly understood due to sample inaccessibility. Here, at a deep-underground fractured hard-rock aquifer, we show that fracture activity leads to altered groundwater flow that drives profound changes in fluid-associated microbial communities by physical transport instead of environmental selection. We thereby identify advection induced by geological activity (a notable trigger for fracture activity) as a prominent yet overlooked mechanism shaping subsurface biogeography with potentially profound implications for life’s evolutionary history. Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.
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16
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Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments. WATER 2022. [DOI: 10.3390/w14101597] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In karst areas, anthropogenic contaminants reach the subsurface with detrimental effects on the groundwater ecosystem and downstream springs, which often serve as drinking water sources for the local human communities. We analyzed the water chemistry and microbial community composition in upstream and downstream locations of five hydrokarst systems (HKS) during four seasons. Conductivity and nitrates were higher in the downstream springs than in the pre-karst waters, whereas the concentration of organic matter, considered here as a pollution indicator, was lower. The microbial community composition varied largely between upstream and downstream locations, with multiple species of potentially pathogenic bacteria decreasing in the HKS. Bacteria indicative of pollution decreased as well when passing through the HKS, but potential biodegraders increased. This suggests that the HKS can filter out part of the polluting organic matter and, with it, part of the associated microorganisms. Nevertheless, the water quality, including the presence of pathogens in downstream springs, must be further monitored to control whether the water is appropriate for consumption. In parallel, the human populations located upstream must be advised of the risks resulting from their daily activities, improper stocking of their various wastes and dumping of their refuse in surface streams.
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17
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Fuentes B, Choque A, Gómez F, Alarcón J, Castro-Nallar E, Arenas F, Contreras D, Mörchen R, Amelung W, Knief C, Moradi G, Klumpp E, Saavedra CP, Prietzel J, Klysubun W, Remonsellez F, Bol R. Influence of Physical-Chemical Soil Parameters on Microbiota Composition and Diversity in a Deep Hyperarid Core of the Atacama Desert. Front Microbiol 2022; 12:794743. [PMID: 35197940 PMCID: PMC8859261 DOI: 10.3389/fmicb.2021.794743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
The extreme environmental conditions and lack of water on the soil surface in hyperarid deserts hamper microbial life, allowing only highly specialized microbial communities to the establish colonies and survive. Until now, the microbial communities that inhabit or have inhabited soils of hyperarid environments at greater depths have been poorly studied. We analyzed for the first time the variation in microbial communities down to a depth of 3.4 m in one of the driest places of the world, the hyperarid Yungay region in the Atacama Desert, and we related it to changes in soil physico-chemical characteristics. We found that the moisture content changed from 2 to 11% with depth and enabled the differentiation of three depth intervals: (i) surface zone A (0–60 cm), (ii) intermediate zone B (60–220 cm), and (iii) deep zone C (220–340 cm). Each zone showed further specific physicochemical and mineralogical features. Likewise, some bacterial phyla were unique in each zone, i.e., members of the taxa Deinococcota, Halobacterota, and Latescibacterota in zone A; Crenarchaeota, Fusobacteriota, and Deltaproteobacterium Sva0485 in zone B; and Fervidibacteria and Campilobacterota in zone C, which indicates taxon-specific preferences in deep soil habitats. Differences in the microbiota between the zones were rather abrupt, which is concomitant with abrupt changes in the physical-chemical parameters. Overall, moisture content, total carbon (TC), pH, and electric conductivity (EC) were most predictive of microbial richness and diversity, while total sulfur (TS) and total phosphorous (TP) contents were additionally predictive of community composition. We also found statistically significant associations between taxa and soil properties, most of which involved moisture and TC contents. Our findings show that under-explored habitats for microbial survival and existence may prevail at greater soil depths near water or within water-bearing layers, a valuable substantiation also for the ongoing search for biosignatures on other planets, such as Mars.
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Affiliation(s)
- Bárbara Fuentes
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Alessandra Choque
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Francisco Gómez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Franko Arenas
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Contreras
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Ramona Mörchen
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Wulf Amelung
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation, Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Ghazal Moradi
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Erwin Klumpp
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jörg Prietzel
- Wissenschaftszentum Weihenstephan, Technical University München, Freising, Germany
| | - Wantana Klysubun
- Synchrotron Light Research Institute, Nakhon Ratchasima, Thailand
| | - Francisco Remonsellez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
- *Correspondence: Francisco Remonsellez,
| | - Roland Bol
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
- School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
- Roland Bol,
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18
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Westmeijer G, Mehrshad M, Turner S, Alakangas L, Sachpazidou V, Bunse C, Pinhassi J, Ketzer M, Åström M, Bertilsson S, Dopson M. Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities. Commun Biol 2022; 5:37. [PMID: 35017653 PMCID: PMC8752596 DOI: 10.1038/s42003-021-02980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/15/2021] [Indexed: 12/20/2022] Open
Abstract
The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions. Westmeijer et al. employ high-throughput sequencing to investigate the connection between deep biosphere groundwaters and surface microbial communities. They suggest that the microbial communities of deep biosphere groundwaters in the Fennoscandian Shield are mostly comprised of autochthonous species, rather than migratory surface representatives.
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Affiliation(s)
- George Westmeijer
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Linda Alakangas
- Swedish Nuclear Fuel and Waste Management Co (SKB), 57 229, Oskarshamn, Sweden
| | - Varvara Sachpazidou
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.,Helmholtz-Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Marcelo Ketzer
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Mats Åström
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
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19
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Sahu RP, Kazy SK, Bose H, Mandal S, Dutta A, Saha A, Roy S, Dutta Gupta S, Mukherjee A, Sar P. Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environ Microbiol 2021; 24:2837-2853. [PMID: 34897962 DOI: 10.1111/1462-2920.15867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 12/20/2022]
Abstract
Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 106 ) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.
