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Zhou J, Zeng X, Shi J, Liu S, Zhao X, Zhang J, Li W, Xi Y, Wang S, Wang X, Jia Y. Aerobic Se(IV) reducing bacteria and their reducing characteristics in estuarine sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173680. [PMID: 38844212 DOI: 10.1016/j.scitotenv.2024.173680] [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: 03/09/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
Microorganisms play a critical role in the biogeochemical cycling of selenium in natural ecosystems, particularly in reducing selenite (Se(IV)) to element selenium (Se(0)) which reduces its mobility and bioavailability. However, Se(IV)-reducing bacteria and their reducing characteristics in estuarine sediments remain inadequately understood. In this study, the reduction of Se(IV) was confirmed to be microbially driven through the cultivation of a mixture of estuarine sediment and Se(IV) under aerobic conditions. Community analysis indicates that Bacillus was primarily involved in the reduction of Se(IV). A strain with high salt tolerance (7.5 % NaCl) and Se(IV) resistance (up to 200 mM), Bacillus cereus SD1, was isolated from an estuarine sediment. The reduction of Se(IV) occurred concomitantly with the onset of microbial growth, and reduction capacity increased approximately 5-fold by adjusting the pH. In addition, Se(IV) reduction in Bacillus cereus SD1 was significantly inhibited by sulfite, and the key enzyme activity tests revealed the possible presence of a sulfite reductase-mediated Se(IV) reduction pathway. These research findings provide new insights into the bioreducing characteristics and the biogeochemical cycling of selenium in estuarine environments.
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Affiliation(s)
- Jiaxing Zhou
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiangfeng Zeng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China.
| | - Junyi Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China
| | - Sijia Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China
| | - Xiaoming Zhao
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China
| | - Jiaxi Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China
| | - Weiming Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China
| | - Yimei Xi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China
| | - Shaofeng Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, PR China
| | - Xin Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China
| | - Yongfeng Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, PR China.
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Li Y, Wang J, Li E, Yang X, Yang J. Shifts in Microbial Community Structure and Co-occurrence Network along a Wide Soil Salinity Gradient. Microorganisms 2024; 12:1268. [PMID: 39065037 PMCID: PMC11278679 DOI: 10.3390/microorganisms12071268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
The response of microbiomes to salinity has been clarified in different geographic scales or ecosystems. However, how soil microbial community structure and interaction respond to salinity across wide salinity range and climatic region is still unclearly resolved. To address this issue, we examined the microbial community's composition in saline soils from two climatic regions (coastal wetland and arid desert). Our research confirms that soil salinity had a negative effect on soil nutrient content. Salinity decreased the relative abundance of bacteria, but increased archaea abundance, leading to the shifts from bacteria dominant community to archaea dominant community. Low-water medium-salinity soil (LWMS) had the most complex archaeal community network, whereas for bacteria, the most complex bacterial community network was observed in low-water high-salinity soils (LWHS). Key microbial taxa differed in three salinity gradients. Salinity, soil water content, pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors for the composition of archaeal and bacterial community. Salinity directly affected archaeal community, but indirectly influenced bacteria community through SOC; pH affected archaeal community indirectly through TN, but directly affected bacterial community. Our study suggests that soil salinity dramatically influences diversity, composition, and interactions within the microbial community.
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Affiliation(s)
- Yan Li
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
| | - Juan Wang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
- Chengdu Institute of Biology, Chinese Academy Sciences, Chengdu 610042, China
| | - Eryang Li
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
| | - Xiaodong Yang
- Department of Geography & Spatial Information Technology, Ningbo University, Ningbo 315211, China
| | - Jianjun Yang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China; (Y.L.)
