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Du Y, Xiong Y, Deng Y, Tao Y, Tian H, Zhang Y, Li Q, Gan Y, Wang Y. Geogenic Phosphorus Enrichment in Groundwater due to Anaerobic Methane Oxidation-Coupled Fe(III) Oxide Reduction. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8032-8042. [PMID: 38670935 DOI: 10.1021/acs.est.4c00267] [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: 04/28/2024]
Abstract
Accumulation of geogenic phosphorus (P) in groundwater is an emerging environmental concern, which is closely linked to coupled processes involving FeOOH and organic matter under methanogenic conditions. However, it remains unclear how P enrichment is associated with methane cycling, particularly the anaerobic methane oxidation (AMO). This study conducted a comprehensive investigation of carbon isotopes in dissolved inorganic carbon (DIC), CO2, and CH4, alongside Fe isotopes, microbial communities, and functions in quaternary aquifers of the central Yangtze River plain. The study found that P concentrations tended to increase with Fe(II) concentrations, δ56Fe, and δ13C-DIC, suggesting P accumulation due to the reductive dissolution of FeOOH under methanogenic conditions. The positive correlations of pmoA gene abundance versus δ13C-CH4 and Fe concentrations versus δ13C-CH4, and the prevalent presence of Candidatus_Methanoperedens, jointly demonstrated the potential significance of Fe(III)-mediated AMO process (Fe-AMO) alongside traditional methanogenesis. The increase of P concentration with δ13C-CH4 value, pmoA gene abundance, and Fe concentration suggested that the Fe-AMO process facilitated P enrichment in groundwater. Redundancy analysis confirmed this assertion, identifying P concentration as the primary determinant and the cooperative influence of Fe-AMO microorganisms such as Candidatus_Methanoperedens and Geobacter on P enrichment. Our work provided new insights into P dynamics in subsurface environments.
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Affiliation(s)
- Yao Du
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yaojin Xiong
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yamin Deng
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yanqiu Tao
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Hao Tian
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yanpeng Zhang
- Wuhan Center of China Geological Survey, Wuhan 430205, China
| | - Qinghua Li
- Wuhan Center of China Geological Survey, Wuhan 430205, China
| | - Yiqun Gan
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yanxin Wang
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
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Bellini R, Vasile NS, Bassani I, Vizzarro A, Coti C, Barbieri D, Scapolo M, Pirri CF, Verga F, Menin B. Investigating the activity of indigenous microbial communities from Italian depleted gas reservoirs and their possible impact on underground hydrogen storage. Front Microbiol 2024; 15:1392410. [PMID: 38725680 PMCID: PMC11079786 DOI: 10.3389/fmicb.2024.1392410] [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: 02/27/2024] [Accepted: 04/09/2024] [Indexed: 05/12/2024] Open
Abstract
H2 produced from renewable energies will play a central role in both greenhouse gas reduction and decarbonization by 2050. Nonetheless, to improve H2 diffusion and utilization as a fuel, large storage capacity systems are needed. Underground storage of natural gas in depleted reservoirs, aquifers and salt caverns is a well-established technology. However, new challenges arise when it comes to storing hydrogen due to the occurrence and activity of indigenous microbial populations in deep geological formations. In a previous study, four Italian natural gas reservoirs were characterized both from a hydro-chemical and microbiological point of view, and predictive functional analyses were carried out with the perspective of underground hydrogen storage (UHS). In the present work, formation waters from the same reservoirs were used as inoculant during batch cultivation tests to characterize microbial activity and its effects on different gas mixtures. Results evidence a predominant acidogenic/acetogenic activity, whilst methanogenic and sulfate reducing activity were only marginal for all tested inoculants. Furthermore, the microbial activation of tested samples is strongly influenced by nutrient availability. Obtained results were fitted and screened in a computational model which would allow deep insights in the study of microbial activity in the context of UHS.
