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Li W, Zhen Y, Yang Y, Wang D, He H. Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea. J Microbiol 2024:10.1007/s12275-024-00166-5. [PMID: 39212864 DOI: 10.1007/s12275-024-00166-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 102 to 2.17 × 106 copies per gram of sediment and from 6.6 × 101 to 7.65 × 104 copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50 °C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.
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Affiliation(s)
- Wenhui Li
- Key Laboratory of Marine Environmental and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
| | - Yu Zhen
- Key Laboratory of Marine Environmental and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, People's Republic of China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, People's Republic of China.
| | - Yuhong Yang
- Key Laboratory of Marine Environmental and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
| | - Daling Wang
- Key Laboratory of Marine Environmental and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
| | - Hui He
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, People's Republic of China
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Wu P, Liu Y, Li C, Zheng Q, Hong Y, Wu J, Xu S, Lin L, Xiao Y, Wang T, Liu Y. Distribution and co-occurrence networks of the bacterial community in sediment cores from the subtropical Daya Bay, China. MARINE POLLUTION BULLETIN 2023; 196:115580. [PMID: 37801799 DOI: 10.1016/j.marpolbul.2023.115580] [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: 06/08/2023] [Revised: 08/01/2023] [Accepted: 09/21/2023] [Indexed: 10/08/2023]
Abstract
The bacterial community plays an important role in biogeochemical cycles in marine sediment. However, little is known about the vertical profiles and co-occurrence patterns of bacterial community in sediment cores from the marine environment. In this study, five sediment cores were taken from a subtropical bay in China, heavily impacted by anthropogenic activities. The bacterial composition in sediment cores was investigated by using high-throughput sequencing of the 16S rRNA gene. A principal coordinates analysis and an adonis analysis of the operational taxonomic unit (OTU) compositions showed that spatial variation, rather than vertical variation, determined the bacterial structure in sediment cores. The bacterial complexity varied greatly across the five sediment cores, and the rare taxa played an important role in supporting the stability of the bacterial network. This study revealed that sediment properties and anthropogenic activities may induce a shift in the bacterial composition in sediment cores of a subtropical bay.
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Affiliation(s)
- Peng Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Yong Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China.
| | - Chunhou Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China.
| | - Qiushi Zheng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Shannan Xu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Lin Lin
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Yayuan Xiao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Teng Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Observation and Research Station of Xisha Island Reef Fishery Ecosystem of Hainan Province/Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province/Sanya Tropical Fisheries Research Institute, Sanya, Hainan 572018, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
| | - Yu Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China; Scientific Observation and Research Station of Pearl River Estuary Ecosystem of Guangdong Province, Guangzhou 510300, China; Guangdong Provincial Key Laboratory of Fishery Ecology Environment, Guangzhou 510300, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
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Ye J, Wu J, Deng W, Li Y, Jiang C, Wang Y, Hong Y. Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea. MARINE POLLUTION BULLETIN 2022; 185:114351. [PMID: 36401947 DOI: 10.1016/j.marpolbul.2022.114351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/26/2022] [Accepted: 11/06/2022] [Indexed: 06/16/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.
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Affiliation(s)
- Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Wenfang Deng
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yiben Li
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Cuihong Jiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
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Zheng M, Mu G, Zhang A, Wang J, Chang F, Niu J, Wang X, Gao T, Zhao Z. Predominance of comammox bacteria among ammonia oxidizers under low dissolved oxygen condition. CHEMOSPHERE 2022; 308:136436. [PMID: 36115478 DOI: 10.1016/j.chemosphere.2022.136436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 08/19/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Although low-oxygen nitrification can significantly cut down the aeration demand in wastewater treatment plants, little is known about the community dynamics of relevant microorganisms under different oxygen concentrations. Here, by conducting a series of bioreactors with oxygen concentrations of 0%, 2%, 5%, 10%, 20%, 40%, and 70%, we provided a comprehensive investigation on the behaviors and performances of comammox bacteria (CMX), ammonia-oxidizing bacteria (AOB) and archaea (AOA) during the nitrification process. Quantitative PCR analysis demonstrated that CMX was the dominant ammonia-oxidizer under low oxygen condition (10%) after the four-month operation with the abundance increased by 8.65 times higher than the initial operation, whereas the growth of AOA and AOB was inhibited. Moreover, Nitrospira nitrosa dominated the CMX species (relative abundance >96%) in low dissolved oxygen concentrations, while Nitrospira nitrificans (3.39%) seemed to prefer high oxygen conditions. Our study indicates the long-term effects of oxygen concentrations on the niche differentiation of ammonia oxidizers, and highlights the significance of CMX in low-oxygen nitrification for reducing global carbon emission and energy consumption.
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Affiliation(s)
- Maosheng Zheng
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Technology, North China Electric Power University, Beijing, 102206, China
| | - Guangli Mu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Technology, North China Electric Power University, Beijing, 102206, China
| | - Anqi Zhang
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Technology, North China Electric Power University, Beijing, 102206, China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, China.
| | - Fang Chang
- Marine Resources Research Centre, Tianjin Research Institute for Water Transport Engineering, M.O.T., Tianjin, 300456, China
| | - Junfeng Niu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Technology, North China Electric Power University, Beijing, 102206, China
| | - Xinwei Wang
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Technology, North China Electric Power University, Beijing, 102206, China
| | - Tian Gao
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Technology, North China Electric Power University, Beijing, 102206, China
| | - Zhirong Zhao
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Technology, North China Electric Power University, Beijing, 102206, China
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Chen J, Zhou Z, Gu JD. Distribution pattern of N-damo bacteria along an anthropogenic nitrogen input gradient from the coastal mangrove wetland to the South China sea sediments. MARINE ENVIRONMENTAL RESEARCH 2022; 181:105739. [PMID: 36084374 DOI: 10.1016/j.marenvres.2022.105739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Microbial nitrite-dependent anaerobic methane oxidation (n-damo) process is important for mitigating methane emission and anthropogenic nitrogen inputs in the marine environment. However, the distribution pattern of n-damo bacteria along an anthropogenic N-input gradient from the coastal wetland to the pristine South China Sea is poorly understood. This study investigated the diversity and abundance of n-damo bacteria in samples collected along a N-input gradient from Mai Po (MP) mangrove wetland sediments of the Pearl River Estuary (PRE) to the deep ocean sediments of the South China Sea (SCS). Retrieved 16S rDNA sequences showed a shift of n-damo community composition of complex structures with both freshwater and marine n-damo lineages in MP intertidal sediments to marine dominated characteristic in SCS sediments. The observed variation of Shannon and Chao1 indexes of n-damo bacteria shared a similar trend of a decrease at first followed by an increase along the targeting gradient with previously investigated methanogens, anaerobic methanotrophic archaea, ammonia-oxidizing archaea and ammonia-oxidizing bacteria, but had a reverse pattern with anammox bacteria. The community structure of pmoA gene sequences contained freshwater lineages only in SCS continental shelf sediments closer to the PRE, and turned to group with other marine samples in deeper and pristine sediments. Results suggested that n-damo bacteria might be a major contributor to anaerobic denitrification in the SCS sediments because their abundances were much higher than previously studied anammox bacteria in the same sample set. The distribution pattern of n-damo bacterial diversity, richness and abundance along the anthropogenic N-input gradient implies that they could be used as a bio-indicator for monitoring the anthropogenic/terrestrial inputs in marine environments.
