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Li T, Wang X, Wang X, Huang J, Shen L. Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone. MICROBIAL ECOLOGY 2023; 86:1829-1846. [PMID: 36702929 DOI: 10.1007/s00248-023-02180-3] [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: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.
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Affiliation(s)
- Tingting Li
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Xiaoyan Wang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China.
| | - Xia Wang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Jingyu Huang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Lei Shen
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
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Wang Z, Li Y, Zheng W, Ji Y, Duan M, Ma L. Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China. Sci Rep 2023; 13:8064. [PMID: 37202434 DOI: 10.1038/s41598-023-35134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/12/2023] [Indexed: 05/20/2023] Open
Abstract
Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha-1 was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha-1 (52.7-56.5%) and when manure was added (72.7-99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha-1 (58.4-84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.
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Affiliation(s)
- Zhan Wang
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- Guyuan Branch, Ningxia Academy of Agricultural and Forestry Sciences, Guyuan, 756000, China
| | - Yinkun Li
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Wengang Zheng
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yuru Ji
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Minjie Duan
- Beijing Key Laboratory of Ecological Function Assessment and Regulation Technology of Green Space, Beijing Urban Ecosystem Positioning Observation and Research Station, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Li Ma
- Wuzhong National Agricultural Science and Technology Park Management Committee, Wuzhong, 751100, Ningxia, China
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Almeida PIND, Jesus HED, Pereira PHF, Vieira CED, Bianchini A, Martins CDMG, Santos HFD. The microbial profile of rivers and lagoons three years after the impact of the world's largest mining disaster (Fundão dam, Brazil). ENVIRONMENTAL RESEARCH 2023; 216:114710. [PMID: 36334830 DOI: 10.1016/j.envres.2022.114710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
The collapse of the Fundão tailings dam (Minas Gerais, Brazil) was the largest environmental disaster in Brazil's history and in the world mining industry. This disaster carried approximately 55 million m3 of iron ore tailings along the rivers and the lagoons of the Doce river basin. Although multiple studies assessed the impact on microbial communities in those rivers and lagoons right after the dam rupture, it is not known whether the microbiome in those environments remains impacted years after the disaster. Assessing the microbiome is very important to evaluate impacts and evaluate the health of the environment, due to the several ecological roles played by microorganisms. Here, we evaluated the impact of the dam failure on water and sediment bacteriome and archaeome by high-throughput next-generation sequencing. Samples were taken from two rivers and six lagoons during the dry and rainy seasons approximately three years post disturbance. The results showed a large number and abundance of microbial groups associated with the presence of heavy metals and mine tailings sediments. Some of these microorganisms were also reported in large abundance in the impacted rivers shortly after the Fundão dam rupture. Among the most abundant microorganisms in the Doce River, we can highlight the bacteria hgcI clade and the archaea Nitrososphera sp. in the water, and the bacteria Anaerolineaceae sp. in the sediment. These results suggest that the microbiome of the rivers and the lagoons in the Doce river basin remains severely impacted by the Fundão tailings dam failure even three years after the disaster. The presence of those microorganisms can also help to assess the occurrence of the Fundão dam sediment in other environments.
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Affiliation(s)
- Pedro Ivo Neves de Almeida
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil
| | - Hugo Emiliano de Jesus
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil
| | - Pedro Henrique Freitas Pereira
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil
| | - Carlos Eduardo Delfino Vieira
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, FURG. Av. Itália, S/n, Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, FURG. Av. Itália, S/n, Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Camila De Martinez Gaspar Martins
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, FURG. Av. Itália, S/n, Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Henrique Fragoso Dos Santos
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ, 24210-201, Brazil.
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Wang X, Ren Y, Yu Z, Shen G, Cheng H, Tao S. Effects of environmental factors on the distribution of microbial communities across soils and lake sediments in the Hoh Xil Nature Reserve of the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156148. [PMID: 35609688 DOI: 10.1016/j.scitotenv.2022.156148] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Comparison of microbial community diversity and composition of terrestrial and aquatic ecosystems in undisturbed regions could expand our understanding on the mechanisms of microbial community assembly and ecosystem responses to environmental change. This study investigated the spatial distribution of bacterial community diversity and composition in the lakeshore soils and lake sediments from one of the best preserved nature reserves, Hoh Xil on the Qinghai-Tibetan Plateau, and explored the corresponding environmental drivers. A total of 36 sediment and soil samples were collected from six alpine lakes and the corresponding shore zones, and their bacterial community structure was identified by high-throughput 16S rRNA gene sequencing. Significant difference (p < 0.05) in diversity and composition of bacterial communities between the soils and sediments was observed. Heterogeneous selection played a dominant role in shaping the spatial variations of bacterial communities between the soils and sediments. Results of canonical correspondence analysis showed that the difference in composition of bacterial communities at OTU level between the soils and sediments was mainly determined by the mean annual temperature, salinity, and contents of total organic carbon and total nitrogen. Structural equation modeling revealed that salinity played a significantly direct role in soil bacterial composition, while mean annual temperature indirectly affected the bacterial composition mainly through changing soil salinity. In contrast, the sediment bacterial composition was directly influenced primarily by the contents of total organic carbon and total nitrogen, while pH also had an important indirect effect on sediment bacterial composition. These results shed light on the distribution patterns of bacterial communities between lakeshore soils and lake sediments in high-altitude permafrost regions, and the major ecological processes and environmental drivers that shaped their bacterial communities, and provide insight into the mechanisms underlying microbial community assembly in such regions.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yuxuan Ren