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830017, China
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Li Y, Si Y, Sun Z, Hu X, Shi Z, Li Y, Wu H. Simulated nitrogen load promoted mineralization of N2P1 compounds and accumulation of N4S2 compounds in soil dissolved organic matter in a typical subtropical estuarine marsh. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172107. [PMID: 38575015 DOI: 10.1016/j.scitotenv.2024.172107] [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: 01/05/2024] [Revised: 03/17/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
Soil dissolved organic matter (DOM) is the most reactive pool in estuarine marshes, playing an important role in the biogeochemical processes of biogenetic elements. To investigate the impacts of enhanced nitrogen (N) load on DOM molecular composition and its interactions with microbes in typical Cyperus malaccensis mashes of the Min River estuary, a field N load experiment with four N levels (0, 37.50, 50 and 100 g exogenous N m-2 yr-1, respectively; applied monthly for a total of seven months) was performed. DOM molecular composition was characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), the microbial community compositions (MCC, including fungi and bacteria) were determined by high-throughput sequencing technique, and their relationships were presented by co-occurrence network analysis. The results indicated that enhanced N load had significant impacts on soil DOM molecular composition, with N/C and P/C of DOM decreasing but S/C increasing markedly. Meanwhile, enhanced N load decreased the percentages of N2P1 compounds (primarily lipids) but increased those of N4S2 compounds (mainly lignins and lipids). The relative abundances of lignins significantly increased with increasing N load levels, whereas the proportions of lipids decreased. The abundance of N2P1 and N4S2 compounds was primarily positively correlated with eutrophic and oligotrophic microorganisms, respectively. Therefore, mineralization of N2P1 compounds might act as a source to replenish inorganic P, while enrichment of N4S2 compounds may make great contribution to organic S accumulation. Overall, enhanced N load promoted P depletion and S enrichment via altering plant growth, litter decomposition and MCC.
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Affiliation(s)
- Yajin Li
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, People's Republic of China; Key Laboratory of Humid Subtropical Eco-Geographical Process (Fujian Normal University), Ministry of Education, Fuzhou 350117, People's Republic of China
| | - Youtao Si
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, People's Republic of China; Key Laboratory of Humid Subtropical Eco-Geographical Process (Fujian Normal University), Ministry of Education, Fuzhou 350117, People's Republic of China; Institute of Geography, Fujian Normal University, Fuzhou 350117, People's Republic of China.
| | - Zhigao Sun
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, People's Republic of China; Key Laboratory of Humid Subtropical Eco-Geographical Process (Fujian Normal University), Ministry of Education, Fuzhou 350117, People's Republic of China; Institute of Geography, Fujian Normal University, Fuzhou 350117, People's Republic of China.
| | - Xingyun Hu
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, People's Republic of China; Key Laboratory of Humid Subtropical Eco-Geographical Process (Fujian Normal University), Ministry of Education, Fuzhou 350117, People's Republic of China
| | - Zixiang Shi
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, People's Republic of China; Key Laboratory of Humid Subtropical Eco-Geographical Process (Fujian Normal University), Ministry of Education, Fuzhou 350117, People's Republic of China
| | - Yanzhe Li
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, People's Republic of China; Key Laboratory of Humid Subtropical Eco-Geographical Process (Fujian Normal University), Ministry of Education, Fuzhou 350117, People's Republic of China
| | - Huihui Wu
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, People's Republic of China; Key Laboratory of Humid Subtropical Eco-Geographical Process (Fujian Normal University), Ministry of Education, Fuzhou 350117, People's Republic of China
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Rasmussen AN, Francis CA. Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay. THE ISME JOURNAL 2024; 18:wrae148. [PMID: 39077992 PMCID: PMC11334935 DOI: 10.1093/ismejo/wrae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/24/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024]
Abstract
Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.
