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Ning Z, Sheng Y, Gan S, Guo C, Wang S, Cai P, Zhang M. Metagenomic and isotopic insights into carbon fixation by autotrophic microorganisms in a petroleum hydrocarbon impacted red clay aquifer. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124824. [PMID: 39197642 DOI: 10.1016/j.envpol.2024.124824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/14/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ13C of dissolved inorganic carbon (δ13C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers.
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Affiliation(s)
- Zhuo Ning
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China; Key Laboratory of Groundwater Remediation of Hebei Province & China Geological Survey, Zhengding, 050083, China
| | - Yizhi Sheng
- Frontiers Science Center for Deep-Time Digital Earth, Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Shuang Gan
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China; Key Laboratory of Groundwater Remediation of Hebei Province & China Geological Survey, Zhengding, 050083, China; Hefei University of Technology, Hefei, 230009, China
| | - Caijuan Guo
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China
| | - Shuaiwei Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China
| | - Pingping Cai
- School of Water Resources and Environment, Hebei GEO University, Shijiazhuang, 050061, China
| | - Min Zhang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China; Key Laboratory of Groundwater Remediation of Hebei Province & China Geological Survey, Zhengding, 050083, China.
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Xing W, Zhou G, Gao D, Zhang Z, Li L, Zheng W, Yao H. Carbon dioxide and weak magnetic field enhance iron-carbon micro-electrolysis combined autotrophic denitrification. BIORESOURCE TECHNOLOGY 2024; 406:131015. [PMID: 38906196 DOI: 10.1016/j.biortech.2024.131015] [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: 04/15/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Combining iron-carbon micro-electrolysis and autotrophic denitrification is promising for nitrate removal from wastewater. In this study, four continuous reactors were constructed using CO2 and weak magnetic field (WMF) to address challenges like iron passivation and pH stability. In the reactors with CO2 + WMF (10 and 35 mT), the increase in total nitrogen removal efficiency was significantly higher (96.2 ± 1.6 % and 94.1 ± 2.7 %, respectively) than that of the control (51.6 ± 2.7 %), and Fe3O4 converted to low-density FeO(OH) and FeCO3, preventing passivation film formation. The WMF application decreased the N2O emissions flux by 8.7 % and 20.5 %, respectively. With CO2 + WMF, the relative enzyme activity and abundance of denitrifying bacteria, especially unclassified_Rhodocyclaceae and Denitratisoma, increased. Thus, this study demonstrates that CO2 and WMF optimize the nitrate removal process, significantly enhancing removal efficiency, reducing greenhouse gas emissions, and improving process stability.
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Affiliation(s)
- Wei Xing
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Environment, Beijing Jiaotong University, Beijing 100044, PR China; Tangshan Research Institute of Beijing Jiaotong University, Hebei 063000, PR China.
| | - Guangxin Zhou
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Environment, Beijing Jiaotong University, Beijing 100044, PR China
| | - Daoqing Gao
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Environment, Beijing Jiaotong University, Beijing 100044, PR China; China Institute of Marine Technology and Economy, Beijing 100081, PR China
| | - Zexi Zhang
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Environment, Beijing Jiaotong University, Beijing 100044, PR China
| | - Longsheng Li
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Environment, Beijing Jiaotong University, Beijing 100044, PR China
| | - Weijia Zheng
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Environment, Beijing Jiaotong University, Beijing 100044, PR China
| | - Hong Yao
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Environment, Beijing Jiaotong University, Beijing 100044, PR China; Tangshan Research Institute of Beijing Jiaotong University, Hebei 063000, PR China.