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Affiliation(s)
- Ruggero Bellini
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Nicolò Santi Vasile
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Ilaria Bassani
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Arianna Vizzarro
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | | | | | | | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Francesca Verga
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- National Research Council, Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Milan, Italy
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Tian H, Du Y, Deng Y, Sun X, Xu J, Gan Y, Wang Y. Identification of methane cycling pathways in Quaternary alluvial-lacustrine aquifers using multiple isotope and microbial indicators. WATER RESEARCH 2024; 250:121027. [PMID: 38113595 DOI: 10.1016/j.watres.2023.121027] [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: 09/06/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Groundwater rich in dissolved methane is often overlooked in the global or regional carbon cycle. Considering the knowledge gap in understanding the biogeochemical behavior of methane in shallow aquifers, particularly those in humid alluvial-lacustrine plains with high organic carbon content, we investigated methane sources and cycling pathways in groundwater systems at the central Yangtze River basins. Composition of multiple stable isotopes (2H/18O in water, 13C in dissolved inorganic carbon, 13C/2H in methane, and 13C in carbon dioxide) was combined with the characteristics of microbes and dissolved organic matter (DOM) in the study. The results revealed significant concentrations of biogenic methane reaching up to 13.05 mg/L in anaerobic groundwater environments with abundant organic matter. Different pathways for methane cycling (methanogenic CO2-reduction and acetate-fermentation, and methane oxidation) were identified. CO2-reduction dominated acetate-fermentation in the two methanogenic pathways primarily associated with humic DOM, while methane oxidation was more closely associated with microbially derived DOM. The abundance of obligate CO2-reduction microorganisms (Methanobacterium and Methanoregula) was higher in samples with substantial CO2-reduction, as indicated by isotopic composition. The obligate acetate-fermentation microorganism (Methanosaeta) was more abundant in samples exhibiting evident acetate-fermentation. Additionally, a high abundance of Candidatus Methanoperedens was identified in samples with apparent methane oxidation. Comparing our findings with those in other areas, we found that various factors, such as groundwater temperature, DOM abundance and types, and hydrogeological conditions, may lead to differences in groundwater methane cycling. This study offered a new perspective and understanding of methane cycling in worldwide shallow alluvial-lacustrine aquifer systems without geothermal disturbance.
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Affiliation(s)
- Hao Tian
- MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, Wuhan 430078, China; School of Environmental Studies, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, China
| | - Yao Du
- MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, Wuhan 430078, China; School of Environmental Studies, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, China.
| | - Yamin Deng
- MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, Wuhan 430078, China; School of Environmental Studies, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, China
| | - Xiaoliang Sun
- MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, Wuhan 430078, China; School of Environmental Studies, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, China
| | - Jiawen Xu
- MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, Wuhan 430078, China; School of Environmental Studies, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, China
| | - Yiqun Gan
- MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, Wuhan 430078, China; School of Environmental Studies, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, China
| | - Yanxin Wang
- MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, Wuhan 430078, China; School of Environmental Studies, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430078, China
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Hanišáková N, Vítězová M, Vítěz T, Kushkevych I, Kotrlová E, Novák D, Lochman J, Zavada R. Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea. Front Microbiol 2023; 14:1293506. [PMID: 38188570 PMCID: PMC10771303 DOI: 10.3389/fmicb.2023.1293506] [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: 09/13/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.
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Affiliation(s)
- Nikola Hanišáková
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Monika Vítězová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tomáš Vítěz
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Ivan Kushkevych
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Kotrlová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Novák
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Roman Zavada
- Innovation Unit, NAFTA a.s., Bratislava, Slovakia
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Zheng J, Yang Y, Li J, Zhang H, Ma Y. The Migration Mechanism of BTEX in Single- and Double-Lithology Soil Columns under Groundwater Table Fluctuation. TOXICS 2023; 11:630. [PMID: 37505595 PMCID: PMC10384195 DOI: 10.3390/toxics11070630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/09/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
The migration of light non-aqueous phase liquids (LNAPLs) trapped in porous media is a complex phenomenon. Groundwater table fluctuation can not only affect contaminant migration but also redox conditions, bacterial communities, and contaminant degradation. Understanding LNAPLs' (e.g., benzene, toluene, ethylbenzene, and xylene (BTEX)) behavior within porous media is critical for the high efficiency of most in situ remediation systems. A laboratory study of single- and double-lithology soil column investigation of the groundwater table fluctuation effect on BTEX transport, using benzene and toluene as typical compounds, in a typical representative model of aquifers subjected to water table fluctuation was undertaken in this study. The results show that benzene and toluene migration in single-lithology soil columns packed with sand was mainly affected by flushing due to the hydraulic force induced by water table fluctuations and that the double-lithology soil column packed with sand and silt was significantly affected by retention due to the higher adsorption induced by 10 cm of silt. The dissolution mainly correlated with the BTEX migration in saturated zones, and the contaminant concentration increased when the water table fell and decreased when the water table rose. For a contaminated site with a single-lithology structure consisting of sand, more attention should be paid to organic contaminant removal within the groundwater, and a double-lithology structure containing silt is more suited to the removal of organic contaminants from the silt layer. The difference in biodegradation kinetics between the groundwater table fluctuation (GTF) zone and the saturated zone should be better understood for the remediation of BTEX compounds.