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Affiliation(s)
- Jing Chen
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, PR China; Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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Zhou Z, Meng H, Gu W, Li J, Deng M, Gu JD. High-throughput sequencing reveals the main drivers of niche-differentiation of bacterial community in the surface sediments of the northern South China sea. MARINE ENVIRONMENTAL RESEARCH 2022; 178:105641. [PMID: 35594805 DOI: 10.1016/j.marenvres.2022.105641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 05/16/2023]
Abstract
Studies on marine bacterial communities have revealed endemism in local communities, yet the underlying mechanisms remained elusive. Environmental gradient settings can benefit the straightaway study of community composition changes and the mechanisms explaining them. Here, MiSeq-based 16S rRNA gene sequencing was performed on 12 surface sediment samples from the northern South China Sea (nSCS) revealing that shallow-sea samples had a higher alpha diversity than deep-sea samples, and were differentiated from them significantly based on beta diversity. Temperature, seawater depth, and salinity were the top three influential factors. Bacterial 16S rRNA gene abundance was positively correlated with temperature, and negatively correlated with salinity. Sulfate-reducing bacteria including Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteraceae were enriched in shallow-sea sediments, co-abundant with nitrite-oxidizing Nitrospira and potential sulfur-oxidizing shallow-sea specific Woeseiaceae/JTB255 clade. Meanwhile, the co-existing and co-abundant of marine anammox and n-damo bacteria were enriched in deep-sea sediments, which was firstly evidenced in this study. The global deep-sea cosmopolitans, OM1 clade, and deep-sea specific Woeseiaceae/JTB255 clade were also found enriched in deep-sea sediments of nSCS. The discovery of novel taxa which were differentially enriched in shallow-/deep-sea sediments not only shed light on enigmatic physiological properties and the natural selection mechanism, but also provided the potential ecological-functional links which invoked further genomics-based metabolic characteristics.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Meng
- School of Environment, Nanjing Normal University, 122 Ninghai Road, Nanjing, Jiangsu, 210023, China
| | - Wenjie Gu
- Insitute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences/Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, 66 Jinying Road, Guangzhou, Guangdong, 510640, China
| | - Jing Li
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Maocheng Deng
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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Patil PK, Baskaran V, Vinay TN, Avunje S, Leo-Antony M, Shekhar MS, Alavandi SV, Vijayan KK. Abundance, community structure and diversity of nitrifying bacterial enrichments from low and high saline brackishwater environments. Lett Appl Microbiol 2021; 73:96-106. [PMID: 33780023 DOI: 10.1111/lam.13480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
The study reports diversity in nitrifying microbial enrichments from low (0·5-5‰) and high (18-35‰) saline ecosystems. Microbial community profiling of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) enrichments was analysed by sequencing 16S rRNA and was processed using Mothur pipeline. The α-diversity indices showed the richness of nitrifying bacterial consortia from the high saline environment and were clustering based on the source of the sample. AOB and NOB enrichments from both the environments showed diverse lineages of phyla distributed in both groups with 38 and 34 phyla from low saline and 53 and 40 phyla in high saline sources, respectively. At class level, α- and γ-proteobacteria were found to be more dominant in both the enrichments. AOBs and NOBs in enrichments from low saline environments were dominated by Nitrosomonadaceae, Gallionellaceae (Nitrotoga sp.) and Ectothiorhodospiraceae and Nitrospira, respectively. Though Chromatiaceae were present in both AOB and NOB enrichments, Nitrosoglobus and Nitrosococcus dominated the AOBs while NOBs were dominated by uncultured genera, whereas Rhizobiales were found in both the enrichments. AOBs and NOBs in enrichments from high saline environments were dominated by Nitrospira-like AOBs, Nitrosomonas and Nitrosococcus genera, whereas ammonia-oxidizing archaea (AOA) group included Nitrosopumilus and Nitrososphaera genera comprising and Nitrospirae, respectively. The majority of the genera obtained in both the salinities were found to be either uncultured or unclassified groups. Results of the study suggest that the AOB and NOB consortia have unique and diverse microbes in each of the enrichments, capable of functioning in aquaculture systems practised at different salinities (0-60 ppt).
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Affiliation(s)
- P K Patil
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - V Baskaran
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - T-N Vinay
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - S Avunje
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - M Leo-Antony
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - M S Shekhar
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - S V Alavandi
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - K K Vijayan
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
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8
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Monthly distribution of ammonia-oxidizing microbes in a tropical bay. J Microbiol 2020; 59:10-19. [PMID: 33201437 DOI: 10.1007/s12275-021-0287-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17-20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17-20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.
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Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary. Appl Environ Microbiol 2020; 86:AEM.00736-20. [PMID: 32631866 DOI: 10.1128/aem.00736-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.