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Gan S, Ning Z, Wang S, Sun W, Xu Z, Di H, Ti J, Guo C, Zhou Y, He Z, Kong S, Zhang M. Identification of carbon fixation microorganisms and pathways in an aquifer contaminated with long-chain petroleum hydrocarbons. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e11078. [PMID: 39087861 DOI: 10.1002/wer.11078] [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: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
Petroleum hydrocarbons (PHCs) can be biodegraded into CO2, and PHC-contaminated aquifers are always deemed as carbon sources. Fortunately, some carbon fixation microorganisms have been found in PHC-contaminated sites. However, most of the studies are related to volatile short-chain PHC, and few studies focus on long-chain PHC-contaminated sites. To reveal the carbon fixation microorganisms in these sites, in the study, a long-chain PHC polluted site in North China was selected. Through hydrochemical and metagenomics analysis, the structure and capacity of carbon fixing microorganisms in the site were revealed. Results showed that there were many kinds of carbon fixed microorganisms that were identified such as Flavobacterium, Pseudomonas. HP/4HB, rTCA, and DC/4HB cycles were dominated carbon fixation pathways. The long-chain PHC were weakly correlated with carbon fixation microorganisms, but it may stimulate the growth of some carbon fixation microorganisms, such as microorganisms involved in rTCA cycle. PRACTITIONER POINTS: The microorganisms with carbon fixation gene exist in the aquifer contaminated by long-chain petroleum hydrocarbon. Microorganisms that have the ability to degrade petroleum also have the ability to carbon fixation. Long-chain petroleum hydrocarbon may promote the growth of carbon fixation microorganisms.
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Affiliation(s)
- Shuang Gan
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Zhuo Ning
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Shuaiwei Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Weichao Sun
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Zhe Xu
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - He Di
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Jinjin Ti
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Caijuan Guo
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
| | - Yahong Zhou
- School of water resources and environment, Hebei GEO University, Shijiazhuang, China
| | - Ze He
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Siyu Kong
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
| | - Min Zhang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, China
- Key Laboratory of Groundwater Remediation of Hebei Province and China Geological Survey, Zhengding, China
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Ning Z, Cai P, Zhang M. Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer. ENVIRONMENTAL RESEARCH 2024; 247:118289. [PMID: 38266905 DOI: 10.1016/j.envres.2024.118289] [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: 07/07/2023] [Revised: 12/23/2023] [Accepted: 01/20/2024] [Indexed: 01/26/2024]
Abstract
As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.
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Affiliation(s)
- Zhuo Ning
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China; Key Laboratory of Groundwater Remediation of Hebei Province & China Geological Survey, China.
| | - Pingping Cai
- School of Water Resources and Environment, Hebei GEO University, China.
| | - Min Zhang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China; Key Laboratory of Groundwater Remediation of Hebei Province & China Geological Survey, China.
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Li J, Xie N, Feng C, Wang C, Huang R, Tao Q, Tang X, Wu Y, Luo Y, Li Q, Li B. Pore size and organic carbon of biochar limit the carbon sequestration potential of Bacillus cereus SR. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 274:116229. [PMID: 38508101 DOI: 10.1016/j.ecoenv.2024.116229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
Carbon-fixing functional strain-loaded biochar may have significant potential in carbon sequestration given the global warming situation. The carbon-fixing functional strain Bacillus cereus SR was loaded onto rice straw biochar pyrolyzed at different temperatures with the anticipation of clarifying the carbon sequestration performance of this strain on biochar and the interaction effects with biochar. During the culture period, the content of dissolved organic carbon (DOC), easily oxidizable organic carbon, and microbial biomass carbon in biochar changed. This finding indicated that B. cereus SR utilized organic carbon for survival and enhanced carbon sequestration on biochar to increase organic carbon, manifested by changes in CO2 emissions and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) enzyme activity. Linear regression analysis showed that the strain was likely to consume DOC on 300 °C biochar, although the Rubisco enzyme activity was higher. In contrast, the strain had a higher carbon sequestration potential on 500 °C biochar. Correlation analysis showed that Rubisco enzyme activity was controlled by the physical structure of the biochar. Our results highlight the differences in the survival mode and carbon sequestration potential of B. cereus SR on biochar pyrolyzed at different temperatures.