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Affiliation(s)
- Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sunanda Mandal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sukanta Roy
- Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, MH, 415114, India
| | - Srimanti Dutta Gupta
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Abhijit Mukherjee
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.,Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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20
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Unravelling unknown cyanobacteria diversity linked with HCN production. Mol Phylogenet Evol 2021; 166:107322. [PMID: 34626811 DOI: 10.1016/j.ympev.2021.107322] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/16/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022]
Abstract
Cyanobacteria are ecologically versatile microorganisms, occupying diverse habitats, from terrestrial caves to coastal shores and from brackish lakes to thermal springs. Cyanobacteria have also been linked with hydrogen cyanide (HCN), mainly for their ability to catabolize HCN by the nitrogenase enzyme. In this context, we sampled disparate environments, spanning from Canary Islands and Iceland to Estonia and Cyprus. Eighty-one (81) strains were isolated and characterised with taxonomic indices and molecular markers (16S-23S rRNA region and cpcBA region), whilst their ability to produce HCN was evaluated. This approach resulted in the description of five new genera (Speleotes, Haliplanktos, Olisthonema, Speos, and Iphianassa) and their type species (S. anchialus, H. antonyquinny, O. eestii, S. fyssassi, I. zackieohae) representing Chroococcales, Chroococcidiopsales, Oscillatoriales, Synechococcales, and Nostocales orders, respectively. We also found unique lineages inside the genera Komarekiella, Stenomitos, Cyanocohniella, and Nodularia, describing four new species (K. chia, S. pantisii, C. hyphalmyra, N. mediterannea). We report for the first time a widespread production of HCN amongst different taxa and habitats. Epilithic lifestyle, where cyanobacteria are more vulnerable to grazers, had the largest relative frequency in HCN production. In this work, we show novel cyanobacteria diversity from various habitats, including an unexplored anchialine cave, and possible correlation of cyanobacteria chemo- with species diversity, which may have implications on strategic focusing of screening programs on underexploited taxa and/or habitats.
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21
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Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide. Microorganisms 2021; 9:microorganisms9091812. [PMID: 34576708 PMCID: PMC8465018 DOI: 10.3390/microorganisms9091812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.
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22
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Yan L, Hermans SM, Totsche KU, Lehmann R, Herrmann M, Küsel K. Groundwater bacterial communities evolve over time in response to recharge. WATER RESEARCH 2021; 201:117290. [PMID: 34130083 DOI: 10.1016/j.watres.2021.117290] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.
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Affiliation(s)
- Lijuan Yan
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Syrie M Hermans
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany
| | - Kai Uwe Totsche
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany.
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23
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Mehrshad M, Lopez-Fernandez M, Sundh J, Bell E, Simone D, Buck M, Bernier-Latmani R, Bertilsson S, Dopson M. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nat Commun 2021; 12:4253. [PMID: 34253732 PMCID: PMC8275790 DOI: 10.1038/s41467-021-24549-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.
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Affiliation(s)
- Maliheh Mehrshad
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Margarita Lopez-Fernandez
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.4489.10000000121678994Present Address: Department of Microbiology, University of Granada, Granada, Spain
| | - John Sundh
- grid.10548.380000 0004 1936 9377Dept of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Emma Bell
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.22072.350000 0004 1936 7697Present Address: Department of Biological Sciences, University of Calgary, Calgary, Alberta Canada
| | - Domenico Simone
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.6341.00000 0000 8578 2742SLU Bioinformatics Infrastructure, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rizlan Bernier-Latmani
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefan Bertilsson
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark Dopson
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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24
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Michel C, Baran N, André L, Charron M, Joulian C. Side Effects of Pesticides and Metabolites in Groundwater: Impact on Denitrification. Front Microbiol 2021; 12:662727. [PMID: 34054765 PMCID: PMC8155494 DOI: 10.3389/fmicb.2021.662727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/30/2021] [Indexed: 01/16/2023] Open
Abstract
The impact of two pesticides (S-metolachlor and propiconazole) and their respective main metabolites (ESA-metolachlor and 1,2,4-triazole) on bacterial denitrification in groundwater was studied. For this, the denitrification activity and the bacterial diversity of a microbial community sampled from a nitrate-contaminated groundwater were monitored during 20 days in lab experiments in the presence or absence of pesticides or metabolites at 2 or 10 μg/L. The kinetics of nitrate reduction along with nitrite and N2O production all suggested that S-metolachlor had no or only little impact, whereas its metabolite ESA-metolachlor inhibited denitrification by 65% at 10 μg/L. Propiconazole and 1,2,4-triazole also inhibited denitrification at both concentrations, but to a lesser extent (29–38%) than ESA-metolachlor. When inhibition occurred, pesticides affected the reduction of nitrate into nitrite step. However, no significant differences were detected on the abundance of nitrate reductase narG and napA genes, suggesting an impact of pesticides/metabolites at the protein level rather than on denitrifying bacteria abundance. 16S rRNA gene Illumina sequencing indicated no major modification of bacterial diversity in the presence or absence of pesticides/metabolites, except for ESA-metolachlor and propiconazole at 10 μg/L that tended to increase or decrease Shannon and InvSimpson indices, respectively. General growth parameters suggested no impact of pesticides, except for propiconazole at 10 μg/L that partially inhibited acetate uptake and induced a decrease in microbial biomass. In conclusion, pesticides and metabolites can have side effects at environmental concentrations on microbial denitrification in groundwater and may thus affect ecosystem services based on microbial activities.
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Affiliation(s)
- Caroline Michel
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Nicole Baran
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Laurent André
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France.,Université d'Orléans, CNRS, BRGM, UMR 7327 Institut des Sciences de la Terre d'Orléans, Orléans, France
| | - Mickael Charron
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Catherine Joulian
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
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25
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Vishnivetskaya TA, Almatari AL, Spirina EV, Wu X, Williams DE, Pfiffner SM, Rivkina EM. Insights into community of photosynthetic microorganisms from permafrost. FEMS Microbiol Ecol 2021; 96:5979775. [PMID: 33181853 DOI: 10.1093/femsec/fiaa229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
This work integrates cultivation studies of Siberian permafrost and analyses of metagenomes from different locations in the Arctic with the aim of obtaining insights into the community of photosynthetic microorganisms in perennially frozen deposits. Cyanobacteria and microalgae have been described in Arctic aquatic and surface soil environments, but their diversity and ability to withstand harsh conditions within the permafrost are still largely unknown. Community structure of photosynthetic organisms in permafrost sediments was explored using Arctic metagenomes available through the MG-RAST. Sequences affiliated with cyanobacteria represented from 0.25 to 3.03% of total sequences, followed by sequences affiliated with Streptophyta (algae and vascular plants) 0.01-0.45% and Chlorophyta (green algae) 0.01-0.1%. Enrichment and cultivation approaches revealed that cyanobacteria and green algae survive in permafrost and they could be revived during prolonged incubation at low light intensity. Among photosynthetic microorganisms isolated from permafrost, the filamentous Oscillatoria-like cyanobacteria and unicellular green algae of the genus Chlorella were dominant. Our findings suggest that permafrost cyanobacteria and green algae are expected to be effective members of the re-assembled community after permafrost thawing and soil collapse.