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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Xing G, Lu J, Xuan L, Chen J, Xiong J. Sediment prokaryotic assembly, methane cycling, and ammonia oxidation potentials in response to increasing antibiotic pollution at shrimp aquafarm. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128885. [PMID: 35421673 DOI: 10.1016/j.jhazmat.2022.128885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 05/28/2023]
Abstract
Antibiotic pollution poses serious threats to public health and ecological processes. However, systematic research regarding the interactive effects of increasing nutrient and antibiotic pollutions on the prokaryotic community, particularly taxa that contribute to greenhouse gas emissions, is lacking. By exploring the complex interactions that occur between interkingdom bacteria and archaea, biotic and abiotic factors, the responses of sediment prokaryotic assembly were determined along a significant antibiotic pollution gradient. Bacterial and archaeal communities were primarily governed by sediment antibiotic pollution, ammonia, phosphate, and redox potential, which further affected enzyme activities. The two communities nonlinearly responded to increasing antibiotic pollution, with significant tipping points of 3.906 and 0.979 mg/kg antibiotics, respectively. The combined antibiotic concentration-discriminatory taxa of bacteria and archaea accurately (98.0% accuracy) diagnosed in situ antibiotic concentrations. Co-abundance analysis revealed that the methanogens, methanotrophs, sulfate-reducing bacteria, and novel players synergistically contributed to methane cycling. Antibiotic pollution caused the dominant role of ammonia-oxidizing archaea in ammonia oxidation at these alkaline sediments. Collectively, the significant tipping points and bio-indicators afford indexes for regime shift and quantitative diagnosis of antibiotic pollution, respectively. Antibiotic pollution could expedite methane cycling and mitigate nitrous oxide yield, which are previously unrecognized ecological effects. These findings provide new insights into the interactive biological and ecological consequences of increasing nutrient and antibiotic pollutions.
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Affiliation(s)
- Guorui Xing
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Lixia Xuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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Temporal and Spatial Patterns of Sediment Microbial Communities and Driving Environment Variables in a Shallow Temperate Mountain River. Microorganisms 2022; 10:microorganisms10040816. [PMID: 35456866 PMCID: PMC9028755 DOI: 10.3390/microorganisms10040816] [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: 03/08/2022] [Revised: 03/24/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Microbial communities in sediment play an important role in the circulation of nutrients in aquatic ecosystems. In this study, the main environmental factors and sediment microbial communities were investigated bimonthly from August 2018 to June 2020 at River Taizicheng, a shallow temperate mountain river at the core area of the 2022 Winter Olympics. Microbial community structure was analyzed using 16S rRNA genes (bacteria 16S V3 + V4 and archaea 16S V4 + V5) and high-throughput sequencing technologies. Structure equation model (SEM) and canonical correspondence analysis (CCA) were used to explore the driving environmental factors of the microbial community. Our results showed that the diversity indices of the microbial community were positively influenced by sediment nutrients but negatively affected by water nutrients. Bacteroidetes and Proteobacteria were the most dominant phyla. The best-fitted SEM model indicated that environmental variables not only affected community abundance directly, but also indirectly through influencing their diversity. Flavobacterium, Arenimonas and Terrimonas were the dominant genera as a result of enriched nutrients. The microbial community had high spatial–temporal autocorrelation. CCA showed that DO, WT and various forms of phosphorus were the main variables affecting the temporal and spatial patterns of the microbial community in the river. The results will be helpful in understanding the driving factors of microbial communities in temperate monsoon areas.
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Liu X, Shao Y, Dong Y, Dong M, Xu Z, Hu X, Liu A. Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:11357-11368. [PMID: 33123879 DOI: 10.1007/s11356-020-11356-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg-1), which showed an antagonistic effect between Cu and SDZ (5 mg · kg-1), while the combined toxicity of high-concentration SDZ (10 mg · kg-1) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg-1 Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg-1 SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg-1 Cu combined with 5 mg · kg-1 SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.
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Affiliation(s)
- Xijuan Liu
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Yifei Shao
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Yuanpeng Dong
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Mengyang Dong
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Ziwen Xu
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Xinxin Hu
- College of Resources and Environmental engineering, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Aiju Liu
- College of Resources and Environmental engineering, Shandong University of Technology, Zibo, 255049, People's Republic of China.
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Li C, Zhong Z, Wang W, Wang H, Yan G, Dong W, Chu Z, Wang H, Chang Y. Distribution characteristics of nitrogen and the related microbial community in the surface sediments of the Songhua River. RSC Adv 2021; 11:26721-26731. [PMID: 35480017 PMCID: PMC9037357 DOI: 10.1039/d1ra04903h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/26/2021] [Indexed: 11/21/2022] Open
Abstract
In this study, temporal and spatial distribution of nitrogen in the Songhua River sediments and distribution characteristics of related microbes as well as the relationship between them were investigated.