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Affiliation(s)
- Jie Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Ningyi Xie
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Changchun Feng
- China National Tobacco Corporation Sichuan, Chengdu 610041, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Rong Huang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyan Tang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yingjie Wu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Youlin Luo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiquan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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Wang Y, Huang Y, Zeng Q, Liu D, An S. Biogeographic distribution of autotrophic bacteria was more affected by precipitation than by soil properties in an arid area. Front Microbiol 2023; 14:1303469. [PMID: 38173682 PMCID: PMC10761425 DOI: 10.3389/fmicb.2023.1303469] [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: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction Autotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood. Methods Herein, we conducted a 391-km north to south transect (mean annual precipitation <600 mm) survey in the Loess Plateau of China, to investigate the biogeographic distributions of autotrophic bacteria (RubisCO cbbL and cbbM genes) and the environmental drivers across different latitude sites with clear vegetational and climatic gradients. Results and discussion The soils in northern region with lower precipitation are dominated by grassland/forest, which is typically separated from the soils in southern region with higher precipitation. The community structure of autotrophic bacterial cbbL and cbbM genes generally differed between the soils in the southern and northern Loess Plateau, suggesting that precipitation and its related land use practices/ecosystem types, rather than local soil properties, are more important in shaping the soil autotrophic microorganisms. The cbbL-containing generalist OTUs were almost equally abundant across the northern and southern Loess Plateau, while the cbbM-containing bacterial taxa were more prevalent in the low precipitation northern region. Such differences indicate differentiate distribution patterns of cbbM- and cbbL-containing bacteria across the north to south transect. Our results suggest that the community composition and the differentiate distributions of soil cbbL- and cbbM-containing bacterial communities depend on precipitation and the related ecosystem types in the north to south transect in the Loess Plateau of China.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Yimei Huang
- College of Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Quanchao Zeng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, Shaanxi Province, China
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Xu X, Van Eygen G, Molina-Fernández C, Nikolaeva D, Depasse Y, Chergaoui S, Hartanto Y, Van der Bruggen B, Coutinho JA, Buekenhoudt A, Luis P. Evaluation of task-specific ionic liquids applied in pervaporation membranes: Experimental and COSMO-RS studies. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2023.121350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Tang H, Wen L, Shi L, Li C, Cheng K, Li W, Xiao X. Effects of Long-Term Fertilizer Practices on Rhizosphere Soil Autotrophic CO 2-Fixing Bacteria under Double Rice Ecosystem in Southern China. J Microbiol Biotechnol 2022; 32:1292-1298. [PMID: 36224752 PMCID: PMC9668096 DOI: 10.4014/jmb.2205.05055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022]
Abstract
Soil autotrophic bacterial communities play a significant role in the soil carbon (C) cycle in paddy fields, but little is known about how rhizosphere soil microorganisms respond to different long-term (35 years) fertilization practices under double rice cropping ecosystems in southern China. Here, we investigated the variation characteristics of rhizosphere soil RubisCO gene cbbL in the double rice ecosystems of in southern China where such fertilization practices are used. For this experiment we set up the following fertilizer regime: without any fertilizer input as a control (CK), inorganic fertilizer (MF), straw returning (RF), and organic and inorganic fertilizer (OM). We found that abundances of cbbL, 16S rRNA genes and RubisCO activity in rhizosphere soil with OM, RF and MF treatments were significantly higher than that of CK treatment. The abundances of cbbL and 16S rRNA genes in rhizosphere soil with OM treatment were 5.46 and 3.64 times higher than that of CK treatment, respectively. Rhizosphere soil RubisCO activity with OM and RF treatments increased by 50.56 and 45.22%, compared to CK treatment. Shannon and Chao1 indices for rhizosphere soil cbbL libraries with RF and OM treatments increased by 44.28, 28.56, 29.60, and 23.13% compared to CK treatment. Rhizosphere soil cbbL sequences with MF, RF and OM treatments mainly belonged to Variovorax paradoxus, uncultured proteobacterium, Ralstonia pickettii, Thermononospora curvata, and Azoarcus sp.KH33C. Meanwhile, cbbL-carrying bacterial composition was obviously influenced by soil bulk density, rhizosphere soil dissolved organic C, soil organic C, and microbial biomass C contents. Fertilizer practices were the principal factor influencing rhizosphere soil cbbL-carrying bacterial communities. These results showed that rhizosphere soil autotrophic bacterial communities were significantly changed under conditions of different long-term fertilization practices Therefore, increasing rhizosphere soil autotrophic bacteria community with crop residue and organic manure practices was found to be beneficial for management of double rice ecosystems in southern China.