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Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
- Oceans Department, Stanford University, Stanford, CA 94305, United States
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Zhou Y, Wang Y, Prangishvili D, Krupovic M. Exploring the Archaeal Virosphere by Metagenomics. Methods Mol Biol 2024; 2732:1-22. [PMID: 38060114 DOI: 10.1007/978-1-0716-3515-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
During the past decade, environmental research has demonstrated that archaea are abundant and widespread in nature and play important ecological roles at a global scale. Currently, however, the majority of archaeal lineages cannot be cultivated under laboratory conditions and are known exclusively or nearly exclusively through metagenomics. A similar trend extends to the archaeal virosphere, where isolated representatives are available for a handful of model archaeal virus-host systems. Viral metagenomics provides an alternative way to circumvent the limitations of culture-based virus discovery and offers insight into the diversity, distribution, and environmental impact of uncultured archaeal viruses. Presently, metagenomics approaches have been successfully applied to explore the viromes associated with various lineages of extremophilic and mesophilic archaea, including Asgard archaea (Asgardarchaeota), ANME-1 archaea (Methanophagales), thaumarchaea (Nitrososphaeria), altiarchaea (Altiarchaeota), and marine group II archaea (Poseidoniales). Here, we provide an overview of methods widely used in archaeal virus metagenomics, covering metavirome preparation, genome annotation, phylogenetic and phylogenomic analyses, and archaeal host assignment. We hope that this summary will contribute to further exploration and characterization of the enigmatic archaeal virome lurking in diverse environments.
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Affiliation(s)
- Yifan Zhou
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - David Prangishvili
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France.
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Kumar Chaudhary D, Bajagain R, Seo D, Hong Y, Han S. Depth-dependent microbial communities potentially mediating mercury methylation and various geochemical processes in anthropogenically affected sediments. ENVIRONMENTAL RESEARCH 2023; 237:116888. [PMID: 37586452 DOI: 10.1016/j.envres.2023.116888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Metal contamination and other geochemical alterations affect microbial composition and functional activities, disturbing natural biogeochemical cycles. Therefore, it is essential to understand the influences of multi-metal and geochemical interactions on microbial communities. This work investigated the distributions of total mercury (THg), methylmercury (MeHg), and trace metals in the anthropogenically affected sediment. The microbial communities and functional genes profiles were further determined to explore their association with Hg-methylation and geochemical features. The levels of THg and MeHg in sediment cores ranged between 10 and 40 mg/kg and 0.01-0.16 mg/kg, respectively, with an increasing trend toward bottom horizons. The major metals present at all depths were Al, Fe, Mn, and Zn. The enrichment and contamination indices confirmed that the trace metals were highly enriched in the anthropogenically affected sediment. Various functional genes were detected in all strata, indicating the presence of active microbial metabolic processes. The microbial community profiles revealed that the phyla Proteobacteria, Bacteroidetes, Bathyarchaeota, and Euryarchaeota, and the genera Thauera, Woeseia, Methanomethylovorans, and Methanosarcina were the dominant microbes. Correlating major taxa with geochemical variables inferred that sediment geochemistry substantially affects microbial community and biogeochemical cycles. Furthermore, archaeal methanogens and the bacterial phyla Chloroflexi and Firmicutes may play crucial roles in enhancing MeHg levels. Overall, these findings shed new light on the microbial communities potentially involved in Hg-methylation process and other biogeochemical cycles.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Rishikesh Bajagain
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - DongGyun Seo
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea.
| | - Seunghee Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
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Hu X, Huang Y, Gu G, Hu H, Yan H, Zhang H, Zhang R, Zhang D, Wang K. Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China. ENVIRONMENTAL MICROBIOME 2023; 18:75. [PMID: 37805516 PMCID: PMC10560434 DOI: 10.1186/s40793-023-00530-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises. RESULTS The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study. CONCLUSIONS Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.
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Affiliation(s)
- Xuya Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yujie Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Gaoke Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Hanjing Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Huizhen Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China.