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Affiliation(s)
- Congyu Li
- Research Center of Environmental Pollution Control Technology
- Chinese Research Academy of Environmental Science
- Beijing 100012
- PR China
| | - Zhen Zhong
- Research Center of Environmental Pollution Control Technology
- Chinese Research Academy of Environmental Science
- Beijing 100012
- PR China
- ChangZhou JiangRun Environmental Protection Technology Co., Ltd
| | - Wenfu Wang
- Shangcai County Environmental Monitoring Station
- China
| | - Haiyan Wang
- Research Center of Environmental Pollution Control Technology
- Chinese Research Academy of Environmental Science
- Beijing 100012
- PR China
| | - Guokai Yan
- Research Center of Environmental Pollution Control Technology
- Chinese Research Academy of Environmental Science
- Beijing 100012
- PR China
| | - Weiyang Dong
- Research Center of Environmental Pollution Control Technology
- Chinese Research Academy of Environmental Science
- Beijing 100012
- PR China
| | - Zhaosheng Chu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration
- Chinese Research Academy of Environmental Sciences
- Beijing 100012
- PR China
| | - Huan Wang
- Research Center of Environmental Pollution Control Technology
- Chinese Research Academy of Environmental Science
- Beijing 100012
- PR China
| | - Yang Chang
- Research Center of Environmental Pollution Control Technology
- Chinese Research Academy of Environmental Science
- Beijing 100012
- PR China
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Wang C, Wu R, Song Y, Guo J, Liu R, Cui Y. Differences in nitrification and ammonium-oxidising prokaryotes in the process of wetland restoration. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 56:136-144. [PMID: 33259261 DOI: 10.1080/10934529.2020.1852845] [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: 05/16/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) are ammonium oxidising prokaryotes that can drive soil nitrification in wetlands. During the restoration of wetlands, different types of land use soils (agricultural soil [AS], restored wetland soil [RS], and natural wetland soil [NWS]) are present. However, studies on the effects of changes in the types of land use in wetlands during restoration on nitrification and the community composition of AOA and AOB are still not well understood. In this study, the differences in the potential nitrification rate (PNR) and community composition of AOA and AOB in AS, RS, and NWS were compared and discussed. The results indicated that the PNRs in the AS, RS, and NWS were on the same order of magnitude. Nitrification was mainly driven by AOB. High-throughput sequencing results showed that the genus Nitrososphaera of AOA and unclassified_o_Nitrosomonadales of AOB were only detected in the AS. Redundancy analysis (RDA) results indicated that the community composition of AOA was mostly influenced by pH, while TC was the most influential variable on the community composition of AOB. Our study provides a basis for distinguishing the roles of ammonium-oxidising prokaryotes in nitrification and further understanding the changes in nitrifying activity in wetlands during restoration.
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Affiliation(s)
- Chunyong Wang
- School of Chemical and Environmental Engineering, Liaoning University of Technology, Jinzhou, PR China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Rui Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yi Song
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Jianbo Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
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Ke Y, Tong T, Chen J, Huang J, Xie S. Influences of hexafluoropropylene oxide (HFPO) homologues on soil microbial communities. CHEMOSPHERE 2020; 259:127504. [PMID: 32650170 DOI: 10.1016/j.chemosphere.2020.127504] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/05/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Hexafluoropropylene oxide (HFPO) homologues, as emerging perfluoroalkyl substances (PFASs) to replace legacy PFASs, have wide applications in the organofluorine industry and have been detected in the global environment. However, it is still unclear what effect HFPO homologues will exert on microbial abundance, community structure and function. The objective of this study was to assess potential impacts of HFPO homologue acids on archaea, bacteria, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the soil environment. Grassland soil microcosms were supplemented with low (0.1 mg/kg) or high (10 mg/kg) dosages of dimer, trimer and tetramer acids of HFPO (HFPO-DA, HFPO-TA, and HFPO-TeA), respectively. The amendment of HFPO homologues acids initially decreased the abundance of archaea and bacteria but increased them in the later period. The addition of HFPO homologues acids raised AOA abundance but restrained AOB growth during the whole incubation. AOA and AOB community structures showed considerable variations. Potential nitrifying rate (PNR) showed an increase in the initial period followed by a decline in the later period. HFPO-DA had a lasting and suppressive effect on AOB and PNR even at a nearly environmental level. Overall, HFPO homologues with different carbon chain lengths had different impacts on soil microbial community and ammonia oxidation.
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Affiliation(s)
- Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jun Huang
- School of Environment, Beijing Key Laboratory for Emerging Organic Contaminants Control (BKLEOC), State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), Tsinghua University, Beijing, 100084, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Xu L, Zhang B, Peng X, Zhang X, Sun B, Sun H, Jiang C, Zhou S, Zeng X, Bai Z, Xu S, Zhuang X. Dynamic variations of microbial community structure in Myriophyllum aquaticum constructed wetlands in response to different NH4+-N concentrations. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Cao L, Yu X, Liu C, Liu M, Chen J, Qin H, Liang C, Xu Q, Penttinen P. Alteration of soil nitrifiers and denitrifiers and their driving factors during intensive management of Moso bamboo (Phyllostachys pubescens). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135236. [PMID: 31841899 DOI: 10.1016/j.scitotenv.2019.135236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
Long-term intensive management, such as inorganic fertilization and soil tillage, have been reported to decrease soil organic carbon content (SOC) and diversity of soil bacterial communities, as well as increase N2O emissions in moso bamboo forests. However, the response of the N-cycling soil microbial community to intensive management remains unclear. To address this, we examined the effects of intensive moso bamboo management on nitrifying and denitrifying microorganisms. Soils receiving non-management (NM) and 10, 15, 20, and 25 years of intensive management (IM10, IM15, IM20, IM25) were characterized using quantitative real-time PCR (qPCR) and high-through sequencing methods. Our results showed that abundances of ammonia monooxygenase (amoA) from ammonia-oxidizing archaea (AOA) significantly increased (P < 0.05) and were greatest in IM15 (8.37 × 107 copies/g dry soils) and IM25 (5.42 × 107 copies/g dry soils) in top- and subsoils, respectively, while nitrous oxide reductase (nosZ) abundance significantly decreased by 59.1% (topsoil) and 36.4% (subsoil) in IM20 (P < 0.05). GroupI.1a-associated affiliating to AOA, and Bradyrhizobium affiliating to nosZ, were keys groups for nitrifiers and denitrifiers, respectively, and showed the greatest variations in response to long-term intensive management. Abundances of ammonia-oxidizing bacteria (AOB) and the nitrite reductase gene nirS were less affected, as were the dominant Nitrosospira species belonging to the AOB community. Except the AOB amoA abundance, soil nitrogen was found to be the main factor influencing the abundance, diversity, and composition of nitrifying genes, while denitrifying genes were mainly affected by SOC and available potassium, indicating that different factors control populations of nitrifiers and denitrifiers. Collectively, our study revealed that groupings of nitrifying and denitrifying microorganisms responded differently to intensive management. This information is of potential value towards identifying strategies to minimize nitrogen loss in moso bamboo plantations.