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Affiliation(s)
- Haiming Tang
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China,Corresponding authors H. Tang Phone: +86 731 84696102 Fax: +86 731 84691581 E-mail:
| | - Li Wen
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Lihong Shi
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China,
L. Shi E-mail:
| | - Chao Li
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Kaikai Cheng
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Weiyan Li
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
| | - Xiaoping Xiao
- Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China
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Wang X, Li W, Cheng A, Shen T, Xiao Y, Zhu M, Pan X, Yu L. Community characteristics of autotrophic CO 2-fixing bacteria in karst wetland groundwaters with different nitrogen levels. Front Microbiol 2022; 13:949208. [PMID: 36046022 PMCID: PMC9421164 DOI: 10.3389/fmicb.2022.949208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Karst wetlands are important in the global carbon and nitrogen cycles as well as in security of water resources. Huixian wetland (Guilin) is the largest natural karst wetland in China. In recent years, groundwater nitrogen pollution has increasingly affected the wetland ecosystem integrity due to anthropogenic activities. In this study, it was hypothesized that autotrophic microbial diversity is impacted with the advent of pollution, adversely affecting autotrophs in the carbon and nitrogen cycles. Autotrophic microbes have important roles in abating groundwater nitrogen pollution. Thus, it is of great significance to study the characteristics of autotrophic bacterial communities and their responses to environmental parameters in nitrogen-polluted karst groundwaters. The abundances of the Calvin-Benson cycle functional genes cbbL and cbbM as well as the autotrophic CO2-fixing bacterial communities were characterized in the karst groundwater samples with different levels of nitrogen pollution. The cbbM gene was generally more abundant than the cbbL gene in the groundwater samples. The cbbL gene abundance was significantly positively correlated with dissolved inorganic nitrogen (DIN) concentration (P < 0.01). In the autotrophic CO2-fixing bacterial communities, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were predominant. At the genus level, Rubrivivax and Methylibium were the dominant cbbL gene containing genera, while Halothiobacillus and Endothiovibrio were the dominant genera for the cbbM gene. The abundance of autotrophic CO2-fixing bacterial communities increased but their diversity decreased with the inflow of nitrogen into the karst groundwater system. The community structure of autotrophic CO2-fixing bacteria in the groundwaters was also significantly affected by environmental factors such as the carbonic anhydrase (CA) activity, dissolved inorganic carbon (DIC) concentration, temperature, and oxidation-reduction potential (ORP). Nitrogen inflow significantly changed the characteristics of autotrophic CO2-fixing bacterial communities in the karst groundwaters. Some key genera such as Nitrosospira and Thiobacillus were clearly abundant in the karst groundwaters with high nitrogen levels. Their respective roles in nitrification and denitrification impact nitrogen removal in this ecosystem. The findings in this study provide an important reference for biological abatement of nitrogen pollution in the karst groundwater system.