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Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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11
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Li Y, Jing H, Kao SJ, Zhang W, Liu H. Metabolic response of prokaryotic microbes to sporadic hypoxia in a eutrophic subtropical estuary. MARINE POLLUTION BULLETIN 2020; 154:111064. [PMID: 32319898 DOI: 10.1016/j.marpolbul.2020.111064] [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: 08/01/2019] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Coastal eutrophication and consequent oxygen depletion (hypoxia) occurs worldwide due to increased human activity. The paucity of genomic information of microbes in hypoxia prone coastal waters have hindered our understanding of microorganism related causation and adaption to the environment. Here, using metagenomic approach, we investigated microbial metabolic capability in heavily polluted Pearl River estuary. Our results highlighted the possible roles of microbial metabolic activity in the formation of bottom water hypoxia by revealing enriched organic degradation related microbial genes in the bottom layer beneath surface phytoplankton bloom. Microbial nitrate reduction in hypoxia layer was low, possibly due to the low pH and fluctuating oxygen level. On contrary, high abundance of sulfate-reducing, and antibiotic and metal resistance related genes were detected in bottom and surface layers, respectively, indicating microbial adaptation to oxygen depletion and pollution. Our study provides gene level information on the interactive relations between microbial functions and environmental stress.
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Affiliation(s)
- Yingdong Li
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Weipeng Zhang
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, China
| | - Hongbin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, China; Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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12
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Zhou Z, Chen J, Gu W, Gu JD. Biogeographic pattern of the nirS gene-targeted anammox bacterial community and composition in the northern South China Sea and a coastal Mai Po mangrove wetland. Appl Microbiol Biotechnol 2020; 104:3167-3181. [PMID: 32036435 DOI: 10.1007/s00253-020-10415-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/19/2020] [Accepted: 01/24/2020] [Indexed: 11/29/2022]
Abstract
Functional genes, namely hzo/hao, nirS, hzs, and ccs gene, are efficient with high specificity for detecting anammox bacteria. Sc-nirS and An-nirS primer sets were proposed for targeting Scalindua/non-Scalindua anammox bacterial groups; previously, they have not been assessed for biogeographic study on marine-terrestrial transitional systems, specifically marine and terrestrial ecosystems. Here, we report phylogenetic distribution pattern of anammox bacteria in both northern South China Sea (nSCS) and Mai Po wetland (a coastal mangrove) using nirS gene-based primers. A well-delineated biogeographic distribution pattern from ocean to continental shelf was evident by combining both gene-based analyses as previously depicted using 16S rRNA as the biomarker. Furthermore, factors affecting the abundance and composition of An-nirS genes in Mai Po wetland were identified as substrate (NO3-/NO2- concentration) and anoxic/oxic condition in association to depth. An-nirS gene abundance was from 2.6 × 103 to 1.2-1.4 × 104 copies/g dry sediment in nSCS; and it was around 5 × 103 and 1-2 × 104 copies/g dry sediment in surface and subsurface sediments of Mai Po wetland, respectively. In addition, nirS gene abundance and distribution pattern of denitrifiers and anammox bacteria in the wetland indicates a competition relationship between them. Mangrove vegetation affected the community composition of An-nirS gene considerably, and a more homogeneous distribution pattern was observed in the mangrove forest than intertidal mudflats. Sc/An-nirS gene-based biogeographic insights on anammox bacteria have shed lights on the compositional and potential functional dynamics and emphasized the importance of molecular tools on refining the current microbial ecological patterns.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Jing Chen
- School of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan Province, People's Republic of China
| | - Wenjie Gu
- Guangdong Academy of Agricultural Sciences, 29 Jinying Road, Guangzhou, 510000, Guangdong Province, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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13
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Hu J, Liu S, Yang W, He Z, Wang J, Liu H, Zheng P, Xi C, Ma F, Hu B. Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone. MICROBIAL ECOLOGY 2019; 78:555-564. [PMID: 30903203 DOI: 10.1007/s00248-019-01359-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (107-108amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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14
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Jiang Q, Xia F, Zhu T, Wang D, Quan Z. Distribution of comammox and canonical ammonia‐oxidizing bacteria in tidal flat sediments of the Yangtze River estuary at different depths over four seasons. J Appl Microbiol 2019; 127:533-543. [DOI: 10.1111/jam.14337] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Q. Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences Fudan University Shanghai P.R. China
| | - F. Xia
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences Fudan University Shanghai P.R. China
- School of Food and Biological Engineering Shaanxi University of Science and Technology Xi’an P.R. China
| | - T. Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences Fudan University Shanghai P.R. China
| | - D. Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences Fudan University Shanghai P.R. China
| | - Z. Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences Fudan University Shanghai P.R. China
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15
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Liu Y, Liu J, Yao P, Ge T, Qiao Y, Zhao M, Zhang XH. Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas. Syst Appl Microbiol 2018; 41:658-668. [PMID: 30172418 DOI: 10.1016/j.syapm.2018.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 01/19/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS). Nitrosopumilus (AOA) and Nitrosospira (AOB) were predominant lineages, but their abundances varied significantly between ECS, and BS and YS. This was mainly attributed to salinity and dissolved oxygen of the bottom water. The discovery of a high abundance of Nitrosophaera at estuarine sites suggested strong terrigenous influence exerted on the AOA community. In contrast, variations in ocean conditions played more important roles in structuring the AOB community, which was separated by bottom water dissolved oxygen into two groups: the south YS, and the north YS and BS. This study provides a comprehensive insight into the spatial distribution pattern of ammonia-oxidizing prokaryotes in ECMS sediments, laying a foundation for understanding their relative roles in nitrification.