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Affiliation(s)
- Linhua Cao
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Xiao Yu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Caixia Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Ming Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Junhui Chen
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Hua Qin
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Chenfei Liang
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Qiufang Xu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Petri Penttinen
- College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
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13
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Zhang S, Liu F, Luo P, Xiao R, Chen J, Chen L, Wu J. Does rice straw application reduce N 2O emissions from surface flow constructed wetlands for swine wastewater treatment? CHEMOSPHERE 2019; 226:273-281. [PMID: 30933736 DOI: 10.1016/j.chemosphere.2019.03.084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/09/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Rice straw was applied often as a carbon source to improve nitrogen removal; however, few studies have considered the effect of rice straw on nitrous oxide (N2O) emission during nitrogen removal in constructed wetlands (CWs). We constructed eighteen combined systems, consisting of rice straw ponds and surface flow CWs to investigate the effect of rice straw application on N2O emission in three strengths of swine wastewater treatments. The results showed rice straw (RS) treatment increased 131.5% of N2O emission factor from low strength CWs, but decreased 37.2-43.7% of N2O emission factors for medium and high strengths compared with no rice straw (NRS) treatment. The RS application led to an average 10.7% increase in the potential denitrification rate, and simultaneously enhanced gene abundances of the total bacteria (16S rRNA), ammonia-oxidising archaea, ammonia-oxidising bacteria, nitrate reductase, and N2O reductase (nosZ) for all strengths CWs. The multiple regression model revealed N2O emissions were strongly related to water temperature, nitrate, chemical oxygen demand, and denitrification genes. The proportion of nosZ gene abundance in 16S rRNA was higher in RS (0.7-1.3%) than NRS (0.4-0.9%) for medium and high strengths, while an opposite trend was observed for low strength. The discrepancy was responsible for increasing or decreasing N2O emission by RS application among different strengths. These findings indicated the effectiveness of RS application to control N2O emissions from the surface flow CWs was related to the pollution level of wastewater.
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Affiliation(s)
- Shunan Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China.
| | - Pei Luo
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
| | - Runlin Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
| | - Junli Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Liang Chen
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Hunan, 410004, PR China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
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14
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Wang S, Zheng X, Xia H, Shi D, Fan J, Wang P, Yan Z. Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing. PLoS One 2019; 14:e0218611. [PMID: 31226149 PMCID: PMC6588238 DOI: 10.1371/journal.pone.0218611] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.
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Affiliation(s)
- Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Huijuan Xia
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Di Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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15
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Sun Y, Zhu L, Xu X, Meng Q, Men M, Xu B, Deng L. Correlation between ammonia-oxidizing microorganisms and environmental factors during cattle manure composting. Rev Argent Microbiol 2019; 51:371-380. [PMID: 30904396 DOI: 10.1016/j.ram.2018.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 11/17/2022] Open
Abstract
Cattle manure composting was performed in an aerated vessel. Community structure and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) techniques targeting the ammonia monooxygenase alpha subunit (amoA) gene and the correlation between AOB and AOA communities and environmental factors was explored. Thirteen (13) AOB sequences were obtained, which were closely related to Nitrosomonas spp., Nitrosomonas eutropha, and Nitrosospira spp. and uncultured bacteria, among which Nitrosomonas spp. were predominant. Excessively high temperature and high ammonium concentration were not favorable for AOB growth. Five AOA sequences, belonging to CandidatusNitrososphaera gargensis and to an uncultured archaeon, were obtained. During composting, community diversity of AOB and AOA fluctuated, with AOA showing a higher Shannon-Wiener index. The AOB community changed more dramatically in the mesophilic stage and the early thermophilic stage, whereas the most obvious AOA community succession occurred in the late thermophilic stage, the cooling stage and the maturity stage. Water content, total nitrogen (TN) and ammonium concentration were more relevant to the AOB community structure, while higher correlations were observed between ammonia, nitrate and TN and the AOA community. AOB community diversity was negatively correlated with pH (r = -0.938, p < 0.01) and water content (r = -0.765, p < 0.05), while positively correlated with TN (r = 0.894, p < 0.01). AOA community diversity was negatively correlated with ammonium concentration (r = -0.901, p < 0.01). Ammonium concentration played an important role in the succession of AOB and AOA communities during composting.