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Affiliation(s)
- Xiayu Wang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Li
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Aoqi Cheng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Taiming Shen
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, China
| | - Yutian Xiao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Min Zhu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaodong Pan
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, China
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Haiming T, Chao L, Lihong S, Kaikai C, Li W, Weiyan L, Xiaoping X. Effects of different short-term tillage managements on rhizosphere soil autotrophic CO 2 -fixing bacteria in a double-cropping rice paddy field. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:245-253. [PMID: 35019234 DOI: 10.1111/1758-2229.13044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/08/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Soil autotrophic bacteria community plays an important role in carbon (C) cycling process in soil, but there is still limited information about how the rhizosphere soil microbe that drives this process respond to combined application of tillage with crop residue incorporation managements under a double-cropping rice (Oryza sativa L.) paddy field in southern China. Therefore, the 6-years short-term tillage treatment on rhizosphere soil autotrophic bacteria community [RubisCO gene (cbbL)] under the double-cropping rice paddy field in southern China was studied using the high-throughput sequencing method in the present article. The field experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that abundance, composition and activity of rhizosphere soil cbbL-carrying bacteria were obviously influenced by application of different tillage treatments. The rhizosphere soil abundant cbbL and 16S rRNA genes as well as RubisCO activity with CT, RT and NT treatments were higher than that of RTO treatment. The cbbL sequences in rhizosphere soil with CT, RT and NT treatments mainly included Azoarcus_sp._KH33C, Ralstonia_pickettii, Thermomonospora_curvata, Variovorax_paradoxus and uncultured_proteobacterium. Meanwhile, the results indicated that cbbL-carrying bacterial composition was significantly affected by soil organic carbon, microbial biomass carbon, dissolved organic carbon contents and soil bulk density. There had an obvious difference in characteristics of rhizosphere soil autotrophic bacteria community between CT, RT, NT treatments and RTO treatment. Therefore, it was a beneficial practice for improving rhizosphere soil autotrophic bacteria community in the double-cropping rice paddy field in southern China by combined application of tillage with crop residue incorporation practices.
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Affiliation(s)
- Tang Haiming
- Hunan Soil and Fertilizer Institute, Changsha, 410125, China
| | - Li Chao
- Hunan Soil and Fertilizer Institute, Changsha, 410125, China
| | - Shi Lihong
- Hunan Soil and Fertilizer Institute, Changsha, 410125, China
| | - Cheng Kaikai
- Hunan Soil and Fertilizer Institute, Changsha, 410125, China
| | - Wen Li
- Hunan Soil and Fertilizer Institute, Changsha, 410125, China
| | - Li Weiyan
- Hunan Soil and Fertilizer Institute, Changsha, 410125, China
| | - Xiao Xiaoping
- Hunan Soil and Fertilizer Institute, Changsha, 410125, China
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11
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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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12
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Liu Z, Lin W, Li Q, Rong Q, Zu H, Sang M. Separation of dimethyl carbonate/methanol azeotropic mixture by pervaporation with dealcoholized room temperature-vulcanized silicone rubber/nanosilica hybrid active layer. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.116926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Zhao Y, Liu P, Rui J, Cheng L, Wang Q, Liu X, Yuan Q. Dark carbon fixation and chemolithotrophic microbial community in surface sediments of the cascade reservoirs, Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134316. [PMID: 31783464 DOI: 10.1016/j.scitotenv.2019.134316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Dark carbon fixation (DCF) by chemolithotrophic microbes can make considerable contribution to inorganic carbon fixation in aquatic ecosystems. However, little is known about the importance and diversity of chemolithotrophic microbes in cascade reservoir sediments. In this study, we determined the potential DCF rates of sediments of three cascade reservoirs in Wujiang River basin by carbon isotopic labeling. The results showed that the DCF rates of the surface sediments ranged from 1.5 to 14.7 mmol C m-2 d-1. The ratio of DCF to mineralization rate of sediment organic matter of surface sediment was between 11.6%~60.9%. High-throughput sequencing analysis of cbbL and cbbM genes involved in Calvin Benson Cycle indicated that cbbL-carrying CO2-assimilating bacteria included diverse functional groups, while cbbM type was mostly involved in sulfur oxidation. The sediments of Hongfeng (HF) reservoir, which has much longer hydraulic residence time (HRT) and locates in most upstream of a major tributary of Wujiang River, have substantially higher DCF rates. The cbbL and cbbM communities in HF were dominated by sulfur oxidizing bacteria, and were largely different from that in the other two reservoirs. Our results suggested that chemolithotrophy plays an important role in carbon cycling of sediments in cascade reservoir. Meanwhile, HRT and relative location of cascade reservoirs are the key control factors of both DCF and composition of autotrophic microbial communities in cascade reservoir sediments.