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Affiliation(s)
- Tatiana A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA.,Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
| | - Abraham L Almatari
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Elena V Spirina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
| | - Xiaofen Wu
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Daniel E Williams
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Elizaveta M Rivkina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
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26
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Diego D, Hannisdal B, Dahle H. On how the power supply shapes microbial survival. Math Biosci 2021; 338:108615. [PMID: 33857526 DOI: 10.1016/j.mbs.2021.108615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/29/2021] [Accepted: 04/04/2021] [Indexed: 10/21/2022]
Abstract
Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.
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Affiliation(s)
- David Diego
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway.
| | - Bjarte Hannisdal
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway
| | - Håkon Dahle
- K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway; Department of Biological Sciences, University of Bergen, Thormøhlens gate 53A, NO-5006 Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
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27
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Kaushik R, Pandit MK, Meyerson LA, Chaudhari DS, Sharma M, Dhotre D, Shouche YS. Contrasting Composition, Diversity and Predictive Metabolic Potential of the Rhizobacterial Microbiomes Associated with Native and Invasive Prosopis Congeners. Curr Microbiol 2021; 78:2051-2060. [PMID: 33837467 DOI: 10.1007/s00284-021-02473-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 03/19/2021] [Indexed: 11/24/2022]
Abstract
Invasive plants are known to alter the soil microbial communities; however, the effects of co-occurring native and invasive congeners on the soil bacterial diversity and their predictive metabolic profiles are not known. Here, we compared the rhizosphere bacterial communities of invasive Prosopis juliflora and its native congener Prosopis cineraria using high-throughput sequencing of the 16S rRNA gene. Unweighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram revealed significant variation in the communities of these co-occurring Prosopis species. Additionally, Canonical Correspondence Analysis (CCA) based on microbial communities in addition to the soil physiochemical parameters viz. soil pH, electrical conductivity, moisture content and sampling depth showed ~ 80% of the variation in bacterial communities of the rhizosphere and control soil. We observed that Proteobacteria was the predominant phylum of P. juliflora rhizosphere and the control soil, while P. cineraria rhizosphere was dominated by Cyanobacteria. Notably, the invasive P. juliflora rhizosphere showed an enhanced abundance of bacterial phyla like Actinobacteria, Chloroflexi, Firmicutes and Acidobacteria compared to the native P. cineraria as well as the control soil. Predictive metagenomics revealed that the bacterial communities of the P. juliflora rhizosphere had a higher abundance of pathways involved in antimicrobial biosynthesis and degradation, suggesting probable exposure to enemy attack and an active response mechanism to counter it as compared to native P. cineraria. Interestingly, the higher antimicrobial biosynthesis predicted in the invasive rhizosphere microbiome is further corroborated by the fact that the bacterial isolates purified from the rhizosphere of P. juliflora belonged to genera like Streptomyces, Isoptericola and Brevibacterium from the phylum Actinobacteria, which are widely reported for their antibiotic production ability. In conclusion, our results demonstrate that the co-occurring native and invasive Prosopis species have significantly different rhizosphere bacterial communities in terms of composition, diversity and their predictive metabolic potentials. In addition, the rhizosphere microbiome of invasive Prosopis proffers it a fitness advantage and influences invasion success of the species.
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Affiliation(s)
- Rishabh Kaushik
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India.,Centre for Interdisciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India
| | - Maharaj K Pandit
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India. .,Centre for Interdisciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India.
| | - Laura A Meyerson
- Department of Natural Resources Science, University of Rhode Island, Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Diptaraj S Chaudhari
- National Centre for Cell Sciences, Pune University Campus, Ganeskhind, Pune, 411007, India
| | - Meesha Sharma
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India.,Centre for Interdisciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India
| | - Dhiraj Dhotre
- National Centre for Cell Sciences, Pune University Campus, Ganeskhind, Pune, 411007, India
| | - Yogesh S Shouche
- National Centre for Cell Sciences, Pune University Campus, Ganeskhind, Pune, 411007, India
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28
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles. Commun Biol 2021; 4:307. [PMID: 33686191 PMCID: PMC7940616 DOI: 10.1038/s42003-021-01810-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/08/2021] [Indexed: 12/22/2022] Open
Abstract
The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles. Karin Holmfeldt et al. sequence metagenomes and metatranscriptomes of viruses in deep groundwaters down to 448 m below the surface. The results reveal ecological dynamics of viruses including slow motion ‘boom and burst’ cycles and a ‘kill the winner’ model potentially driven by viral predation.