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Affiliation(s)
- Jingwei Zheng
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
| | - Yang Yang
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China
| | - Juan Li
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China
| | - Hao Zhang
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China
| | - Yan Ma
- School of Chemical and Environmental Engineering, China University of Mining and Technology-Beijing, Beijing 100083, China
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Alsabti B, Sabarathinam C, Svv DR. Identification of high nitrate concentration in shallow groundwater of an arid region: a case study of South Kuwait's Bay. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 195:143. [PMID: 36418655 DOI: 10.1007/s10661-022-10698-1] [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: 04/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Coastal aquifer is a fragile environment due to the interaction of groundwater with seawater, especially in arid environments. Groundwater along Kuwait's Bay is polluted due to discharge of waste from desalination plants, power plants, and other anthropogenic activities. Earlier studies on submarine groundwater discharge in Kuwait's Bay region have reported the transfer of nutrient flux from the groundwater to Kuwait's Bay. The current study focused on nitrate sources and processes governing their distribution in groundwater samples collected from the southern part of Kuwait's Bay. The concentration of nitrate in the samples ranged from 22.7 to 803.9 mg/L. Higher values were noted in the samples collected inland and a few samples adjacent to the Bay. Spearman's correlation analysis of the data indicated that NO3- has a strong positive correlation with SO42- and moderate positive correlation with Na + , TDS/EC. The PCA analysis and factor scores revealed the different sources for groundwater nitrate contamination as follows: leakage of sewer lines in the urban region has led to the infiltration of contaminated sewage, high saline environment due to seawater intrusion, chemical weathering, and influence of denitrifying bacteria. The health risk has resulted due to the NO3- concentration being above the standard limit for adults. Furthermore, the nitrate concentration was higher in the region adjoining the landfills. In addition, the discharge of groundwater with higher nitrate to the adjacent open water in the Bay may lead to eutrophication. Hence, proper management strategies are to be adopted to control the nitrate pollution in groundwater.
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Affiliation(s)
- Bedour Alsabti
- Water Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait.
| | | | - Dhanu Radha Svv
- Water Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait
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Fan D, Zhao Z, Wang Y, Ma J, Wang X. Crop-type-driven changes in polyphenols regulate soil nutrient availability and soil microbiota. Front Microbiol 2022; 13:964039. [PMID: 36090073 PMCID: PMC9449698 DOI: 10.3389/fmicb.2022.964039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Crop rotation is a typical agronomic practice to mitigate soil deterioration caused by continuous cropping. However, the mechanisms of soil biotic and abiotic factors in response to different cropping patterns in acidic and polyphenol-rich tea nurseries remain unclear. In this study, the composition and function of microbial communities were comparatively investigated in soils of tea seedlings continuously planted for 2 years (AC: autumn-cutting; SC: summer-cutting) and in soils rotation with strawberries alternately for 3 years (AR: autumn-cutting). The results showed that AR significantly improved the survival of tea seedlings but greatly reduced the contents of soil polyphenols. The lower soil polyphenol levels in AR were associated with the decline of nutrients (SOC, TN, Olsen-P) availability, which stimulates the proliferation of nutrient cycling-related bacteria and mixed-trophic fungi, endophytic fungi and ectomycorrhizal fungi, thus further satisfying the nutrient requirements of tea seedlings. Moreover, lower levels of polyphenols facilitated the growth of plant beneficial microorganisms (Bacillus, Mortierella, etc.) and suppressed pathogenic fungi (Pseudopestalotiopsis, etc.), creating a more balanced microbial community that is beneficial to plant health. Our study broadens the understanding of the ecological role of plant secondary metabolites and provides new insights into the sustainability of tea breeding.