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Affiliation(s)
- Yuan Zhao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Liu
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Junpeng Rui
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, China
| | - Qian Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
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14
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Cai P, Ning Z, Zhang N, Zhang M, Guo C, Niu M, Shi J. Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis. Microorganisms 2019; 7:microorganisms7100412. [PMID: 31581560 PMCID: PMC6843334 DOI: 10.3390/microorganisms7100412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/06/2019] [Accepted: 09/25/2019] [Indexed: 11/16/2022] Open
Abstract
In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.
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Affiliation(s)
- Pingping Cai
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
- School of Resources and Environmental Engineering, HeFei University of Technology, Hefei 230009, China.
| | - Zhuo Ning
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
- Key Laboratory of Groundwater Remediation of Hebei Province, Zhengding 050083, China.
| | - Ningning Zhang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China.
| | - Min Zhang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
| | - Caijuan Guo
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
| | - Manlan Niu
- School of Resources and Environmental Engineering, HeFei University of Technology, Hefei 230009, China.
| | - Jiansheng Shi
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
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15
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Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments. ISME JOURNAL 2019; 13:2475-2488. [PMID: 31182769 DOI: 10.1038/s41396-019-0439-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022]
Abstract
Almost all the inorganic carbon on Earth is converted into biomass via the Calvin-Benson-Bassham (CBB) cycle. Here, the central carboxylation reaction is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which can be found in numerous primary producers including plants, algae, cyanobacteria, and many autotrophic bacteria. Although RubisCO possesses a crucial role in global biomass production, it is not a perfect catalyst. Therefore, research interest persists on accessing the full potential of yet unexplored RubisCOs. We recently developed an activity-based screen suited to seek active recombinant RubisCOs from the environment-independent of the native host's culturability. Here, we applied this screen to twenty pre-selected genomic fosmid clones from six cultured proteobacteria to demonstrate that a broad range of phylogenetically distinct RubisCOs can be targeted. We then screened 12,500 metagenomic fosmid clones from six distinct hydrothermal vents and identified forty active RubisCOs. Additional sequence-based screening uncovered eight further RubisCOs, which could then also be detected by a modified version of the screen. Seven were active form III RubisCOs from yet uncultured Archaea. This indicates the potential of the activity-based screen to detect RubisCO enzymes even from organisms that would not be expected to be targeted.
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16
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Kumar S, Herrmann M, Blohm A, Hilke I, Frosch T, Trumbore SE, Küsel K. Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiol Ecol 2018; 94:5056153. [DOI: 10.1093/femsec/fiy141] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/18/2018] [Indexed: 01/17/2023] Open
Affiliation(s)
- Swatantar Kumar
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Annika Blohm
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, D-07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Torsten Frosch
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, D-07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Albert-Einstein-Strasse 6, D-07745, Jena, Germany
| | - Susan E Trumbore
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Strasse 10, D-07745 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
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17
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Alfreider A, Baumer A, Bogensperger T, Posch T, Salcher MM, Summerer M. CO 2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs. Environ Microbiol 2017; 19:2754-2768. [PMID: 28474482 PMCID: PMC5619642 DOI: 10.1111/1462-2920.13786] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 11/23/2022]
Abstract
While mechanisms of different carbon dioxide (CO2) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO2 fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin-Benson-Bassham (CBB) cycle, the reductive tricarboxylic acid (rTCA) cycle, and the recently discovered archaeal 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) pathway. Eleven primer sets were used to amplify and sequence genes coding for selected key enzymes in the three pathways. Whereas the CBB pathway with different forms of RubisCO (IA, IC and II) was ubiquitous and related to diverse bacterial taxa, encompassing a wide range of potential physiologies, the rTCA cycle in Epsilonproteobacteria and Chloribi was exclusively detected in anoxic water layers. Nitrifiying Nitrosospira and Thaumarchaeota, using the rTCA and HP/HB cycle respectively, are important residents in the aphotic and (micro-)oxic zone of deep lakes. Both taxa were of minor importance in surface waters and in smaller lakes characterized by an anoxic hypolimnion. Overall, this study provides a first insight on how different CO2 fixation strategies and chemical gradients in lakes are associated to the distribution of chemoautotrophic prokaryotes with different functional traits.