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29
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Ruiz-González C, Rodellas V, Garcia-Orellana J. The microbial dimension of submarine groundwater discharge: current challenges and future directions. FEMS Microbiol Rev 2021; 45:6128669. [PMID: 33538813 PMCID: PMC8498565 DOI: 10.1093/femsre/fuab010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC). Passeig Marítim de la Barceloneta 37-49, E08003 Barcelona, Spain
| | - Valentí Rodellas
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
| | - Jordi Garcia-Orellana
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain.,Departament de Física, Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
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30
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Stanish LF, Sherwood OA, Lackey G, Osborn S, Robertson CE, Harris JK, Pace N, Ryan JN. Microbial and Biogeochemical Indicators of Methane in Groundwater Aquifers of the Denver Basin, Colorado. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:292-303. [PMID: 33296185 DOI: 10.1021/acs.est.0c04228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The presence of methane and other hydrocarbons in domestic-use groundwater aquifers poses significant environmental and human health concerns. Isotopic measurements are often relied upon as indicators of groundwater aquifer contamination with methane. While these parameters are used to infer microbial metabolisms, there is growing evidence that isotopes present an incomplete picture of subsurface microbial processes. This study examined the relationships between microbiology and chemistry in groundwater wells located in the Denver-Julesburg Basin of Colorado, a rapidly urbanizing area with active oil and gas development. A primary goal was to determine if microbial data can reliably indicate the quantities and sources of groundwater methane. Comprehensive chemical and molecular analyses were performed on 39 groundwater well samples from five aquifers. Elevated methane concentrations were found in only one aquifer, and both isotopic and microbial data support a microbial origin. Microbial parameters had similar explanatory power as chemical parameters for predicting sample methane concentrations. Furthermore, a subset of samples with unique microbiology corresponded with unique chemical signatures that may be useful indicators of methane gas migration, potentially from nearby coal seams interacting with the aquifer. Microbial data may allow for more accurate determination of groundwater contamination and improved long-term water quality monitoring compared solely to isotopic and chemical data in areas with microbial methane.
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Affiliation(s)
- Lee F Stanish
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Owen A Sherwood
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Greg Lackey
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Stephen Osborn
- Department of Geological Sciences, California State Polytechnic University, Pomona, California 91768, United States
| | | | | | - Norman Pace
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Joseph N Ryan
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
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31
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Seto M, Iwasa Y. How Thermodynamics Illuminates Population Interactions in Microbial Communities. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.602809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In traditional population models of microbial ecology, there are two central players: producers and consumers (including decomposers that depend on organic carbon). Producers support surface ecosystems by generating adenosine triphosphate (ATP) from sunlight, part of which is used to build new biomass from carbon dioxide. In contrast, the productivity of subsurface ecosystems with a limited supply of sunlight must rely on bacteria and archaea that are able generate ATP solely from chemical or electric energy to fix inorganic carbon. These “light-independent producers” are frequently not included in traditional food webs, even though they are ubiquitous in nature and interact with one another through the utilization of the by-products of others. In this review, we introduce theoretical approaches based on population dynamics that incorporate thermodynamics to highlight characteristic interactions in the microbial community of subsurface ecosystems, which may link community structures and ecosystem expansion under conditions of a limited supply of sunlight. In comparison with light-dependent producers, which compete with one another for light, the use of Gibbs free energy (chemical energy) can lead cooperative interactions among light-independent producers through the effects of the relative quantities of products and reactants on the available chemical energy, which is termed abundant resource premium. The development of a population theory that incorporates thermodynamics offers fundamental ecological insights into subsurface microbial ecosystems, which may be applied to fields of study such as environmental science/engineering, astrobiology, or the microbial ecosystems of the early earth.
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32
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics. Front Microbiol 2020; 11:572252. [PMID: 33013807 PMCID: PMC7509429 DOI: 10.3389/fmicb.2020.572252] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/13/2020] [Indexed: 01/08/2023] Open
Abstract
To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic Methanobacteriaceae; acetoclastic and methylotrophic lineages were less abundant. ANME archaea were not found. The most numerous bacteria were the Firmicutes, Ignavibacteriae, Deltaproteobacteria, Chloroflexi, and Armatimonadetes. Most of the community was composed of anaerobic heterotrophs. Only six MAGs belonged to sulfate reducers. These MAGs accounted for 5% of the metagenome and were assigned to the Firmicutes, Deltaproteobacteria, Candidatus Kapabacteria, and Nitrospirae. Organotrophic bacteria carrying cytochrome c oxidase genes and presumably capable of aerobic respiration mostly belonged to the Chloroflexi, Ignavibacteriae, and Armatimonadetes. They accounted for 13% of the community. The first complete closed genomes were obtained for members of the Ignavibacteriae SJA-28 lineage and the candidate phylum Kapabacteria. Metabolic reconstruction of the SJA-28 bacterium, designated Candidatus Tepidiaquacella proteinivora, predicted that it is an anaerobe growing on proteinaceous substrates by fermentation or anaerobic respiration. The Ca. Kapabacteria genome contained both the sulfate reduction pathway and cytochrome c oxidase. Presumably, the availability of buried organic matter of Mesozoic marine sediments, long-term recharge of the aquifer with meteoric waters and its spatial heterogeneity provided the conditions for the development of microbial communities, taxonomically and functionally more diverse than those found in oligotrophic underground ecosystems.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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33
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Ivarsson M, Drake H, Bengtson S, Rasmussen B. A Cryptic Alternative for the Evolution of Hyphae. Bioessays 2020; 42:e1900183. [DOI: 10.1002/bies.201900183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/03/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Magnus Ivarsson
- Department of BiologyUniversity of Southern Denmark Campusvej 55 Odense M DK 5230 Denmark
- Department of PaleobiologySwedish Museum of Natural History Box 50007 Stockholm SE‐104 05 Sweden
| | - Henrik Drake
- Department of Biology and Environmental ScienceLinnaeus University Kalmar 391 82 Sweden
| | - Stefan Bengtson
- Department of PaleobiologySwedish Museum of Natural History Box 50007 Stockholm SE‐104 05 Sweden
| | - Birger Rasmussen
- School of Earth SciencesThe University of Western Australia Nedlands WA 6009 Australia
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Purkamo L, Kietäväinen R, Nuppunen-Puputti M, Bomberg M, Cousins C. Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context. Life (Basel) 2020; 10:E2. [PMID: 31947979 PMCID: PMC7175195 DOI: 10.3390/life10010002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/31/2019] [Accepted: 01/01/2020] [Indexed: 01/06/2023] Open
Abstract
The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.