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Affiliation(s)
- Dongmei Fan
- Department of Tea Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhumeng Zhao
- Department of Tea Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
| | - Yu Wang
- Department of Tea Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Junhui Ma
- Administration of Agriculture and Rural Affairs of Lishui, Lishui, China
| | - Xiaochang Wang
- Department of Tea Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Xiaochang Wang,
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Microbial Communities in Underground Gas Reservoirs Offer Promising Biotechnological Potential. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Securing new sources of renewable energy and achieving national self-sufficiency in natural gas have become increasingly important in recent times. The study described in this paper focuses on three geologically diverse underground gas reservoirs (UGS) that are the natural habitat of methane-producing archaea, as well as other microorganisms with which methanogens have various ecological relationships. The objective of this research was to describe the microbial metabolism of methane in these specific anoxic environments during the year. DNA sequencing analyses revealed the presence of different methanogenic communities and their metabolic potential in all sites studied. Hydrogenotrophic Methanobacterium sp. prevailed in Lobodice UGS, members of the hydrogenotrophic order Methanomicrobiales predominated in Dolní Dunajovice UGS and thermophilic hydrogenotrophic members of the Methanothermobacter sp. were prevalent in Tvrdonice UGS. Gas composition and isotope analyses were performed simultaneously. The results suggest that the biotechnological potential of UGS for biomethane production cannot be neglected.
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Macro-seepage based potential new hydrocarbon prospects in Assam-Arakan Basin, India. Sci Rep 2022; 12:2273. [PMID: 35145130 PMCID: PMC8831647 DOI: 10.1038/s41598-022-06045-6] [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: 04/23/2021] [Accepted: 01/04/2022] [Indexed: 11/20/2022] Open
Abstract
Active macro seepages of methane that occur in between the north bank of the Brahmaputra river and Himalayan foothill region of Assam Arakan Basin, India, indicate the presence of hydrocarbon accumulation in the subsurface, but the hydrocarbon prospects in this region are not well studied. We carried out an extensive field sampling, which included a total of 58 sediment core collections from an active gas seepage location and nearby areas at a depth of 2–2.5 m. Our sample locations are placed at 1 km intervals laterally. We performed laboratory investigations and mapped near-surface chemical alterations associated with active macro seepages and microseepages. The analysis of geochemical composition of hydrocarbon gases in the sediment indicates both the biogenic and thermogenic origins of seeped hydrocarbons. The stable isotope analysis of methane suggests the presence of thermogenic as well as mixed biogenic-thermogenic gases. The presence of such mixing of gases is caused by the secondary alteration processes during their migration through potential faults and fractures. The trace elements of the sediments show anomalous concentrations at different parts of the study area, with a wide range of concentrations for Ba (54 to 492 ppm), Cu (1–25 ppm), Cr (61–329 ppm), Ni (1–42 ppm), Pb (2–48 ppm), Th (2–32 ppm), U (4–39 ppm), V (19–133 ppm) and U (0.87–6.5 ppm). There are higher concentrations of adsorbed gases, trace elements, and microbes along the identified lineaments. Such higher concentration can be triggered by high hydrocarbon-oxidizing bacteria count, which is greater than 104 cfu/gm of soil of bacterial growth around the lineaments. We identified potential hydrocarbon prospects based on the macro and micro seepage analysis using integrated geological, geochemical and microbial techniques in the study area.