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Affiliation(s)
- Albin Alfreider
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andreas Baumer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | | | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Michaela M Salcher
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.,Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Monika Summerer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
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18
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Seston SL, Beinart RA, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ. Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes. Front Microbiol 2016; 7:1074. [PMID: 27486438 PMCID: PMC4949241 DOI: 10.3389/fmicb.2016.01074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 12/26/2022] Open
Abstract
Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.
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Affiliation(s)
| | - Roxanne A Beinart
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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19
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Herrmann M, Rusznyák A, Akob DM, Schulze I, Opitz S, Totsche KU, Küsel K. Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl Environ Microbiol 2015; 81:2384-94. [PMID: 25616797 PMCID: PMC4357952 DOI: 10.1128/aem.03269-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/17/2015] [Indexed: 11/20/2022] Open
Abstract
The traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed-upper and lower-limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO2 via the Calvin cycle, with abundances of cbbM and cbbL genes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 10(3) to 6 × 10(6) genes liter(-1) over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO2-assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO2 fixation in environments with strong oxygen and CO2 fluctuations. The genera Sulfuricella and Nitrosomonas were represented by read fractions of up to 78 and 33%, respectively, within the cbbM and cbbL transcript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO2 fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds.
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Affiliation(s)
- Martina Herrmann
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Anna Rusznyák
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Denise M Akob
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany U.S. Geological Survey, Reston, Virginia, USA
| | - Isabel Schulze
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Sebastian Opitz
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Uwe Totsche
- Department of Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, 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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20
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Liu JF, Sun XB, Yang GC, Mbadinga SM, Gu JD, Mu BZ. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration. Front Microbiol 2015; 6:236. [PMID: 25873911 PMCID: PMC4379918 DOI: 10.3389/fmicb.2015.00236] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.
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Affiliation(s)
- Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Xiao-Bo Sun
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Guang-Chao Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, University of Hong Kong Hong Kong, China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology Shanghai, China
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21
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Yousuf B, Kumar R, Mishra A, Jha B. Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities. PLoS One 2014; 9:e107025. [PMID: 25225969 PMCID: PMC4167329 DOI: 10.1371/journal.pone.0107025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/07/2014] [Indexed: 11/23/2022] Open
Abstract
Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO2 concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.
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Affiliation(s)
- Basit Yousuf
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - Raghawendra Kumar
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - Avinash Mishra
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
- * E-mail: (AM); (BJ)
| | - Bhavanath Jha
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi, India
- * E-mail: (AM); (BJ)
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22
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Xiao KQ, Bao P, Bao QL, Jia Y, Huang FY, Su JQ, Zhu YG. Quantitative analyses of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit genes (cbbL) in typical paddy soils. FEMS Microbiol Ecol 2013; 87:89-101. [DOI: 10.1111/1574-6941.12193] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ke-Qing Xiao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Peng Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Qiong-Li Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Yan Jia
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Fu-Yi Huang
- University of Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
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Wu X, Ge T, Yuan H, Li B, Zhu H, Zhou P, Sui F, O’Donnell AG, Wu J. Changes in bacterial CO2 fixation with depth in agricultural soils. Appl Microbiol Biotechnol 2013; 98:2309-19. [DOI: 10.1007/s00253-013-5179-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/04/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
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Application of targeted metagenomics to explore abundance and diversity of CO₂-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea. Gene 2012; 506:18-24. [PMID: 22766402 DOI: 10.1016/j.gene.2012.06.083] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 06/25/2012] [Indexed: 11/23/2022]
Abstract
Sequestration of CO(2) by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO(2). Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed <95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real-time PCR (qRT PCR), was 9.38 ± 0.75 × 10(7) and 5.43 ± 0.79 × 10(8) (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO(2)-fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management.
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