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Affiliation(s)
- Yuyang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Tiantian Ge
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Successive transitory distribution of Thaumarchaeota and partitioned distribution of Bathyarchaeota from the Pearl River estuary to the northern South China Sea. Appl Microbiol Biotechnol 2018; 102:8035-8048. [PMID: 29946932 DOI: 10.1007/s00253-018-9147-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 05/05/2018] [Accepted: 05/23/2018] [Indexed: 01/09/2023]
Abstract
Thaumarchaeota and Bathyarchaeota (formerly named Miscellaneous Crenarchaeotal Group, MCG) are globally occurring archaea playing potential roles in nitrogen and carbon cycling, especially in marine benthic biogeochemical cycle. Information on their distributional and compositional patterns could provide critical clues to further delineate their physiological and biochemical characteristics. Profiles of thaumarchaeotal and the total archaeal community in the northern South China Sea surface sediments revealed a successively transitional pattern of Thaumarchaeota composition using MiSeq sequencing. Shallow-sea sediment enriched phylotypes decreased gradually along the slope from estuarine and coastal marine region to the deep-sea, while deep-sea sediment enriched phylotypes showed a trend of increasing. Proportion of Thaumarchaeota within the total archaea increased with seawater depth. Phylotypes enriched in shallow- and deep-sea sediments were affiliated to OTUs originated from similar niches, suggesting that physiological adaption not geographical distance shaped the distribution of Thaumarchaeota lineages. Quantitative PCR also depicted a successive decrease of thaumarchaeotal 16S rRNA gene abundance from the highest at shallow-sea sites E708S and E709S (2.57 × 106 and 2.73 × 106 gene copies/g of dry sediment) to the lowest at deep-sea sites E525S and E407S (1.97 × 106 and 2.14 × 106 gene copies/g of dry sediment). Both of the abundance fractions of Bathyarchaeota subgroups (including subgroups 1, 6, 8, 10, 13, 15, 17, and ungrouped Bathyarchaeota) and the total Bathyarchaeota in the total archaea showed a negative distribution to seawater depth. Partitioned distribution of Bathyarchaeota fraction in the total archaea is documented for the first time in this study, and the shallow- and deep-sea Bathyarchaeota could account for 17.8 and 0.8%, respectively, on average. Subgroups 6 and 8, enriched subgroups in shallow-sea sediments, largely explained this partitioned distribution pattern according to seawater depth. Their prevalence in shallow-sea and suboxic estuarine sediments rather than deep-sea sediments hints that their metabolic properties of carbon metabolism are adapted to carbon substrates in these environments.
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17
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He H, Zhen Y, Mi T, Fu L, Yu Z. Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China. Front Microbiol 2018; 9:116. [PMID: 29456526 PMCID: PMC5801408 DOI: 10.3389/fmicb.2018.00116] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.
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Affiliation(s)
- Hui He
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Lulu Fu
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, China
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18
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Wu RN, Meng H, Wang YF, Lan W, Gu JD. A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils. MICROBIAL ECOLOGY 2017; 74:910-922. [PMID: 28808742 DOI: 10.1007/s00248-017-1045-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/13/2017] [Indexed: 05/20/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4+ equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al3+. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.
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Affiliation(s)
- Ruo-Nan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Han Meng
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Yong-Feng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
- Laboratory of Microbial Ecology and Toxicology, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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19
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Wang J, Kan J, Zhang X, Xia Z, Zhang X, Qian G, Miao Y, Leng X, Sun J. Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean-from the Equator to the Bay of Bengal. Front Microbiol 2017; 8:415. [PMID: 28360898 PMCID: PMC5352681 DOI: 10.3389/fmicb.2017.00415] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.
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Affiliation(s)
- Jing Wang
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Jinjun Kan
- Stroud Water Research Center Avondale, PA, USA
| | - Xiaodong Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Zhiqiang Xia
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Xuecheng Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Gang Qian
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Yanyi Miao
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology Tianjin, China
| | - Xiaoyun Leng
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and TechnologyTianjin, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and TechnologyTianjin, China
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20
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New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria. Appl Microbiol Biotechnol 2016; 101:1267-1287. [PMID: 28032194 DOI: 10.1007/s00253-016-8013-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 01/13/2023]
Abstract
PCR primers targeting genes encoding the two proteins of anammox bacteria, hydrazine synthase and cytochrome c biogenesis protein, were designed and tested in this study. Three different ecotypes of samples, namely ocean sediments, coastal wetland sediments, and wastewater treatment plant (WWTP) samples, were used to assess the primer efficiency and the community structures of anammox bacteria retrieved by 16S ribosomal RNA (rRNA) and the functional genes. Abundances of hzsB gene of anammox bacteria in South China Sea (SCS) samples were significantly correlated with 16S rRNA gene by qPCR method. And hzsB and hzsC gene primer pair hzsB364f-hzsB640r and hzsC745f-hzsC862r in combination with anammox bacterial 16S rRNA gene primers were recommended for quantifying anammox bacteria. Congruent with 16S rRNA gene-based community study, functional gene hzsB could also delineate the coastal-ocean distributing pattern, and seawater depth was positively associated with the diversity and abundance of anammox bacteria from shallow- to deep-sea. Both hzsC and ccsA genes could differentiate marine samples between deep and shallow groups of the Scalindua sp. clades. As for WWTP samples, non-Scalindua anammox bacteria reflected by hzsB, hzsC, ccsA, and ccsB gene-based libraries showed a similar distribution pattern with that by 16S rRNA gene. NH4+ and NH4+/Σ(NO3- + NO2-) positively correlated with anammox bacteria gene diversity, but organic matter contents correlated negatively with anammox bacteria gene diversity in SCS. Salinity was positively associated with diversity indices of hzsC and ccsB gene-harboring anammox bacteria communities and could potentially differentiate the distribution patterns between shallow- and deep-sea sediment samples. SCS surface sediments harbored considerably diverse community of Scalindua. A new Mai Po clade representing coastal estuary wetland anammox bacteria group based on 16S rRNA gene phylogeny is proposed. Existence of anammox bacteria within wider coverage of genera in Mai Po wetland indicates this unique niche is very complex, and species of anammox bacteria are niche-specific with different physiological properties towards substrates competing and chemical tolerance capability.
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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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Zhang Y, Chen L, Sun R, Dai T, Tian J, Zheng W, Wen D. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay. Appl Microbiol Biotechnol 2016; 100:6035-45. [PMID: 26960319 DOI: 10.1007/s00253-016-7421-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/20/2016] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.
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Affiliation(s)
- Yan Zhang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Lujun Chen
- School of Environment, Tsinghua University, Beijing, 100084, China.,Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, 314050, China
| | - Renhua Sun
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.,Rural Energy & Environment Agency, Ministry of Agriculture, Beijing, 100125, China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jinping Tian
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Wei Zheng
- Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, 314050, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Yu S, Yao P, Liu J, Zhao B, Zhang G, Zhao M, Yu Z, Zhang XH. Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas. Front Microbiol 2016; 7:137. [PMID: 26904010 PMCID: PMC4751261 DOI: 10.3389/fmicb.2016.00137] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO[Formula: see text]), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ(15)NTN and SiO[Formula: see text], and nitrate and δ(13)C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO[Formula: see text]. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.