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Lee YY, Seo Y, Ha M, Lee J, Yang H, Cho KS. Evaluation of rhizoremediation and methane emission in diesel-contaminated soil cultivated with tall fescue (Festuca arundinacea). ENVIRONMENTAL RESEARCH 2021; 194:110606. [PMID: 33345896 DOI: 10.1016/j.envres.2020.110606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/24/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Rhizoremediation, CH4 emission, and bacterial community dynamics were evaluated in diesel-contaminated soil cultivated with tall fescue via a pot experiment. At the beginning of the experiment, total petroleum hydrocarbons (TPHs) removal efficiency was 30.2% in tall fescue-cultivated soil, which was significantly higher than that of unplanted soil (19.4%). However, when compost was added as a soil amendment, TPHs removal efficiency increased to 39.2% in tall fescue-cultivated soil. Interestingly, potential CH4 emissions were more affected by the initial diesel concentration than by compost addition or tall fescue planting. Specifically, the potential CH4 emission was approximately 3.8 times higher in the treatment with the highest initial diesel concentration (T-WC38) than that of the treatment with the lowest initial diesel concentration (T-WC5). Functional gene analysis revealed that TPHs removal had a linear correlation with the alkB/16S gene ratio, whereas potential CH4 emission had a linear correlation with pmoA gene copy numbers. Initial diesel concentrations in soil also affected bacterial community structures and the genera Rhizobium, Halothiobacillus, and Geobacter were found to be positively linked to diesel-contaminated soil rhizoremediation. Therefore, this study provides useful insights into the development of strategies to enhance rhizoremediation efficiency and CH4 emission mitigation in diesel-contaminated soils.
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Affiliation(s)
- Yun-Yeong Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Yoonjoo Seo
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Minyoung Ha
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jiho Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyoju Yang
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.
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Chen F, Zheng Y, Hou L, Niu Y, Gao D, An Z, Zhou J, Yin G, Dong H, Han P, Liang X, Liu M. Microbial abundance and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in estuarine and intertidal wetlands: Heterogeneity and driving factors. WATER RESEARCH 2021; 190:116737. [PMID: 33326895 DOI: 10.1016/j.watres.2020.116737] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is a crucial link between carbon and nitrogen cycles in estuarine and coastal ecosystems. However, the factors that affect the heterogeneous variability in n-DAMO microbial abundance and activity across estuarine and intertidal wetlands remain unclear. This study examined the spatiotemporal variations in n-DAMO microbial abundance and associated activity in different estuarine and intertidal habitats via quantitative PCR and 13C stable isotope experiments. The results showed that Candidatus 'Methylomirabilis oxyfera' (M. oxyfera)-like DAMO bacteria and Candidatus 'Methanoperedens nitroreducens' (M. nitroreducens)-like DAMO archaea cooccurred in estuarine and intertidal wetlands, with a relatively higher abundance of the M. oxyfera-like bacterial pmoA gene (4.0 × 106-7.6 × 107 copies g-1 dry sediment) than the M. nitroreducens-like archaeal mcrA gene (4.5 × 105-9.4 × 107 copies g-1 dry sediment). The abundance of the M. oxyfera-like bacterial pmoA gene was closely associated with sediment pH and ammonium (P<0.05), while no significant relationship was detected between M. nitroreducens-like archaeal mcrA gene abundance and the measured environmental parameters (P>0.05). High n-DAMO microbial activity was observed, which varied between 0.2 and 84.3 nmol 13CO2 g-1 dry sediment day-1 for nitrite-DAMO bacteria and between 0.4 and 32.6 nmol 13CO2 g-1 dry sediment day-1 for nitrate-DAMO archaea. The total n-DAMO potential tended to be higher in the warm season and in the upstream freshwater and low-salinity estuarine habitats and was significantly related to sediment pH, total organic carbon, Fe(II), and Fe(III) contents (P<0.05). In addition to acting as an important methane (CH4) sink, n-DAMO microbes had the potential to consume a substantial amount of reactive N in estuarine and intertidal environments, with estimated nitrogen elimination rates of 0.5-224.7 nmol N g-1 dry sediment day-1. Overall, our investigation reveals the distribution pattern and controlling factors of n-DAMO bioprocesses in estuarine and intertidal marshes and gains a better understanding of the coupling mechanisms between carbon and nitrogen cycles.