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Affiliation(s)
- Yu Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Liping Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China.
| | - Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengqi Men
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Benshu Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
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16
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Li N, Chen Y, Zhang Z, Chang S, Huang D, Chen S, Guo Q, Xie S, Bing Y. Response of ammonia-oxidizing archaea to heavy metal contamination in freshwater sediment. J Environ Sci (China) 2019; 77:392-399. [PMID: 30573104 DOI: 10.1016/j.jes.2018.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 06/09/2023]
Abstract
It has been well-documented that the distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soils can be affected by heavy metal contamination, whereas information about the impact of heavy metal on these ammonia-oxidizing microorganisms in freshwater sediment is still lacking. The present study explored the change of sediment ammonia-oxidizing microorganisms in a freshwater reservoir after being accidentally contaminated by industrial discharge containing high levels of metals. Bacterial amoA gene was found to be below the quantitative PCR detection and was not successfully amplified by conventional PCR. The number of archaeal amoA gene in reservoir sediments were 9.62 × 102-1.35 × 107 copies per gram dry sediment. AOA abundance continuously decreased, and AOA richness, diversity and community structure also considerably varied with time. Therefore, heavy metal pollution could have a profound impact on freshwater sediment AOA community. This work could expand our knowledge of the effect of heavy metal contamination on nitrification in natural ecosystems.
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Affiliation(s)
- Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China..
| | - Yao Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Zhengke Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Sha Chang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Dawei Huang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China..
| | - Yongxin Bing
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China.
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17
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Vipindas PV, Jabir T, Jasmin C, Balu T, Rehitha TV, Adarsh BM, Nair S, Abdulla MH, Abdulaziz A. Diversity and seasonal distribution of ammonia-oxidizing archaea in the water column of a tropical estuary along the southeast Arabian Sea. World J Microbiol Biotechnol 2018; 34:188. [PMID: 30511184 DOI: 10.1007/s11274-018-2570-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/27/2018] [Indexed: 01/28/2023]
Abstract
Diversity and distribution pattern of ammonia-oxidizing archaea (AOA) were studied across a salinity gradient in the water column of Cochin Estuary (CE), a tropical monsoonal estuary along the southeast Arabian Sea. The water column of CE was found to be nutrient rich with high bacterial (3.7-6.7 × 108 cells L-1) and archaeal abundance (1.9-4.5 × 108 cells L-1). Diversity and seasonal variation in the distribution pattern of AOA were studied using clone library analysis and Denaturing gradient gel electrophoresis (DGGE). Clone library analysis of both the amoA and 16S rRNA gene sequences showed similar diversity pattern, however the diversity was more clear when the 16S rRNA gene sequences were analyzed. More than 70% of the sequences retrieved were clustered under uncultured Thaumarchaeota group 1 lineage and the major fractions of the remaining sequences were grouped into the Nitrosopumilus lineage and Nitrosopelagicus lineage. The AOA community in the CE was less adaptable to changing environmental conditions and its distribution showed seasonal variations within the DGGE banding pattern with higher diversity during the pre-monsoon period. The distribution of AOA also showed its preference to intermediate salinity for their higher diversity. Summer monsoon associated runoff and flushing played a critical role in regulating the seasonality of AOA distribution.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India. .,Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India.
| | - Thajudeen Jabir
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Chekidhenkuzhiyil Jasmin
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Tharakan Balu
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Thekkendavida Velloth Rehitha
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Balakrishnan Meenakshikutty Adarsh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Shanta Nair
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Mohamed Hatha Abdulla
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anas Abdulaziz
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
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18
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Nho SW, Abdelhamed H, Paul D, Park S, Mauel MJ, Karsi A, Lawrence ML. Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi. Front Microbiol 2018; 9:2855. [PMID: 30524416 PMCID: PMC6262407 DOI: 10.3389/fmicb.2018.02855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/06/2018] [Indexed: 11/19/2022] Open
Abstract
Metagenomic analyses of microbial communities from aquatic sediments are relatively few, and there are no reported metagenomic studies on sediment from inland ponds used for aquaculture. Catfish ponds in the southeastern U.S. are eutrophic systems. They are fertilized to enhance algae growth and encourage natural food production, and catfish are fed with commercial feed from spring to fall. As result, catfish pond sediment (CPS) contains a very dense, diverse microbial community that has significant effects on the physiochemical parameters of pond dynamics. Here we conducted an in-depth metagenomic analysis of the taxonomic and metabolic capabilities of a catfish pond sediment microbiome from a southeastern U.S. aquaculture farm in Mississippi using Illumina next-generation sequencing. A total of 3.3 Gbp of sequence was obtained, 25,491,518 of which encoded predicted protein features. The pond sediment was dominated by Proteobacteria sequences, followed by Bacteroidetes, Firmicutes, Chloroflexi, and Actinobacteria. Enzyme pathways for methane metabolism/methanogenesis, denitrification, and sulfate reduction appeared nearly complete in the pond sediment metagenome profile. In particular, a large number of Deltaproteobacteria sequences and genes encoding anaerobic functional enzymes were found. This is the first study to characterize a catfish pond sediment microbiome, and it is expected to be useful for characterizing specific changes in microbial flora in response to production practices. It will also provide insight into the taxonomic diversity and metabolic capabilities of microbial communities in aquaculture. Furthermore, comparison with other environments (i.e., river and marine sediments) will reveal habitat-specific characteristics and adaptations caused by differences in nutrients, vegetation, and environmental stresses.