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Affiliation(s)
- Shaolan Yu
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Peng Yao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of ChinaQingdao, China; Qingdao Collaborative Innovation Center of Marine Science and Technology, Ocean University of ChinaQingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Jiwen Liu
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Bin Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Guiling Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Meixun Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of ChinaQingdao, China; Qingdao Collaborative Innovation Center of Marine Science and Technology, Ocean University of ChinaQingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Zhigang Yu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Xiao-Hua Zhang
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China Qingdao, China
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Bao L, Wang X, Chen Y. Abundance and distribution of ammonia-oxidizing microorganisms in the sediments of Beiyun River, China. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1191-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Zhang Q, Tang F, Zhou Y, Xu J, Chen H, Wang M, Laanbroek HJ. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China. Front Microbiol 2015; 6:1180. [PMID: 26579089 PMCID: PMC4621301 DOI: 10.3389/fmicb.2015.01180] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/12/2015] [Indexed: 12/11/2022] Open
Abstract
Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira.
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Affiliation(s)
- Qiufang Zhang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Fangyuan Tang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Yangjing Zhou
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Jirong Xu
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Heping Chen
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Mingkuang Wang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Hendrikus J Laanbroek
- Department of Microbial Wetland Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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Luo ZH, Xu W, Li M, Gu JD, Zhong TH. Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean. Antonie van Leeuwenhoek 2015; 108:329-42. [PMID: 26014493 DOI: 10.1007/s10482-015-0485-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 05/18/2015] [Indexed: 12/23/2022]
Abstract
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.
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Affiliation(s)
- Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen, 361005, People's Republic of China,
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Puthiya Veettil V, Abdulaziz A, Chekidhenkuzhiyil J, Kalanthingal Ramkollath L, Karayadi Hamza F, Kizhakkepat Kalam B, Kallungal Ravunnikutty M, Nair S. Bacterial domination over archaea in ammonia oxidation in a monsoon-driven tropical estuary. MICROBIAL ECOLOGY 2015; 69:544-553. [PMID: 25344857 DOI: 10.1007/s00248-014-0519-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 10/09/2014] [Indexed: 06/04/2023]
Abstract
Autotrophic ammonia oxidizing microorganisms, which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale.
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Zhou Z, Chen J, Cao H, Han P, Gu JD. Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes. Front Microbiol 2015; 5:789. [PMID: 25774150 PMCID: PMC4343527 DOI: 10.3389/fmicb.2014.00789] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/22/2014] [Indexed: 11/17/2022] Open
Abstract
Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 106 copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 106 copies per gram dry weight) was observed, but higher abundance (6.9 × 106 to 1.02 × 108 copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 105 copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 105 copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 108 copies per gram dry weight) and pmoA gene (1.56 × 107 copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Jing Chen
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Huiluo Cao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong China
| | - Ping Han
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
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Potential contribution of anammox to nitrogen loss from paddy soils in Southern China. Appl Environ Microbiol 2014; 81:938-47. [PMID: 25416768 DOI: 10.1128/aem.02664-14] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anaerobic oxidation of ammonium (anammox) process has been observed in diverse terrestrial ecosystems, while the contribution of anammox to N2 production in paddy soils is not well documented. In this study, the anammox activity and the abundance and diversity of anammox bacteria were investigated to assess the anammox potential of 12 typical paddy soils collected in southern China. Anammox bacteria related to "Candidatus Brocadia" and "Candidatus Kuenenia" and two novel unidentified clusters were detected, with "Candidatus Brocadia" comprising 50% of the anammox population. The prevalence of the anammox was confirmed by the quantitative PCR results based on hydrazine synthase (hzsB) genes, which showed that the abundance ranged from 1.16 × 10(4) to 9.65 × 10(4) copies per gram of dry weight. The anammox rates measured by the isotope-pairing technique ranged from 0.27 to 5.25 nmol N per gram of soil per hour in these paddy soils, which contributed 0.6 to 15% to soil N2 production. It is estimated that a total loss of 2.50 × 10(6) Mg N per year is linked to anammox in the paddy fields in southern China, which implied that ca. 10% of the applied ammonia fertilizers is lost via the anammox process. Anammox activity was significantly correlated with the abundance of hzsB genes, soil nitrate concentration, and C/N ratio. Additionally, ammonia concentration and pH were found to be significantly correlated with the anammox bacterial structure.
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Hou M, Xiong J, Wang K, Ye X, Ye R, Wang Q, Hu C, Zhang D. Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea. MARINE POLLUTION BULLETIN 2014; 86:147-153. [PMID: 25110045 DOI: 10.1016/j.marpolbul.2014.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/08/2014] [Accepted: 07/20/2014] [Indexed: 06/03/2023]
Abstract
Anthropogenic nitrogen (N) discharges has caused eutrophication in coastal zones. Ammonia-oxidizing bacteria (AOB) convert ammonia to nitrite and play important roles in N transformation. Here, we used pyrosequencing based on the amoA gene to investigate the response of the sediment AOB community to an N pollution gradient in the East China Sea. The results showed that AOB assemblages were primarily affiliated with Nitrosospira-like lineages, and only 0.4% of those belonged to Nitrosomonas-like lineage. The Nitrosospira-like lineage was separated into four clusters that were most similar to the sediment AOB communities detected in adjacent marine regions. Additionally, one clade was out grouped from the AOB lineages, which shared the high similarities with pmoA gene. The AOB community structures substantially changed along the pollution gradient, which were primarily shaped by NH4(+)-N, NO3(-)-N, SO4(2)(-)-S, TP and Eh. These results demonstrated that coastal pollution could dramatically influence AOB communities, which, in turn, may change ecosystem function.
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Affiliation(s)
- Manhua Hou
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China
| | - Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China
| | - Xiansen Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Ran Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Qiong Wang
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Changju Hu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China.
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Hu Z, Meng H, Shi JH, Bu NS, Fang CM, Quan ZX. Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem. Front Microbiol 2014; 5:371. [PMID: 25101072 PMCID: PMC4107847 DOI: 10.3389/fmicb.2014.00371] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 07/02/2014] [Indexed: 11/30/2022] Open
Abstract
Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition.