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Affiliation(s)
- Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Yuhui Niu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhirui An
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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12
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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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13
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Methane Derived Authigenic Carbonate (MDAC) Aragonite Cemented Quaternary Hardground from a Methane Cold Seep, Rathlin Basin, Northern Ireland: δ13C and δ18O Isotopes, Environment, Porosity and Permeability. GEOSCIENCES 2020. [DOI: 10.3390/geosciences10070255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A block of sandstone retrieved by divers from near Rathlin Island, Co. Antrim, Northern Ireland, represents an aragonite cemented sand formed during the Quaternary. Strongly negative δ13C of the aragonite cement (−50 to −60‰ δ13C) indicates that the hardground was formed by the anaerobic oxidation of methane (AOM), resulting in the formation of a methane-derived authigenic carbonate (MDAC) hardground. Such hardgrounds have previously been recorded as forming extensive pavements in deeper waters in the mid Irish Sea (e.g., Croker Carbonate Slabs), although the latter also contains high-magnesium calcite. Sand was initially deposited as part of a storm lag deposit, with a reworked bivalve and gastropod fauna. This sand was then colonised by a probable crustacean fauna, producing horizontal open dwelling burrows (Thalassinoides). After aragonite cementation, the hardground was colonised by boring bivalves, with slightly negatively elevated levels of δ13C. Finally, the hardground was colonised by an encrusting fauna (bryozoans, calcareous algae and serpulids), by then in warmer seas. Continued depleted levels of δ13C present within the encrusting fauna (−1 to −5‰ δ13C) indicate continued methane generation and seepage, which may still be active to the present day, and to the possibility of shallow gas reserves. The δ18O values change between macro-infauna vs. encrusters, indicating a warming in water temperature, reflecting glacial and post-glacial environments. The aragonite cemented sandstone has a highly variable porosity, with large vugs (open burrows and borings), smaller mouldic porosity within gastropods and bivalves and complex micro-porosity associated with acicular aragonite cements. Overall permeability was recorded at the 2.5 to 23 Darcies level, reflecting the highly variable vuggy porosity, although matrix permeability was around 100 mD and controlled by the MDAC fabric. Actual permeability will likely be controlled by the extent to which larger pores are interconnected. The sea around the Rathlin Island area contains a diverse fauna, which is worthy of future study in the context of cold seep and MDAC pavement formation.
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14
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Reid T, Droppo IG, Weisener CG. Tracking functional bacterial biomarkers in response to a gradient of contaminant exposure within a river continuum. WATER RESEARCH 2020; 168:115167. [PMID: 31639591 DOI: 10.1016/j.watres.2019.115167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/11/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
Within all aquatic environments, aside from the physical dispersal of dissolved and/or particulate phase contaminants, alteration from both biological and chemical processes are shown to change the chemistry of the parent compounds. Often these alterations can lead to secondary influences because of cooperative microbial processes (i.e. coupled respiratory pathways and/or energy and biodegradation cycles), complicating our understanding of the biological impact that these mobile compounds impose on ecosystem health. The McMurray Formation (MF) (the formation constituting the minable bituminous oil sands) is a natural, ongoing source of hydrocarbon-bound sediments to river ecosystems in the region (via terrestrial and aquatic erosion), providing a natural "mesocosm" to track and characterize the effects of these compounds on regional aquatic primary productivity. Here we characterize the natural, in-situ microbial response to increasing hydrocarbon exposure along a river continuum in the downstream direction. Using the Steepbank River (STB), suspended and bed sediment samples were collected at 3 sites from upstream to downstream, as the water flows into and through the MF. Samples were then analyzed for the active, in-situ gene expression of the microbial communities. Results from both suspended and bed sediments show clear and significant shifts in the microbial metabolic processes within each respective compartment, in response to the elevated polycyclic aromatic compound (PAC) concentrations. Specific genes likely responsible for hydrocarbon breakdown (Alkane Monooxygenase, Benzoyl-CoA Reductase etc.) experience elevated expression levels, while certain energy metabolism genes (nitrogen, sulfur, methane) reveal fundamental shifts in their pathway specificity, indicating an adaptation response in their basic energy metabolism. Expression from suspended sediments reveal subtle yet delayed metabolic response further downstream compared to bed sediments, indicative of the erosion and transport dynamics within a lotic system. These results provide insight into the use of novel clusters of gene biomarkers to track the active, in-situ microbial response of both emerging and legacy contaminants. Such information will be important in determining the best management strategies for the monitoring and assessment of aquatic health in both natural and contaminated ecosystems.