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Affiliation(s)
- Lotta Purkamo
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews KY16 9AL, UK
- Geological Survey of Finland, 02151 Espoo, Finland
| | - Riikka Kietäväinen
- Geological Survey of Finland, 02151 Espoo, Finland
- Department of Geosciences and Geography, University of Helsinki, 00014 Helsinki, Finland
| | | | - Malin Bomberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Claire Cousins
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews KY16 9AL, UK
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Bižić M, Klintzsch T, Ionescu D, Hindiyeh MY, Günthel M, Muro-Pastor AM, Eckert W, Urich T, Keppler F, Grossart HP. Aquatic and terrestrial cyanobacteria produce methane. SCIENCE ADVANCES 2020; 6:eaax5343. [PMID: 31998836 PMCID: PMC6962044 DOI: 10.1126/sciadv.aax5343] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that cyanobacteria living in marine, freshwater, and terrestrial environments produce methane at substantial rates under light, dark, oxic, and anoxic conditions, linking methane production with light-driven primary productivity in a globally relevant and ancient group of photoautotrophs. Methane production, attributed to cyanobacteria using stable isotope labeling techniques, was enhanced during oxygenic photosynthesis. We suggest that the formation of methane by cyanobacteria contributes to methane accumulation in oxygen-saturated marine and limnic surface waters. In these environments, frequent cyanobacterial blooms are predicted to further increase because of global warming potentially having a direct positive feedback on climate change. We conclude that this newly identified source contributes to the current natural methane budget and most likely has been producing methane since cyanobacteria first evolved on Earth.
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Affiliation(s)
- M. Bižić
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Corresponding author. (M.B.); (H.-P.G.)
| | - T. Klintzsch
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
| | - D. Ionescu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
| | - M. Y. Hindiyeh
- Department of Water and Environmental Engineering, German Jordanian University, Amman, Jordan
| | - M. Günthel
- Department of Biosciences, Swansea University, SA2 8PP Swansea, UK
- Medical University of Gdańsk, Department of International Research Agenda 3P–Medicine, Marii Skłodowskiej-Curie 3a, 80-210 Gdańsk, Poland
| | - A. M. Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - W. Eckert
- Israel Oceanographic and Limnological Research, Yigal Allon Kinneret Limnological Laboratory, Migdal 14650, Israel
| | - T. Urich
- Institute of Microbiology, Center for Functional Genomics, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - F. Keppler
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, 69120 Heidelberg, Germany
| | - H.-P. Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
- Corresponding author. (M.B.); (H.-P.G.)
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Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters. mBio 2019; 10:mBio.01470-19. [PMID: 31409677 PMCID: PMC6692508 DOI: 10.1128/mbio.01470-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth’s carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water. Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two “modern marine” waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic “thoroughly mixed” water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or “geogases.”
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Dutta A, Sar P, Sarkar J, Dutta Gupta S, Gupta A, Bose H, Mukherjee A, Roy S. Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India. Front Microbiol 2019; 10:1362. [PMID: 31379755 PMCID: PMC6646420 DOI: 10.3389/fmicb.2019.01362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 05/31/2019] [Indexed: 11/13/2022] Open
Abstract
Archaeal community structure and potential functions within the deep, aphotic, oligotrophic, hot, igneous provinces of ∼65 Myr old basalt and its Archean granitic basement was explored through archaeal 16S rRNA gene amplicon sequencing from extracted environmental DNA of rocks. Rock core samples from three distinct horizons, basaltic (BS), transition (weathered granites) (TZ) and granitic (GR) showed limited organic carbon (4–48 mg/kg) and varied concentrations (<1.0–5000 mg/kg) of sulfate, nitrate, nitrite, iron and metal oxides. Quantitative PCR estimated the presence of nearly 103–104 archaeal cells per gram of rock. Archaeal communities within BS and GR horizons were distinct. The absence of any common OTU across the samples indicated restricted dispersal of archaeal cells. Younger, relatively organic carbon- and Fe2O3-rich BS rocks harbor Euryarchaeota, along with varied proportions of Thaumarchaeota and Crenarchaeota. Extreme acid loving, thermotolerant sulfur respiring Thermoplasmataceae, heterotrophic, ferrous-/H-sulfide oxidizing Ferroplasmaceae and Halobacteriaceae were more abundant and closely interrelated within BS rocks. Samples from the GR horizon represent a unique composition with higher proportions of Thaumarchaeota and uneven distribution of Euryarchaeota and Bathyarchaeota affiliated to Methanomicrobia, SAGMCG-1, FHMa11 terrestrial group, AK59 and unclassified taxa. Acetoclastic methanogenic Methanomicrobia, autotrophic SAGMCG-1 and MCG of Thaumarcheaota could be identified as the signature groups within the organic carbon lean GR horizon. Sulfur-oxidizing Sulfolobaceae was relatively more abundant in sulfate-rich amygdaloidal basalt and migmatitic gneiss samples. Methane-oxidizing ANME-3 populations were found to be ubiquitous, but their abundance varied greatly between the analyzed samples. Changes in diversity pattern among the BS and GR horizons highlighted the significance of local rock geochemistry, particularly the availability of organic carbon, Fe2O3 and other nutrients as well as physical constraints (temperature and pressure) in a niche-specific colonization of extremophilic archaeal communities. The study provided the first deep sequencing-based illustration of an intricate association between diverse extremophilic groups (acidophile-halophile-methanogenic), capable of sulfur/iron/methane metabolism and thus shed new light on their potential role in biogeochemical cycles and energy flow in deep biosphere hosted by hot, oligotrophic igneous crust.