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Affiliation(s)
- Ziye Hu
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
| | - Han Meng
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
| | - Jin-Huan Shi
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
| | - Nai-Shun Bu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityShanghai, China
| | - Chang-Ming Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityShanghai, China
| | - Zhe-Xue Quan
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
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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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Zeng J, Zhao D, Yu Z, Huang R, Wu QL. Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms. PLoS One 2014; 9:e100653. [PMID: 24959960 PMCID: PMC4069112 DOI: 10.1371/journal.pone.0100653] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/27/2014] [Indexed: 12/03/2022] Open
Abstract
In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups.
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Affiliation(s)
- Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- * E-mail:
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Rui Huang
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Qinglong L. Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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Xu W, Li M, Ding JF, Gu JD, Luo ZH. Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean. Appl Microbiol Biotechnol 2014; 98:7993-8004. [DOI: 10.1007/s00253-014-5833-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 01/29/2023]
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Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea. Appl Microbiol Biotechnol 2014; 98:7971-82. [DOI: 10.1007/s00253-014-5838-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
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36
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Chen Y, Zhen Y, He H, Lu X, Mi T, Yu Z. Diversity, abundance, and spatial distribution of ammonia-oxidizing β-proteobacteria in sediments from Changjiang Estuary and its adjacent area in East China Sea. MICROBIAL ECOLOGY 2014; 67:788-803. [PMID: 24362769 DOI: 10.1007/s00248-013-0341-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
Changjiang Estuary, the largest estuary in China, encompasses a wide range of nutrient loading and trophic levels from the rivers to the sea, providing an ideal natural environment to explore relationships between functional diversity, physical/chemical complexity, and ecosystem function. In this study, molecular biological techniques were used to analyze the community structure and diversity of ammonia-oxidizing bacteria (AOB) in the sediments of Changjiang Estuary and its adjacent waters in East China Sea. The amoA gene (encoding ammonia monooxygenase subunit A) libraries analysis revealed extensive diversity within the β-Proteobacteria group of AOB, which were grouped into Nitrosospira-like and Nitrosomonas-like lineages. The majority of amoA gene sequences fell within Nitrosospira-like clade, and only a few sequences were clustered with the Nitrosomonas-like clade, indicating that Nitrosospira-like lineage may be more adaptable than Nitrosomonas-like lineage in this area. Multivariate statistical analysis indicated that the spatial distribution of the sedimentary β-Proteobacterial amoA genotype assemblages correlated significantly with nitrate, nitrite, and salinity. The vertical profile of amoA gene copies in gravity cores showed that intense sediment resuspension led to a deeper mixing layer. The horizontal distribution pattern of amoA gene copies was nearly correlated with the clayey mud belt in Changjiang Estuary and its adjacent area in East China Sea, where higher β-Proteobacteria phylogenetic diversity was observed. Meanwhile, those areas with high amoA copies in the surface sediments nearly matched those with low concentrations of dissolved oxygen and ammonium in the bottom water.
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Affiliation(s)
- Yangyang Chen
- College of Environmental Science and Engineering, Ocean University of China, 238 Songling Road, Qingdao, 266100, People's Republic of 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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Wang J, Dong H, Wang W, Gu JD. Reverse-transcriptional gene expression of anammox and ammonia-oxidizing archaea and bacteria in soybean and rice paddy soils of Northeast China. Appl Microbiol Biotechnol 2014; 98:2675-86. [PMID: 24077726 DOI: 10.1007/s00253-013-5242-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 09/03/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
Abstract
The relative gene expression of hydrazine oxidoreductase encoding gene (hzo) for anaerobic ammonium oxidizing bacteria (anammox) and ammonia monooxygenase encoding gene (amoA) for both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in Sanjiang Plain soybean and rice paddy soils of Northeast China was investigated by using real-time reverse-transcriptional quantitative PCR. Metabolically active populations of anammox, AOA, and AOB in rice paddy soils were evident by the presence and successful quantification of hzo mRNA and amoA mRNA genes. The expression ratio of amoA gene for both AOA and AOB varied between soybean soils and different rice paddy soils while the expression of hzo gene for anammox was detectable only in rice paddy soils by showing a diverse relative expression ratio in each soil sample. Gene expression of both archaeal and bacterial amoA genes in rice paddy soils differed among the three sampling depths, but that of hzo was not. Both archaeal and bacterial amoA genes showed an increase trend of expression level with continuation of rice paddy cultivation, but the low expression ratio of hzo gene indicated a relatively small contribution of anammox in overall removal of inorganic nitrogen through N2 even under anoxic and high nitrogen input in agriculture. Bacterial amoA gene from two soybean fields and three rice paddy fields were also analyzed for community composition by denaturing gradient gel electrophoresis fingerprint. Community shift was observed between soybean and paddy fields and within each of them. The consistent occurrence of three bands 5, 6, and 7 in all samples showed their high adaptability for both arid cultivation and continuous rice paddy cultivation. Our data suggest that AOA and AOB are playing a more important role in nitrogen transformation in agricultural soils in oxic or anoxic environment and anammox bacteria may also contribute but in a less extent to N transformation in these agricultural soils under anoxic condition.
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Wang J, Wang W, Gu JD. Community structure and abundance of ammonia-oxidizing archaea and bacteria after conversion from soybean to rice paddy in albic soils of Northeast China. Appl Microbiol Biotechnol 2014; 98:2765-78. [PMID: 24092004 DOI: 10.1007/s00253-013-5213-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 01/31/2023]
Abstract
Community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the albic soil grown with soybean and rice for different years was investigated by construction of clone libraries, denaturing gradient gel electrophoresis (DGGE), and quantitative polymerase chain reaction (q-PCR) by PCR amplification of the ammonia monooxygenase subunit A (amoA) gene. Soil samples were collected at two layers (0-5 and 20-25 cm) from a soybean field and four rice paddy fields with 1, 5, 9, and 17 years of continuous rice cultivation. Both the community structures and abundances of AOA and AOB showed detectable changes after conversion from soybean to rice paddy judged by clone library, DGGE, and q-PCR analyses. In general, the archaeal amoA gene abundance increased after conversion to rice cultivation, while bacterial amoA gene abundance decreased. The abundances of both AOA and AOB were higher in the surface layer than the bottom one in the soybean field, but a reverse trend was observed for AOB in all paddy samples regardless of the duration of paddy cultivation. Phylogenetic analysis identified nine subclusters of AOA and seven subclusters of AOB. Community composition of both AOA and AOB was correlated with available ammonium and increased pH value caused by flooding in multiple variance analysis. Community shift of AOB was also observed in different paddy fields, but the two layers did not show any detectable changes in DGGE analysis. Conversion from soybean to rice cultivation changed the community structure and abundance of AOA and AOB in albic agricultural soil, which requires that necessary cultivation practice be followed to manage the N utilization more effectively.