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Zhang S, Wang F, Wang Y, Chen X, Xu P, Miao H. Shifts of soil archaeal nitrification and methanogenesis with elevation in water level fluctuation zone of the three Gorges Reservoir, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 339:117871. [PMID: 37030237 DOI: 10.1016/j.jenvman.2023.117871] [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: 01/04/2023] [Revised: 03/27/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023]
Abstract
The water level fluctuation zone is a unique ecological zone exposed to long-term drying and flooding and plays a critical role in the transport and transformation of carbon and nitrogen materials in reservoir-river systems. Archaea are a vital component of soil ecosystems in the water level fluctuation zones, however, the distribution and function of archaeal communities in responde to long-term wet and dry alternations are still unclear. The community structure of archaea in the drawdown areas at various elevations of the Three Gorges Reservoir was investigated by selecting surface soils (0-5 cm) of different inundation durations at three sites from upstream to downstream according to the flooding pattern. The results revealed that prolonged flooding and drying increased the community diversity of soil archaea, with ammonia-oxidizing archaea being the dominant species in non-flooded regions, while methanogenic archaea were abundant in soils that had been flooded for an extended period of time. Long-term alternation of wetting and drying increases methanogenesis but decreases nitrification. It was determined that soil pH, NO3--N, TOC and TN are significant environmental factors affecting the composition of soil archaeal communities (P = 0.02). Long-term flooding and drying changed the community composition of soil archaea by altering environmental factors, which in turn influenced nitrification and methanogenesis in soils at different elevations. These findings contribute to our understanding of soil carbon and nitrogen transport transformation processes in the water level fluctuation zone as well as the effects of long-term wet and dry alternation on soil carbon and nitrogen cycles. The results of this study can provide a basis for ecological management, environmental management, and long-term operation of reservoirs in water level fluctuation zones.
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Affiliation(s)
- Shengman Zhang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Yuchun Wang
- China Institute of Water Resources and Hydropower Research, Beijing, 100038, China.
| | - Xueping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Peifan Xu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
| | - Haocheng Miao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
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Lin X, Zhang C, Xie W. Deterministic processes dominate archaeal community assembly from the Pearl River to the northern South China Sea. Front Microbiol 2023; 14:1185436. [PMID: 37426005 PMCID: PMC10324572 DOI: 10.3389/fmicb.2023.1185436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms.
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Affiliation(s)
- Xizheng Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, China
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de la Garza Varela A, Aguirre-Macedo ML, García-Maldonado JQ. Changes in the Rhizosphere Prokaryotic Community Structure of Halodule wrightii Monospecific Stands Associated to Submarine Groundwater Discharges in a Karstic Costal Area. Microorganisms 2023; 11:microorganisms11020494. [PMID: 36838457 PMCID: PMC9963909 DOI: 10.3390/microorganisms11020494] [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: 01/25/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Belowground seagrass associated microbial communities regulate biogeochemical dynamics in the surrounding sediments and influence seagrass physiology and health. However, little is known about the impact of environmental stressors upon interactions between seagrasses and their prokaryotic community in coastal ecosystems. Submerged groundwater discharges (SGD) at Dzilam de Bravo, Yucatán, Mexico, causes lower temperatures and salinities with higher nutrient loads in seawater, resulting in Halodule wrightii monospecific stands. In this study, the rhizospheric archaeal and bacterial communities were characterized by 16S rRNA Illumina sequencing along with physicochemical determinations of water, porewater and sediment in a 400 m northwise transect from SGD occurring at 300 m away from coastline. Core bacterial community included Deltaproteobacteria, Bacteroidia and Planctomycetia, possibly involved in sulfur metabolism and organic matter degradation while highly versatile Bathyarchaeia was the most abundantly represented class within the archaeal core community. Beta diversity analyses revealed two significantly different clusters as result of the environmental conditions caused by SGD. Sites near to SGD presented sediments with higher redox potentials and sand contents as well as lower organic matter contents and porewater ammonium concentrations compared with the furthest sites. Functional profiling suggested that denitrification, aerobic chemoheterotrophy and environmental adaptation processes could be better represented in these sites, while sulfur metabolism and genetic information processing related profiles could be related to SGD uninfluenced sites. This study showed that the rhizospheric prokaryotic community structure of H. wrightii and their predicted functions are shaped by environmental stressors associated with the SGD. Moreover, insights into the archaeal community composition in seagrasses rhizosphere are presented.