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Affiliation(s)
- Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.,School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Jayeeta Sarkar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Srimanti Dutta Gupta
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Abhishek Gupta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Abhijit Mukherjee
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India.,Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sukanta Roy
- Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, India.,CSIR-National Geophysical Research Institute, Hyderabad, India
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Herrmann M, Wegner CE, Taubert M, Geesink P, Lehmann K, Yan L, Lehmann R, Totsche KU, Küsel K. Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions. Front Microbiol 2019; 10:1407. [PMID: 31281301 PMCID: PMC6596338 DOI: 10.3389/fmicb.2019.01407] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms of the formation of a groundwater microbiome and the subsequent differentiation of Cand. Patescibacteria. In the Hainich Critical Zone Exploratory, Germany, we trace the input of microorganisms from forested soils of preferential recharge areas through fractured aquifers along a 5.4 km hillslope well transect. Cand. Patescibacteria were preferentially mobilized from soils and constituted 66% of species-level OTUs shared between seepage and shallow groundwater. These OTUs, mostly related to Cand. Kaiserbacteraceae, Cand. Nomurabacteraceae, and unclassified UBA9983 at the family level, represented a relative abundance of 71.4% of the Cand. Patescibacteria community at the shallowest groundwater well, and still 44.4% at the end of the transect. Several Cand. Patescibacteria subclass-level groups exhibited preferences for different conditions in the two aquifer assemblages investigated: Cand. Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Cand. Nomurabacteraceae were negatively correlated. Co-occurrence network analysis revealed a central role of Cand. Patescibacteria in the groundwater microbial communities and pointed to potential associations with specific organisms, including abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling. Strong associations among Cand. Patescibacteria themselves further suggested that for many groups within this phylum, distribution was mainly driven by conditions commonly supporting a fermentative life style without direct dependence on specific hosts. We propose that import from soil, and community differentiation driven by hydrochemical conditions, including the availability of organic resources and potential hosts, determine the success of Cand. Patescibacteria in groundwater environments.
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Affiliation(s)
- Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Patricia Geesink
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Katharina Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Lijuan Yan
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Uwe Totsche
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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39
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Purkamo L, Kietäväinen R, Miettinen H, Sohlberg E, Kukkonen I, Itävaara M, Bomberg M. Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater. FEMS Microbiol Ecol 2019; 94:5035813. [PMID: 29893836 DOI: 10.1093/femsec/fiy116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/08/2018] [Indexed: 01/19/2023] Open
Abstract
The diversity and metabolic functions of deep subsurface ecosystems remain relatively unexplored. Microbial communities in previously studied deep subsurface sites of the Fennoscandian Shield are distinctive to each site. Thus, we hypothesized that the microbial communities of the deep Archaean bedrock fracture aquifer in Romuvaara, northern Finland, differ both in community composition and metabolic functionality from the other sites in the Fennoscandian Shield. We characterized the composition, functionality and substrate preferences of the microbial communities at different depths in a 600 m deep borehole. In contrast to other Fennoscandian deep biosphere communities studied to date, iron-oxidizing Gallionella dominated the bacterial communities, while methanogenic and ammonia-oxidizing archaea were the most prominent archaea, and a diverse fungal community was also detected. Potential for methane cycling and sulfate and nitrate reduction was confirmed by detection of the functional genes of these metabolic pathways. Organotrophs were less abundant, although carbohydrates were the most preferred of the tested substrates. The microbial communities shared features with those detected from other deep groundwaters with similar geochemistry, but the majority of taxa distinctive to Romuvaara are different from the taxa previously detected in saline deep groundwater in the Fennoscandian Shield, most likely because of the differences in water chemistry.
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Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Riikka Kietäväinen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Elina Sohlberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Ilmo Kukkonen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Merja Itävaara
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
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40
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Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation. PLoS One 2019; 14:e0212937. [PMID: 30865693 PMCID: PMC6415789 DOI: 10.1371/journal.pone.0212937] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/12/2019] [Indexed: 11/19/2022] Open
Abstract
Light driven primary production by plants is the main source of biomass in terrestrial ecosystems. But also in subsurface habitats like aquifers, life is fueled largely by this plant-derived biomass. Here, we investigate the degradation of plant-derived polysaccharides in a groundwater microbiome to identify the microbial key players involved, and compare them to those from soil of the groundwater recharge area. We quantified the activities of enzymes degrading the abundant plant polymers starch, cellulose and hemicellulose in oligotrophic groundwater samples, despite the low cell numbers present. Normalized to 16S rRNA gene copy numbers, these activities were only one order of magnitude lower than in soil. Stimulation of the groundwater microbiome with either starch or cellulose and hemicellulose led to changes of the enzymatic activity ratios, indicating autochthonous production of enzymes in response to the plant polymers. Furthermore, DNA stable isotope probing with 13C labelled plant polymers allowed us to identify microbes involved in the degradation of these compounds. In (hemi)cellulose microcosms, Bacteroidia and Candidatus Parcubacteria were active, while the active community in starch microcosms mostly comprised Candidatus Saccharibacteria, Cytophagia, and Actinobacteria. Not a single one of the active OTUs was also found to be labelled in soil microcosms. This indicates that the degradation of plant-derived polysaccharides in groundwater is driven by organisms completely distinct from those active in soil. The involvement of members of the candidate phyla Cand. Parcubacteria and Cand. Saccharibacteria, organisms known to be abundant in groundwater, in plant-derived organic matter degradation might strongly impact subsurface carbon cycling.
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Gregory SP, Barnett MJ, Field LP, Milodowski AE. Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry. Microorganisms 2019; 7:E53. [PMID: 30769950 PMCID: PMC6407114 DOI: 10.3390/microorganisms7020053] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 12/21/2022] Open
Abstract
Hydrogen is a key energy source for subsurface microbial processes, particularly in subsurface environments with limited alternative electron donors, and environments that are not well connected to the surface. In addition to consumption of hydrogen, microbial processes such as fermentation and nitrogen fixation produce hydrogen. Hydrogen is also produced by a number of abiotic processes including radiolysis, serpentinization, graphitization, and cataclasis of silicate minerals. Both biotic and abiotically generated hydrogen may become available for consumption by microorganisms, but biotic production and consumption are usually tightly coupled. Understanding the microbiology of hydrogen cycling is relevant to subsurface engineered environments where hydrogen-cycling microorganisms are implicated in gas consumption and production and corrosion in a number of industries including carbon capture and storage, energy gas storage, and radioactive waste disposal. The same hydrogen-cycling microorganisms and processes are important in natural sites with elevated hydrogen and can provide insights into early life on Earth and life on other planets. This review draws together what is known about microbiology in natural environments with elevated hydrogen, and highlights where similar microbial populations could be of relevance to subsurface industry.