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Affiliation(s)
- Jing Wang
- School of Marine Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
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40
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Wang YF, Gu JD. Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms. Appl Microbiol Biotechnol 2013; 98:3257-74. [DOI: 10.1007/s00253-013-5399-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/02/2013] [Accepted: 11/09/2013] [Indexed: 10/26/2022]
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Community dynamics and activity of ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze estuary. Appl Environ Microbiol 2013; 80:408-19. [PMID: 24185847 DOI: 10.1128/aem.03035-13] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments.
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42
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Wang YF, Li XY, Gu JD. Differential responses of ammonia/ammonium-oxidizing microorganisms in mangrove sediment to amendment of acetate and leaf litter. Appl Microbiol Biotechnol 2013; 98:3165-80. [PMID: 24169949 DOI: 10.1007/s00253-013-5318-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/03/2013] [Indexed: 02/07/2023]
Abstract
The effects of acetate and leaf litter powder on ammonia/ammonium-oxidizing microorganisms (AOMs) in mangrove sediment were investigated in a laboratory incubation study for a period of 60 days. The results showed that different AOMs responded differently to the addition of acetate and leaf litter. A higher diversity of anaerobic ammonium-oxidizing (anammox) bacteria was observed when acetate or leaf litter was added than the control. However, acetate and leaf litter generally inhibited the growth of anammox bacteria despite that leaf litter promoted their growth in the first 5 days. The inhibitory effects on anammox bacteria were more pronounced by acetate than by leaf litter. Neither acetate nor leaf litter affected ammonia-oxidizing archaea (AOA) community structures, but promoted their growth. For ammonia-oxidizing bacteria (AOB), the addition of acetate or leaf litter resulted in changes of community structures and promoted their growth in the early phase of the incubation. In addition, the promoting effects by leaf litter on AOB growth were more obvious than acetate. These results indicated that organic substances affect AOM community structures and abundances. The study suggests that leaf litter has an important influence on the community structures and abundances of AOMs in mangrove sediment and affects the nitrogen cycle in such ecosystem.
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Affiliation(s)
- Yong-Feng Wang
- Laboratory of Microbial Ecology, Guangdong Academy of Forestry, No. 233, Guangshan 1st Road, Guangzhou, People's Republic of China
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Zhu D, Tanabe SH, Yang C, Zhang W, Sun J. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes. PLoS One 2013; 8:e78501. [PMID: 24205246 PMCID: PMC3804488 DOI: 10.1371/journal.pone.0078501] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/14/2013] [Indexed: 01/12/2023] Open
Abstract
Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.
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Affiliation(s)
- Daochen Zhu
- School of Environmental Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- State Key Laboratory of Applied Microbiology in South China (Ministry-Guangdong Province Jointly Breeding Base), Guangdong Institute of Microbiology, Guangzhou, China
- * E-mail: (DZ); (WZ)
| | - Shoko-Hosoi Tanabe
- School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga, Japan
| | - Chong Yang
- Department of R&D, Zhenjiang Bio-innova Biotech Co, Ltd., Zhenjiang, Jiangsu, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology in South China (Ministry-Guangdong Province Jointly Breeding Base), Guangdong Institute of Microbiology, Guangzhou, China
- * E-mail: (DZ); (WZ)
| | - Jianzhong Sun
- School of Environmental Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
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44
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Han P, Li M, Gu JD. Biases in community structures of ammonia/ammonium-oxidizing microorganisms caused by insufficient DNA extractions from Baijiang soil revealed by comparative analysis of coastal wetland sediment and rice paddy soil. Appl Microbiol Biotechnol 2013; 97:8741-56. [DOI: 10.1007/s00253-013-5169-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 07/30/2013] [Accepted: 07/31/2013] [Indexed: 11/28/2022]
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45
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Wang X, Wang C, Bao L, Xie S. Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils. Appl Microbiol Biotechnol 2013; 98:1883-92. [PMID: 23949998 DOI: 10.1007/s00253-013-5174-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 07/25/2013] [Accepted: 08/01/2013] [Indexed: 12/01/2022]
Abstract
Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson's correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems.
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Affiliation(s)
- Xiaoyan Wang
- College of Resources, Environment & Tourism, Capital Normal University, Beijing, 100048, China
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46
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Li M, Hong Y, Cao H, Gu JD. Community structures and distribution of anaerobic ammonium oxidizing and nirS-encoding nitrite-reducing bacteria in surface sediments of the South China Sea. MICROBIAL ECOLOGY 2013; 66:281-296. [PMID: 23354291 DOI: 10.1007/s00248-012-0175-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 12/26/2012] [Indexed: 06/01/2023]
Abstract
Anaerobic ammonium oxidation (anammox) and denitrification are two important processes responsible for nitrogen loss; monitoring of microbial communities carrying out these two processes offers a unique opportunity to understand the microbial nitrogen cycle. The aim of the current study was to characterize community structures and distribution of anammox and nirS-encoding nitrite-reducing bacteria in surface sediments of the northern South China Sea (SCS). The consistent phylogenetic results of three biomarkers of anammox bacteria, including 16S rRNA, hzo, and Scalindua-nirS genes, showed that Scalindua-like bacteria were the only anammox group presenting in surface sediments of the SCS. However, a relatively high micro-diversity was found within this group, including several SCS habitat-specific phylotypes, Candidatus "Scalindua zhenghei". Comparing to 16S rRNA gene, hzo and Scalindua-nirS genes provided a relatively higher resolution to elucidate anammox bacteria. For the nirS-encoding nitrite-reducing bacteria, the detected nirS gene sequences were closely related to various marine nirS denitrifiers, especially those which originated from coastal and estuarine sediments with a much higher diversity than anammox bacteria. Anammox bacterial communities shifted along with the seawater depth, while nirS-encoding nitrite-reducing bacteria did not. Although nirS-encoding nitrite-reducing bacteria have a much higher abundance and diversity than anammox bacteria, they showed similar abundance variation patterns in research sites, suggesting the two microbial groups might be affected by the similar environmental factors. The significant correlations among the abundance of the two microbial groups with the molar ratio of NH4 (+) to (NO2 (-) + NO3 (-)), pH, and organic matters of sediments strongly supported this hypothesis.