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Affiliation(s)
- Seong Won Nho
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Hossam Abdelhamed
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Debarati Paul
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Seongbin Park
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
| | - Michael J Mauel
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
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19
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Dai L, Liu C, Yu L, Song C, Peng L, Li X, Tao L, Li G. Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds. Front Microbiol 2018; 9:2290. [PMID: 30319588 PMCID: PMC6165866 DOI: 10.3389/fmicb.2018.02290] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/07/2018] [Indexed: 01/28/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms.
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Affiliation(s)
- Lili Dai
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chengqing Liu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Liqin Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chaofeng Song
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Liang Peng
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xiaoli Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Ling Tao
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Gu Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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20
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Yin X, Liu G, Peng L, Hua Y, Wan X, Zhou W, Zhao J, Zhu D. Microbial community of nitrogen cycle-related genes in aquatic plant rhizospheres of Lake Liangzi in winter. J Basic Microbiol 2018; 58:998-1006. [DOI: 10.1002/jobm.201800220] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Xingjia Yin
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Lei Peng
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Xiaoqiong Wan
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Wenbing Zhou
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
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Li B, Yang Y, Chen J, Wu Z, Liu Y, Xie S. Nitrifying activity and ammonia-oxidizing microorganisms in a constructed wetland treating polluted surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:310-318. [PMID: 29444483 DOI: 10.1016/j.scitotenv.2018.02.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/03/2018] [Accepted: 02/03/2018] [Indexed: 06/08/2023]
Abstract
Ammonia oxidation, performed by both ammonia oxidizing bacteria (AOB) and archaea (AOA), is an important step for nitrogen removal in constructed wetlands (CWs). However, little is known about the distribution of these ammonia oxidizing organisms in CWs and the associated wetland environmental variables. Their relative importance to nitrification in CWs remains still controversial. The present study investigated the seasonal dynamics of AOA and AOB communities in a free water surface flow CW (FWSF-CW) used to ameliorate the quality of polluted river water. Strong seasonality effects on potential nitrification rate (PNR) and the abundance, richness, diversity and structure of AOA and AOB communities were observed in the river water treatment FWSF-CW. PNR was positively correlated to AOB abundance. AOB (6.76×105-6.01×107 bacterial amoA gene copies per gram dry sediment/soil) tended to be much more abundant than AOA (from below quantitative PCR detection limit to 9.62×106 archaeal amoA gene copies per gram dry sediment/soil). Both AOA and AOB abundance were regulated by the levels of nitrogen, phosphorus and organic carbon. Different wetland environmental variables determined the diversity and structure of AOA and AOB communities. Wetland AOA communities were mainly composed of unknown species and Nitrosopumilus-like organisms, while AOB communities were mainly represented by both Nitrosospira and Nitrosomonas.
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Affiliation(s)
- Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary. Sci Rep 2018; 8:1584. [PMID: 29371667 PMCID: PMC5785527 DOI: 10.1038/s41598-018-20044-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/12/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the distribution patterns of ammonia-oxidizing microorganisms (AOMs) between different habitats in the same area remain unclear. The present study investigated the AOMs’ abundance and community compositions in both sediment and water habitats of the Yellow River estuary. Quantitative PCR (qPCR) revealed that AOA showed significant higher abundance than AOB both in sediment and water samples. AOA and AOB abundance distribution trends were consistent in sediment but distinct in water along the sampling sites. Clone library-based analyses showed that AOA sequences were affiliated with Nitrososphaera, Nitrosopumilus and Nitrosotalea clusters. Generally, Nitrososphaera was predominant in sediment, while Nitrosopumilus and Nitrosotalea dominated in water column. AOB sequences were classified into genera Nitrosospira and Nitrosomonas, and Nitrosospira dominated in both habitats. Principal coordinate analysis (PCoA) also indicated AOA community structures exhibited significant differences between two habitats, while AOB were not. Ammonium and carbon contents were the potential key factors to influence AOMs’ abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat. These findings increase the understanding of the AOMs’ distribution patterns in estuarine ecosystems.
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Li X, Zhang M, Liu F, Chen L, Li Y, Li Y, Xiao R, Wu J. Seasonality distribution of the abundance and activity of nitrification and denitrification microorganisms in sediments of surface flow constructed wetlands planted with Myriophyllum elatinoides during swine wastewater treatment. BIORESOURCE TECHNOLOGY 2018; 248:89-97. [PMID: 28673518 DOI: 10.1016/j.biortech.2017.06.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 06/17/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Surface flow constructed wetlands (SFCWs) planted with Myriophyllum elatinoides for treatment of swine wastewater were examined to evaluate the effect of season, segment (site S1, S2, and S3), and treatment (100mgL-1 TN, T1; 300mgL-1 TN, T2; 500mgL-1 TN, T3) on the activity, and abundances of nitrifying and, denitrifying microorganisms, and on the abundance of sediment bacteria. The activity and abundances of nitrifiers, denitrifiers, and the abundance of bacteria were the highest in T3 samples, especially in S1 (P<0.05). The potential nitrification rate (PNR) was highest in the summer and potential denitrification rate (PDR) showed an increasing trend over seasons. The abundance of ammonia-oxidizing bacteria (AOB) was strongly correlated with PNR, while abundance of denitrifying gene (nirK) was strongly correlated with PDR. These results indicate that M. elatinoides SFCWs for swine wastewater treatment stimulate the growth of nitrifiers, denitrifiers and bacteria in sediments.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Miaomiao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China.
| | - Liang Chen
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, Hunan Province, PR China
| | - Yuyuan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Rulin Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
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Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies. Sci Rep 2017; 7:12006. [PMID: 28931901 PMCID: PMC5607297 DOI: 10.1038/s41598-017-12275-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 08/30/2017] [Indexed: 11/18/2022] Open
Abstract
The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.