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Affiliation(s)
- T Reid
- Environment and Climate Change Canada, 867 Lakeshore Rd., Burlington, Ontario, L7S 1A1, Canada.
| | - I G Droppo
- Environment and Climate Change Canada, 867 Lakeshore Rd., Burlington, Ontario, L7S 1A1, Canada
| | - C G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, Ontario, N9B 3P4, Canada
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15
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Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments. mSystems 2019; 4:mSystems00091-18. [PMID: 30834326 PMCID: PMC6392090 DOI: 10.1128/msystems.00091-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022] Open
Abstract
Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction. Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages. IMPORTANCE Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.
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16
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Menéndez-Serra M, Triadó-Margarit X, Castañeda C, Herrero J, Casamayor EO. Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:343-353. [PMID: 30199680 DOI: 10.1016/j.scitotenv.2018.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Soil microbial communities (both Bacteria and Archaea) were studied after 16S rRNA genes massive sequencing in two hypersaline and gypsum-rich contrasted sites located in NE Spain. Soil microbial communities were also locally analysed according to environmental variables, including geological, physico-chemical, biogeochemically, and climatic data. Typical soil characteristics, climate data, and plant composition clearly split the two sites and major differences among the microbial communities for the areas were initially expected. Overall, high values of microbial species richness (up to 2300 taxa) and ecological diversity was detected in both sites. High genetic novelty levels were found mostly to environmental sequences, highlighting the high potential for microbiological studies. In contrast to the initial expectations, a substantial overlapping between Monegros and Gallocanta microbes was observed, indicating a high similarity despite of the geographical, botanical and environmental distances between sites, in agreement with both high dispersal and local selection inherent to the microbial world. The potential biogeochemical cycling showed small differences between sites, with presence of photosynthetic green and purple sulfur bacteria, cyanobacteria and aerobic and anaerobic chemolitotrophs. Potential for aerobic methane oxidation and anaerobic methanogenesis was observed in both sites, with predominance of potential nitrification mostly by ammonia-oxidizing archaea, nitrite oxidation and denitrification, and minor contribution for nitrate reduction and nitrate ammonification. The predicted functions based on the taxonomic composition showed high overlapping between the two studied regions, despite their difference in gypsum richness.
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Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Carmen Castañeda
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Juan Herrero
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain.
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17
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Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, Chen IMA, Kyrpides NC, Reddy TBK. Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res 2019; 47:D649-D659. [PMID: 30357420 PMCID: PMC6323969 DOI: 10.1093/nar/gky977] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022] Open
Abstract
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 33 415 Studies, 49 826 Biosamples, 313 324 Organisms, 215 881 Sequencing Projects and 174 454 Analysis Projects with a total of 541 metadata fields, of which 80 are based on controlled vocabulary (CV) terms. GOLD provides a user-friendly web interface to browse sequencing projects and launch advanced search tools across four classification levels. Users submit metadata on a wide range of Sequencing and Analysis Projects in GOLD before depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis. GOLD conforms with and supports the rules set by the Genomic Standards Consortium (GSC) Minimum Information standards. The current version of GOLD (v.7) has seen the number of projects and associated metadata increase exponentially over the years. This paper provides an update on the current status of GOLD and highlights the new features added over the last two years.