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Affiliation(s)
- Simon P Gregory
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Megan J Barnett
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Lorraine P Field
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Antoni E Milodowski
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
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42
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Savio D, Stadler P, Reischer GH, Demeter K, Linke RB, Blaschke AP, Mach RL, Kirschner AKT, Stadler H, Farnleitner AH. Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community. Front Microbiol 2019; 10:28. [PMID: 30828319 PMCID: PMC6385617 DOI: 10.3389/fmicb.2019.00028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/09/2019] [Indexed: 11/13/2022] Open
Abstract
Alpine karst aquifers are important groundwater resources for the provision of drinking water all around the world. Yet, due to difficult accessibility and long-standing methodological limitations, the microbiology of these systems has long been understudied. The aim of the present study was to investigate the structure and dynamics of bacterial communities in spring water of an alpine limestone karst aquifer (LKAS2) under different hydrological conditions (base vs. event flow). The study was based on high-throughput 16S rRNA gene amplicon sequencing, study design and sample selection were guided by hydrology and pollution microbiology data. Spanning more than 27 months, our analyses revealed a taxonomically highly stable bacterial community, comprising high proportions of yet uncultivated bacteria in the suspended bacterial community fraction. Only the three candidate phyla Parcubacteria (OD1), Gracilibacteria (GN02), Doudnabacteria (SM2F11) together with Proteobacteria and Bacteroidetes contributed between 70.0 and 88.4% of total reads throughout the investigation period. A core-community of 300 OTUs consistently contributed between 37.6 and 56.3% of total reads, further supporting the hypothesis of a high temporal stability in the bacterial community in the spring water. Nonetheless, a detectable response in the bacterial community structure of the spring water was discernible during a high-discharge event. Sequence reads affiliated to the class Flavobacteriia clearly increased from a mean proportion of 2.3% during baseflow to a maximum of 12.7% during the early phase of the studied high-discharge event, suggesting direct impacts from changing hydrological conditions on the bacterial community structure in the spring water. This was further supported by an increase in species richness (Chao1) at higher discharge. The combination of these observations allowed the identification and characterization of three different discharge classes (Q1-Q3). In conclusion, we found a taxonomically stable bacterial community prevailing in spring waters from an alpine karst aquifer over the entire study period of more than 2 years. Clear response to changing discharge conditions could be detected for particular bacterial groups, whereas the most responsive group - bacteria affiliated to the class of Flavobacteriia - might harbor potential as a valuable natural indicator of "system disturbances" in karst aquifers.
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Affiliation(s)
- Domenico Savio
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
| | - Philipp Stadler
- Centre for Water Resource Systems, TU Wien, Vienna, Austria.,Research Unit for Water Quality Management, Institute for Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Georg H Reischer
- Molecular Diagnostics Group, Institute of Chemical, Environmental and Bioscience Engineering, Department of Agrobiotechnology, IFA-Tulln, TU Wien, Tulln an der Donau, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Katalin Demeter
- Centre for Water Resource Systems, TU Wien, Vienna, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Rita B Linke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alfred P Blaschke
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Vienna, Austria
| | - Robert L Mach
- Research Division of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alexander K T Kirschner
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Hermann Stadler
- Department for Water Resources Management and Environmental Analytics, Institute for Water, Energy and Sustainability, Joanneum Research, Graz, Austria
| | - Andreas H Farnleitner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Interuniversity Cooperation Centre for Water and Health, Vienna, Austria.,Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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43
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Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol Ecol 2018; 94:5107865. [PMID: 30265315 PMCID: PMC6192502 DOI: 10.1093/femsec/fiy191] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.
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Affiliation(s)
- H J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A J Zelaya
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - K B De León
- Department of Biochemistry, University of Missouri, Columbia, MO
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - R Chakraborty
- Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - D A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - T C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Civil Engineering, Montana State University, Montana State University, Bozeman, MT
| | - M W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
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Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India. Sci Rep 2018; 8:17459. [PMID: 30498254 PMCID: PMC6265293 DOI: 10.1038/s41598-018-35940-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/05/2018] [Indexed: 11/08/2022] Open
Abstract
Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.
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45
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Lopez-Fernandez M, Åström M, Bertilsson S, Dopson M. Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers. Front Microbiol 2018; 9:2880. [PMID: 30538690 PMCID: PMC6277548 DOI: 10.3389/fmicb.2018.02880] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022] Open
Abstract
The continental deep biosphere is suggested to contain a substantial fraction of the earth's total biomass and microorganisms inhabiting this environment likely have a substantial impact on biogeochemical cycles. However, the deep microbial community is still largely unknown and can be influenced by parameters such as temperature, pressure, water residence times, and chemistry of the waters. In this study, 21 boreholes representing a range of deep continental groundwaters from the Äspö Hard Rock Laboratory were subjected to high-throughput 16S rRNA gene sequencing to characterize how the different water types influence the microbial communities. Geochemical parameters showed the stability of the waters and allowed their classification into three groups. These were (i) waters influenced by infiltration from the Baltic Sea with a "modern marine (MM)" signature, (ii) a "thoroughly mixed (TM)" water containing groundwaters of several origins, and (iii) deep "old saline (OS)" waters. Decreasing microbial cell numbers positively correlated with depth. In addition, there was a stronger positive correlation between increased cell numbers and dissolved organic carbon for the MM compared to the OS waters. This supported that the MM waters depend on organic carbon infiltration from the Baltic Sea while the ancient saline waters were fed by "geogases" such as carbon dioxide and hydrogen. The 16S rRNA gene relative abundance of the studied groundwaters revealed different microbial community compositions. Interestingly, the TM water showed the highest dissimilarity compared to the other two water types, potentially due to the several contrasting water types contributing to this groundwater. The main identified microbial phyla in the groundwaters were Gammaproteobacteria, unclassified sequences, Campylobacterota (formerly Epsilonproteobacteria), Patescibacteria, Deltaproteobacteria, and Alphaproteobacteria. Many of these taxa are suggested to mediate ferric iron and nitrate reduction, especially in the MM waters. This indicated that nitrate reduction may be a neglected but important process in the deep continental biosphere. In addition to the high number of unclassified sequences, almost 50% of the identified phyla were archaeal or bacterial candidate phyla. The percentage of unknown and candidate phyla increased with depth, pointing to the importance and necessity of further studies to characterize deep biosphere microbial populations.