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Wang HL, Zhang J, Sun QL, Lian C, Sun L. A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields. PLoS One 2017; 12:e0181048. [PMID: 28704556 PMCID: PMC5507547 DOI: 10.1371/journal.pone.0181048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 06/26/2017] [Indexed: 12/02/2022] Open
Abstract
Currently, little is known about the microbial diversity in the sediments of Pacmanus and Desmos hydrothermal fields in Manus Basin. In this study, Illumina-based sequencing of 16S rRNA gene amplicons and metagenomic analysis were conducted to investigate the microbial populations and metabolic profiles in the sediments from four different regions in Pacmanus and Desmos hydrothermal fields. It was found that Gammaproteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal populations, respectively. The autotrophic prokaryotes in the four communities probably fixed CO2 via four major pathways, i.e. Calvin-Benson-Bassham cycle, reductive acetyl-CoA cycle, rTCA cycle, and 3-hydroxypropionate/4-hydroxybutyrate cycle. Ammonia-oxidizing Thaumarchaeota, nitrifiers, denitrifiers, and sulfur oxidizers belonging to the subgroups of Proteobacteria (e.g., alpha, beta, gamma, and epsilon), Nitrospira, and Nitrospina, and sulfate-reducing Desulfobacterales likely played critical roles in nitrogen and sulfur cycling, in which ammonia, sulfur compounds, and hydrogen could be utilized as potential energy sources. These findings revealed new insights into the operational mechanism of the microbial communities associated with Pacmanus and Desmos hydrothermal fields.
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Affiliation(s)
- Hai-liang Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qing-lei Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chao Lian
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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26
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Yang Y, Li N, Zhao Q, Yang M, Wu Z, Xie S, Liu Y. Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:15358-15369. [PMID: 27109114 DOI: 10.1007/s11356-016-6707-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qun Zhao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Mengxi Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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27
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Zhang J, Zhou X, Chen L, Chen Z, Chu J, Li Y. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes. World J Microbiol Biotechnol 2016; 32:85. [DOI: 10.1007/s11274-016-2042-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/29/2016] [Indexed: 11/24/2022]
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Yang Y, Zhang J, Zhao Q, Zhou Q, Li N, Wang Y, Xie S, Liu Y. Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States. MICROBIAL ECOLOGY 2016; 71:257-265. [PMID: 26111964 DOI: 10.1007/s00248-015-0642-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jingxu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qun Zhao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qiheng Zhou
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ningning Li
- Yuanpei College, Peking University, Beijing, 100871, China
| | - Yilin Wang
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Lu S, Liu X, Ma Z, Liu Q, Wu Z, Zeng X, Shi X, Gu Z. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond. Front Microbiol 2016; 6:1539. [PMID: 26834709 PMCID: PMC4718984 DOI: 10.3389/fmicb.2015.01539] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster.
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Affiliation(s)
- Shimin Lu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xingguo Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhuojun Ma
- Chinese Academy of Fishery Sciences Beijing, China
| | - Qigen Liu
- College of Fisheries and Life, Shanghai Ocean University Shanghai, China
| | - Zongfan Wu
- Tongren Municipal Agricultural Commission (Government, Public) Tongren, China
| | - Xianlei Zeng
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xu Shi
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhaojun Gu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
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Dai Y, Wu Z, Zhou Q, Zhao Q, Li N, Xie S, Liu Y. Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils. Res Microbiol 2015; 166:655-63. [DOI: 10.1016/j.resmic.2015.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 11/30/2022]
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31
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Xing Y, Si YX, Hong C, Li Y. Multiple factors affect diversity and abundance of ammonia-oxidizing microorganisms in iron mine soil. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2015; 69:20-31. [PMID: 25860433 DOI: 10.1007/s00244-015-0144-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 02/28/2015] [Indexed: 06/04/2023]
Abstract
Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. In this study, four soil samples collected from a desert zone in an iron-exploration area and others from farmland and planted forest soil in an iron mine surrounding area. We analyzed the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in iron-mining area near the Miyun reservoir using ammonia monooxygenase. A subunit gene (amoA) as molecular biomarker. Quantitative polymerase chain reaction was applied to explore the relationships between the abundance of AOA and AOB and soil physicochemical parameters. The results showed that AOA were more abundant than AOB and may play a more dominant role in the ammonia-oxidizing process in the whole region. PCR-denaturing gradient gel electrophoresis was used to analyze the structural changes of AOA and AOB. The results showed that AOB were much more diverse than AOA. Nitrosospira cluster three constitute the majority of AOB, and AOA were dominated by group 1.1b in the soil. Redundancy analysis was performed to explore the physicochemical parameters potentially important to AOA and AOB. Soil characteristics (i.e. water, ammonia, organic carbon, total nitrogen, available phosphorus, and soil type) were proposed to potentially contribute to the distributions of AOB, whereas Cd was also closely correlated to the distributions of AOB. The community of AOA correlated with ammonium and water contents. These results highlight the importance of multiple drivers in microbial niche formation as well as their affect on ammonia oxidizer composition, both which have significant consequences for ecosystem nitrogen functioning.