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Zou D, Li H, Du P, Wang B, Lin H, Liu H, Chen J, Li M. Distinct Features of Sedimentary Archaeal Communities in Hypoxia and Non-Hypoxia Regions off the Changjiang River Estuary. Microbiol Spectr 2022; 10:e0194722. [PMID: 36066619 PMCID: PMC9602602 DOI: 10.1128/spectrum.01947-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 12/31/2022] Open
Abstract
Water hypoxia (DO < 2 mg/L) is a growing global environmental concern that has the potential to significantly influence not only the aquatic ecosystem but also the benthic sedimentary ecosystem. The Changjiang River Estuary hypoxia, classified as one of the world's largest seasonal hypoxic water basins, has been reported to be expanding rapidly in recent decades. However, the microbial community dynamics and responses to this water hypoxia are still unclear. In this study, we examined the abundance, community composition, and distribution of sedimentary archaea, one important component of microbial communities in the Changjiang River Estuary and the East China Sea (ECS). Our results indicated that Thaumarchaeota and Bathyarchaeota were predominant archaeal groups in these research areas, with their 16S rRNA gene abundance ranged from 8.55 × 106 to 7.51 × 108 and 3.18 × 105 to 1.11 × 108 copies/g, respectively. The sedimentary archaeal community was mainly influenced by DO, together with the concentration of ammonium, nitrate, and sulfide. In addition, distinct differences in the archaeal community's composition, abundance, and driving factors were discovered between samples from hypoxia and non-hypoxia stations. Furtherly, microbial networks suggest various microbes leading the different activities in hypoxic and normoxic environments. Bathyarchaeota and Thermoprofundales were "key stone" archaeal members of the low-DO network, whereas Thaumarchaeota constituted a significant component of the high-DO network. Our results provide a clear picture of the sedimentary archaeal community in coastal hypoxia zones and indicates potential distinctions of archaea in hypoxia and non-hypoxia environments, including ecological niches and metabolic functions. IMPORTANCE In this study, the sedimentary archaeal community composition and abundance were detailed revealed and quantified based on 16S rRNA genes off the Changjiang River Estuary. We found that the community composition was distinct between hypoxia and non-hypoxia regions, while Thaumarchaeota and Bathyarchaeota dominated in non-hypoxia and hypoxia samples, respectively. In hypoxia regions, the sedimentary archaea were mainly affected by salinity, ammonium, and nitrate, whereas total organic carbon, total nitrogen, and sulfide were major influencing factors in non-hypoxia regions. The distinct microbial network may suggest the niche difference of archaeal community under various oxygen level.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Bin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hua Lin
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
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Response of Prokaryotic Communities to Freshwater Salinization. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Each year, millions of tons of sodium chloride are dumped on roads, contributing to the salinization of freshwater environments. Thus, we sought to understand the effect of sodium chloride (NaCl) on freshwater lake prokaryotic communities, an important and understudied component of food webs. Using mesocosms with 0.01–2.74 ppt NaCl (0.27–1110.86 mg/L Cl−), we evaluated the effect generated on the diversity and absolute abundance of prokaryotic populations after three and six weeks. A positive relationship between Cl− values and absolute bacterial abundance was found after three weeks. The influence of eukaryotic diversity variation was observed as well. Significant differentiation of bacterial communities starting at 420 mg/L Cl− was observed after three weeks, levels lower than the Canadian and US recommendations for acute chloride exposure. The partial recovery of a “pre-disturbance” community was observed following a drop in salinity at the threshold level of 420 mg/L Cl−. A gradual transition of dominance from Betaproteobacteria and Actinobacteria to Bacteroidia and Alphaproteobacteria was observed and is overall similar to the natural transition observed in estuaries.