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Affiliation(s)
| | - Mats Åström
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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46
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Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere. mBio 2018; 9:mBio.01792-18. [PMID: 30459191 PMCID: PMC6247080 DOI: 10.1128/mbio.01792-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the Äspö Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes. The continental subsurface is suggested to contain a significant part of the earth’s total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Äspö Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as “modern marine,” and an “old saline” groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available.
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47
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Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8110418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited.
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48
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Puente-Sánchez F, Arce-Rodríguez A, Oggerin M, García-Villadangos M, Moreno-Paz M, Blanco Y, Rodríguez N, Bird L, Lincoln SA, Tornos F, Prieto-Ballesteros O, Freeman KH, Pieper DH, Timmis KN, Amils R, Parro V. Viable cyanobacteria in the deep continental subsurface. Proc Natl Acad Sci U S A 2018; 115:10702-10707. [PMID: 30275328 PMCID: PMC6196553 DOI: 10.1073/pnas.1808176115] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cyanobacteria are ecologically versatile microorganisms inhabiting most environments, ranging from marine systems to arid deserts. Although they possess several pathways for light-independent energy generation, until now their ecological range appeared to be restricted to environments with at least occasional exposure to sunlight. Here we present molecular, microscopic, and metagenomic evidence that cyanobacteria predominate in deep subsurface rock samples from the Iberian Pyrite Belt Mars analog (southwestern Spain). Metagenomics showed the potential for a hydrogen-based lithoautotrophic cyanobacterial metabolism. Collectively, our results suggest that they may play an important role as primary producers within the deep-Earth biosphere. Our description of this previously unknown ecological niche for cyanobacteria paves the way for models on their origin and evolution, as well as on their potential presence in current or primitive biospheres in other planetary bodies, and on the extant, primitive, and putative extraterrestrial biospheres.
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Affiliation(s)
- Fernando Puente-Sánchez
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain;
| | - Alejandro Arce-Rodríguez
- Institute of Microbiology, Technical University Braunschweig, D-38023 Braunschweig, Germany
- Microbial Interactions and Processes Group, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Monike Oggerin
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Miriam García-Villadangos
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
| | - Nuria Rodríguez
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Laurence Bird
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802
| | - Sara A Lincoln
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802
| | - Fernando Tornos
- Instituto de Geociencias, CSIC-Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Olga Prieto-Ballesteros
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Katherine H Freeman
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802
| | - Dietmar H Pieper
- Microbial Interactions and Processes Group, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, D-38023 Braunschweig, Germany
| | - Ricardo Amils
- Department of Planetology and Habitability, Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial-Consejo Superior de Investigaciones Científicas (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain
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49
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Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong W, Hettich RL, Balmer L, Frutschi M, Sommer G, Bernier-Latmani R. Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater. Front Microbiol 2018; 9:2129. [PMID: 30245678 PMCID: PMC6137086 DOI: 10.3389/fmicb.2018.02129] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and elevated concentrations of sulphide are observed when sulphate-rich and methane-rich groundwaters mix. Particularly high sulphide is observed in methane-rich groundwater from a fracture at 530.6 mbsl, where mixing with sulphate-rich groundwater occurred as the result of an open drill hole connecting two different fractures at different depths. To determine the electron donors fuelling sulphidogenesis, we combined geochemical, isotopic, metagenomic and metaproteomic analyses. This revealed a low diversity microbial community fuelled by hydrogen and organic carbon. Sulphur and carbon isotopes of sulphate and dissolved inorganic carbon, respectively, confirmed that sulphate reduction was ongoing and that CO2 came from the degradation of organic matter. The results demonstrate the impact of introducing sulphate to a methane-rich groundwater with limited electron acceptors and provide insight into extant metabolisms in the terrestrial subsurface.
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Affiliation(s)
- Emma Bell
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Johannes Alneberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chen Qian
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Louise Balmer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Manon Frutschi
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Guillaume Sommer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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50
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Katayama T, Yoshioka H, Yamanaka T, Takeuchi M, Muramoto Y, Usami J, Ikeda H, Sakata S. Microbial community structure in deep natural gas-bearing aquifers subjected to sulfate-containing fluid injection. J Biosci Bioeng 2018; 127:45-51. [PMID: 30082219 DOI: 10.1016/j.jbiosc.2018.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
Abstract
In the natural gas field located in central Japan, high concentrations of natural gases and iodide ions are dissolved in formation water and commercially produced in deep aquifers. In the iodine recovery process, the produced formation water is amended with sulfate, and this fluid is injected into gas-bearing aquifers, which may lead to infrastructure corrosion by hydrogen sulfide. In this study, we examined the microbial community in aquifers subjected to sulfate-containing fluid injection. Formation water samples were collected from production wells located at different distances from the injection wells. The chemical analysis showed that the injection fluid contained oxygen, nitrate, nitrite and sulfate, in contrast to the formation water, which had previously been shown to be depleted in these components. Sulfur isotopic analysis indicated that sulfate derived from the injection fluid was present in the sample collected from near the injection wells. Quantitative and sequencing analysis of dissimilatory sulfite reductase and 16S rRNA genes revealed that sulfate-reducing bacteria (SRB), sulfur-oxidizing bacteria, and anaerobic methanotrophic archaea (ANME) in the wells located near injection wells were more abundant than those in wells located far from the injection wells, suggesting that fluid injection stimulated these microorganisms through the addition of oxygen, nitrate, nitrite and sulfate to the methane-rich aquifers. The predominant taxa were assigned to the ANME-2 group, its sulfate-reducing partner SEEP-SRB1 cluster and sulfur-oxidizing Epsilonproteobacteria. These results provide important insights for future studies to support the development of natural gas and iodine resources in Japan.
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Affiliation(s)
- Taiki Katayama
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Hideyoshi Yoshioka
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan.
| | - Toshiro Yamanaka
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Mio Takeuchi
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Yoshiyuki Muramoto
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Jun Usami
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Hidefumi Ikeda
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
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