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Affiliation(s)
- Yi Xing
- School of Civil and Environmental Engineering, and Key Laboratory of Metal and Mine Efficiently Exploiting and Safety, Ministry of Education, University of Science and Technology Beijing, Xueyuan Road No.30, Haidian District, Beijing, 100083, China,
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32
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Distribution of ammonia-oxidizing archaea and bacteria in plateau soils across different land use types. Appl Microbiol Biotechnol 2015; 99:6899-909. [DOI: 10.1007/s00253-015-6625-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/13/2015] [Accepted: 04/16/2015] [Indexed: 10/23/2022]
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33
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Zhang HH, Huang TL, Chen SN, Yang X, Lv K, Sekar R. Abundance and diversity of bacteria in oxygen minimum drinking water reservoir sediments studied by quantitative PCR and pyrosequencing. MICROBIAL ECOLOGY 2015; 69:618-629. [PMID: 25502074 DOI: 10.1007/s00248-014-0539-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
Reservoir sediment is one of the most stressful environments for microorganisms due to periodically oxygen minimum conditions. In this study, the abundance and composition of bacteria associated with sediments from three drinking water reservoirs (Zhoucun, ZCR; Shibianyu, SBYR; and Jinpen, JPR) were investigated by quantitative polymerase chain reaction and 16S rRNA-based 454 pyrosequencing. The results of physico-chemical analysis of sediments showed that the organic matter and total nitrogen were significantly higher in ZCR as compared to JPR (P < 0.01). The bacterial abundance was 9.13 × 10(6), 1.14 × 10(7), and 6.35 × 10(6) copies/ng DNA in sediments of SBYR, ZCR, and JPR, respectively (P < 0.01). The pyrosequencing revealed a total of 9,673 operational taxonomic units, which were affiliated with 17 phyla. The dominant phylum was Firmicutes (56.83%) in JPR; whereas, the dominance of Proteobacteria was observed in SBYR with 40.38% and ZCR with 39.56%. The Shannon-Wiener diversity (H') was high in ZCR; whereas, Chao 1 richness was high in SBYR. The dominant genera were Clostridium with 42.15% and Bacillus with 20.44% in JPR. Meanwhile, Dechloromonas with 14.80% and Smithella with 7.20% were dominated in ZCR, and Bacillus with 45.45% and Acinetobacter with 5.15% in SBYR. The heat map profiles and redundancy analysis indicated substantial differences in sediment bacterial community composition among three reservoirs. Moreover, it appears from the results that physico-chemical variables of sediments including pH, organic matter, total nitrogen, and available phosphorous played key roles in shaping the bacterial community diversity. The results obtained from this study will broaden our understanding on the bacterial community structure of sediments in oxygen minimum and stressful freshwater environments.
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Affiliation(s)
- Hai-han Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, Shaanxi Province, China
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Liu Y, Zhang J, Zhao L, Li Y, Dai Y, Xie S. Distribution of sediment ammonia-oxidizing microorganisms in plateau freshwater lakes. Appl Microbiol Biotechnol 2015; 99:4435-44. [DOI: 10.1007/s00253-014-6341-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 01/16/2023]
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Zhang J, Yang Y, Zhao L, Li Y, Xie S, Liu Y. Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes. Appl Microbiol Biotechnol 2014; 99:3291-302. [PMID: 25432677 DOI: 10.1007/s00253-014-6262-x] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 11/30/2022]
Abstract
Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.
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Affiliation(s)
- Jingxu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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Impact of carbon source amendment on ammonia-oxidizing microorganisms in reservoir riparian soil. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0979-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils. Appl Microbiol Biotechnol 2014; 98:10197-209. [PMID: 25030456 DOI: 10.1007/s00253-014-5942-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/02/2014] [Accepted: 07/06/2014] [Indexed: 10/25/2022]
Abstract
Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment ecosystems.
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Liu B, Li Y, Zhang J, Zhou X, Wu C. Abundance and diversity of ammonia-oxidizing microorganisms in the sediments of Jinshan Lake. Curr Microbiol 2014; 69:751-7. [PMID: 25008777 DOI: 10.1007/s00284-014-0646-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/12/2014] [Indexed: 11/25/2022]
Abstract
Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH4-N, NO3-N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment.
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Affiliation(s)
- Biao Liu
- Department of Environment Engineering, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China,
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Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland. Appl Microbiol Biotechnol 2014; 98:5697-707. [PMID: 24619246 DOI: 10.1007/s00253-014-5651-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 02/25/2014] [Accepted: 02/26/2014] [Indexed: 11/27/2022]
Abstract
Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) might be the key microorganisms in ammonia conversion in ecosystems. However, the depth-related change of AOA and AOB in sediment ecosystem is still not clear. The relative contribution of AOA and AOB to nitrification in wetland sediment remains also unclear. Moreover, information about ammonia-oxidizing microorganisms in high-altitude freshwater wetland is still lacking. The present study investigated the relative abundances and community structures of AOA and AOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China). Variations of the relative abundances and community structures of AOA and AOB were found in the wetland sediments, dependent on both sampling site and sediment depth. The relative abundances of AOA and AOB (0.04-3.84 and 0.01-0.52 %) and the AOA/AOB ratio (0.12-4.65) showed different depth-related change patterns. AOB community size was usually larger than AOA community size. AOB diversity was usually higher than AOA diversity. AOA diversity decreased with the increase of sediment depth, while AOB diversity showed no obvious link with the sediment depth. Pearson's correlation analysis showed that AOA diversity had a positive significant correlation with available phosphorus. Nitrosospira-like sequences, with different compositions, predominated in the wetland sediment AOB communities. This work could provide some new insights toward nitrification in freshwater sediment ecosystems.
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