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Affiliation(s)
- Meng Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
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47
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Han P, Gu JD. More refined diversity of anammox bacteria recovered and distribution in different ecosystems. Appl Microbiol Biotechnol 2013; 97:3653-63. [PMID: 23515834 DOI: 10.1007/s00253-013-4756-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 01/30/2013] [Accepted: 02/02/2013] [Indexed: 11/29/2022]
Abstract
A newly reported 16S rRNA gene-based PCR primer set was successfully applied to detect anammox bacteria from four ecosystem samples, including sediments from marine, reservoir, mangrove wetland, and wastewater treatment plant sludge. This primer set showed ability to amplify a much wider coverage of all reported anammox bacterial genera. Based on the phylogenetic analyses of 16S rRNA gene of anammox bacteria, two new clusters were obtained, one closely related to Candidatus Scalindua, and the other in a previously reported novel genus related to Candidatus Brocadia. In the Scalindua cluster, four new subclusters were also found in this study, mainly by sequences of the South China Sea sediments, presenting a higher diversity of Candidatus Scalindua in marine environment. Community structure analyses indicated that samples were grouped together based on ecosystems, showing a niche-specific distribution. Phylogenetic analyses of anammox bacteria in samples from the South China Sea also indicated distinguished community structure along the depth. Pearson correlation analysis showed that the amount of anammox bacteria in the detected samples was positively correlated with the nitrate concentration. According to Canonical Correspondence Analysis, pH, temperature, nitrite, and nitrate concentration strongly affected the diversity and distribution of anammox bacteria in South China Sea sediments. Results collectively indicated a promising application of this new primer set and higher anammox bacteria diversity in the marine environment.
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Affiliation(s)
- Ping Han
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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48
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Chen CH, Gao DW, Tao Y. Diversity and distribution of ammonia-oxidizing Archaea in the seasonally frozen soils in Northeastern China. Appl Microbiol Biotechnol 2012; 97:6571-9. [PMID: 23053098 DOI: 10.1007/s00253-012-4448-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 11/25/2022]
Abstract
The genetic diversity and distribution of ammonia-oxidizing Archaea (AOA) in nine seasonally frozen soils sampled around the city of Harbin, China, is analyzed based on archaeal amoA gene. Soil samples are divided into four groups by its properties: fertilized/unfertilized mesic (well-balanced supply of moisture) soils and fertilized/unfertilized hydric (abundant of moisture) soils. Clone libraries based on AOA amoA gene polymerase chain reaction products are constructed, and the phylogenetic analysis at 5 % cutoff level shows that AOA members mainly belong to the soil/sediment lineage which includes four clusters, and very few archaeal amoA gene sequences fall into the marine lineage. The four groups of soils have different archaeal amoA gene assemblage, and the available nitrogen and organic carbon are significantly correlated with diversity indexes. The result shows that long-term artificial amendment such as fertilization and agriculture cultivation has an important impact on AOA community shift in terrestrial environment. Moisture may drive the shape of different AOA communities by changing the aerobic environment into anaerobic. Soil composition is another noticeable factor effect AOA community, which can help the shape of a special AOA community with only two species.
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Affiliation(s)
- Chun-Hong Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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Wang J, Gu JD. Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China. Appl Microbiol Biotechnol 2012; 97:1785-98. [PMID: 22526793 PMCID: PMC3562551 DOI: 10.1007/s00253-012-4036-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/14/2012] [Accepted: 03/15/2012] [Indexed: 11/09/2022]
Abstract
The anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the oxygen-limited zone for nitrogen cycling, but their roles in agricultural ecosystems are still poorly understood. In this study, soil samples were taken from the rhizosphere and non-rhizosphere and from surface (0–5 cm) and subsurface (20–25 cm) layers with 1, 4, and 9 years of rice cultivation history on the typical albic soil of Northeast China to examine the diversity and distribution of anammox bacteria based on 16S rRNA gene and hydrazine oxidoreductase encoding gene (hzo). By comparing these soil samples, no obvious difference was observed in community composition between the rhizosphere and non-rhizosphere or the surface and subsurface layers. Surprisingly, anammox bacterial communities of these rice paddy soils were consisted of mainly Candidatus Scalindua species, which are best known to be dominant in marine and pristine environments. The highest diversity was revealed in the 4-year paddy soil based on clone library analysis. Phylogenetic analysis of 16S rRNA gene and deduced HZO from the corresponding encoding gene showed that most of the obtained clones are grouped together with Candidatus Scalindua sorokinii, Candidatus Scalindua brodae, and Candidatus Scalindua spp. of seawater. The obtained clone sequences from all samples are distributed in two subclusters that contain sequences from environmental samples only. Tentative new species were also discovered in this paddy soil. This study provides the first evidence on the existence of anammox bacteria with limited diversity in agricultural ecosystems in Northern China.
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Affiliation(s)
- Jing Wang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
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Cao H, Hong Y, Li M, Gu JD. Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the western Pacific. MICROBIAL ECOLOGY 2011; 62:813-823. [PMID: 21748268 PMCID: PMC3206191 DOI: 10.1007/s00248-011-9901-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/17/2011] [Indexed: 05/28/2023]
Abstract
The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean.
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Affiliation(s)
- Huiluo Cao
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Yiguo Hong
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
- State Key Laboratory of Oceanography in the Tropics, South China Sea Institute of Oceanography, Chinese Academy of Sciences, 164 Xingang Road West, Guangzhou, 510301 China
| | - Meng Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
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