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Affiliation(s)
- Supratim Mukherjee
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Dimitri Stamatis
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jon Bertsch
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Galina Ovchinnikova
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Hema Y Katta
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alejandro Mojica
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - I-Min A Chen
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nikos C Kyrpides
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - TBK Reddy
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
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18
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Pavlik I, Gersl M, Bartos M, Ulmann V, Kaucka P, Caha J, Unc A, Hubelova D, Konecny O, Modra H. Nontuberculous mycobacteria in the environment of Hranice Abyss, the world's deepest flooded cave (Hranice karst, Czech Republic). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:23712-23724. [PMID: 29872987 DOI: 10.1007/s11356-018-2450-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Nontuberculous mycobacteria (NTM) are widely distributed in the environment. On one hand, they are opportunistic pathogens for humans and animals, and on the other hand, they are effective in biodegradation of some persistent pollutants. Following the recently recorded large abundance of NTM in extreme geothermal environments, the aim of the study was to ascertain the occurrence of NTM in the extreme environment of the water zone of the Hranice Abyss (HA). The HA mineral water is acidic, with large concentrations of free CO2, and bacterial slimes creating characteristic mucilaginous formations. Both culture and molecular methods were used to compare the mycobacterial diversity across the linked but distinct ecosystems of HA and the adjacent Zbrašov Aragonite Caves (ZAC) with consideration of their pathogenic relevance. Six slowly growing NTM species (M. arupense, M. avium, M. florentinum, M. gordonae, M. intracellulare) and two rapidly growing NTM species (M. mucogenicum, M. sediminis) were identified in the water and in the dry zones at both sites. Proteobacteria were dominant in all the samples from both the HA and the ZAC. The bacterial microbiomes of the HA mineral water and HA slime were similar, but both differed from the microbiome in the ZAC mineral water. Actinobacteria, a phylum containing mycobacteria, was identified in all the samples at low proportional abundance. The majority of the detected NTM species belong among environmental opportunistic pathogens.
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Affiliation(s)
- Ivo Pavlik
- Faculty of Regional Development and International Studies, Mendel University in Brno, tr. Generala Piky 7, 61300, Brno, Czech Republic
| | - Milan Gersl
- Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Milan Bartos
- Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Vit Ulmann
- Public Health Institute Ostrava, Partyzanske nam. 7, 702 00, Ostrava, Czech Republic
| | - Petra Kaucka
- Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1, 612 42, Brno, Czech Republic
| | - Jan Caha
- Faculty of Regional Development and International Studies, Mendel University in Brno, tr. Generala Piky 7, 61300, Brno, Czech Republic
| | - Adrian Unc
- School of Science and the Environment, Memorial University of Newfoundland, 20 University Drive, Corner Brook, A2H 5G4, Canada
| | - Dana Hubelova
- Faculty of Regional Development and International Studies, Mendel University in Brno, tr. Generala Piky 7, 61300, Brno, Czech Republic
| | - Ondrej Konecny
- Faculty of Regional Development and International Studies, Mendel University in Brno, tr. Generala Piky 7, 61300, Brno, Czech Republic
| | - Helena Modra
- Faculty of Regional Development and International Studies, Mendel University in Brno, tr. Generala Piky 7, 61300, Brno, Czech Republic.
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Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico. Sci Rep 2017; 7:16015. [PMID: 29167487 PMCID: PMC5700182 DOI: 10.1038/s41598-017-16375-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/10/2017] [Indexed: 11/18/2022] Open
Abstract
Oil and gas percolate profusely through the sediments of the Gulf of Mexico, leading to numerous seeps at the seafloor, where complex microbial, and sometimes animal communities flourish. Sediments from three areas (two cold seeps with contrasting hydrocarbon composition and a site outside any area of active seepage) of the Gulf of Mexico were investigated and compared. Consistent with the existence of a seep microbiome, a distinct microbial community was observed in seep areas compared to sediment from outside areas of active seepage. The microbial community from sediments without any influence from hydrocarbon seepage was characterized by Planctomycetes and the metabolic potential was consistent with detrital marine snow degradation. By contrast, in seep samples with methane as the principal hydrocarbon, methane oxidation by abundant members of ANME-1 was likely the predominant process. Seep samples characterized by fluids containing both methane and complex hydrocarbons, were characterized by abundant Chloroflexi (Anaerolinaceae) and deltaproteobacterial lineages and exhibited potential for complex hydrocarbon degradation. These different metabolic capacities suggested that microorganisms in cold seeps can potentially rely on other processes beyond methane oxidation and that the hydrocarbon composition of the seep fluids may be a critical factor structuring the seafloor microbial community composition and function.
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