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Li Y, Wei J, Yang H, Zhang D, Hu C. Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts. Front Microbiol 2022; 13:848908. [PMID: 35495652 PMCID: PMC9042396 DOI: 10.3389/fmicb.2022.848908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea exhibit strong community heterogeneity with microhabitat gradients and are a non-negligible part of biocrust’s microorganisms. The study on archaeal biogeography in biocrusts could provide new insights for its application in environmental restoration. However, only a few studies on assembly processes and co-occurrence patterns of the archaeal community in patchy biocrusts have been reported, especially considering the number of species pools (SPs). Here, we comprehensively collected biocrusts across 3,500 km of northern China. Different successional biocrusts from various regions contain information of local climate and microenvironments, which can shape multiple unique archaeal SPs. The archaeal community differences in the same successional stage exceeded the variations between successional stages, which was due to the fact that the heterogeneous taxa tended to exchange between unknown patches driven by drift. We also comparatively studied the driving forces of community heterogeneity across three to ten SPs, and assembly and co-occurrence patterns were systematically analyzed. The results revealed that the impact of spatial factors on biogeographic patterns was greater than that of environmental and successional factors and that impact decreased with the number of SPs considered. Meanwhile, community heterogeneity at the phylogenetic facet was more sensitive to these driving factors than the taxonomic facet. Subgroups 1 (SG1) and 2 (SG2) of the archaeal communities in biocrusts were dominated by Nitrososphaeraceae and Haloarchaea, respectively. The former distribution pattern was associated with non-salinity-related variables and primarily assembled by drift, whereas the latter was associated with salinity-related variables and primarily assembled by homogeneous selection. Finally, network analysis indicated that the SG1 network had a higher proportion of competition and key taxa than the SG2 network, but the network of SG2 was more complex. Our study suggested that the development of the archaeal community was not consistent with biocrusts succession. The dominant taxa may determine the patterns of community biogeography, assembly, and co-occurrence.
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Affiliation(s)
- Yuanlong Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Wei
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Delu Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Ferrer A, Heath KD, Mosquera SL, Suaréz Y, Dalling JW. Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats. FEMS Microbiol Ecol 2022; 98:6566339. [PMID: 35404430 DOI: 10.1093/femsec/fiac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022] Open
Abstract
Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine, and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9, and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that taxa either dispersed to both terrestrial and aquatic habitats, or that microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.
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Affiliation(s)
- Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sergio L Mosquera
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Yaraví Suaréz
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
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Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station. Int Microbiol 2022; 25:571-586. [DOI: 10.1007/s10123-022-00244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022]
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High Abundance of Thaumarchaeota Found in Deep Metamorphic Subsurface in Eastern China. Microorganisms 2022; 10:microorganisms10030542. [PMID: 35336118 PMCID: PMC8950554 DOI: 10.3390/microorganisms10030542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Members of the Thaumarchaeota phylum play a key role in nitrogen cycling and are prevalent in a variety of environments including soil, sediment, and seawater. However, few studies have shown the presence of Thaumarchaeota in the terrestrial deep subsurface. Using high-throughput 16S rRNA gene sequencing, this study presents evidence for the high relative abundance of Thaumarchaeota in a biofilm sample collected from the well of Chinese Continental Scientific Drilling at a depth of 2000 m. Phylogenetic analysis showed a close relationship of these thaumarchaeotal sequences with known ammonia-oxidizing archaea (AOA) isolates, suggesting the presence of AOA in the deep metamorphic environment of eastern China which is believed to be oxic. Based on fluid geochemistry and FAProTax functional prediction, a pathway of nitrogen cycling is proposed. Firstly, heterotrophic nitrogen fixation is executed by diazotrophic bacteria coupled with methane oxidation. Then, ammonia is oxidized to nitrite by AOA, and nitrite is further oxidized to nitrate by bacteria within the phylum Nitrospirae. Denitrification and anaerobic ammonia oxidation occur slowly, leading to nitrate accumulation in the subsurface. With respect to biogeochemistry, the reaction between downward diffusing O2 and upward diffusing CH4 potentially fuels the ecosystem with a high relative abundance of Thaumarchaeota.
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