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Xia F, Jiang QY, Zhu T, Zou B, Liu H, Quan ZX. Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148470. [PMID: 34166901 DOI: 10.1016/j.scitotenv.2021.148470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH4+ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.
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Affiliation(s)
- Fei Xia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiu-Yue Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Huan Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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Wang DQ, Zhou CH, Nie M, Gu JD, Quan ZX. Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144993. [PMID: 33736320 DOI: 10.1016/j.scitotenv.2021.144993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.
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Affiliation(s)
- Dan-Qi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chen-Hao Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.
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Effects of Spartina alterniflora Invasion on Soil Microbial Community Structure and Ecological Functions. Microorganisms 2021; 9:microorganisms9010138. [PMID: 33435501 PMCID: PMC7827921 DOI: 10.3390/microorganisms9010138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/23/2022] Open
Abstract
It has been reported that the invasion of Spartina alterniflora changed the soil microbial community in the mangrove ecosystem in China, especially the bacterial community, although the response of soil fungal communities and soil microbial ecological functions to the invasion of Spartina alterniflora remains unclear. In this study, we selected three different communities (i.e., Spartina alterniflora community (SC), Spartina alterniflora–mangrove mixed community (TC), and mangrove community (MC)) in the Zhangjiangkou Mangrove Nature Reserve in China. High-throughput sequencing technology was used to analyze the impact of Spartina alterniflora invasion on mangrove soil microbial communities. Our results indicate that the invasion of Spartina alterniflora does not cause significant changes in microbial diversity, but it can alter the community structure of soil bacteria. The results of the LEfSe (LDA Effect Size) analysis show that the relative abundance of some bacterial taxa is not significantly different between the MC and SC communities, but different changes have occurred during the invasion process (i.e., TC community). Different from the results of the bacterial community, the invasion of Spartina alterniflora only cause a significant increase in few fungal taxa during the invasion process, and these taxa are at some lower levels (such as family, genus, and species) and classified into the phylum Ascomycota. Although the invasion of Spartina alterniflora changes the taxa with certain ecological functions, it may not change the potential ecological functions of soil microorganisms (i.e., the potential metabolic pathways of bacteria, nutritional patterns, and fungal associations). In general, the invasion of Spartina alterniflora changes the community structure of soil microorganisms, but it may not affect the potential ecological functions of soil microorganisms.
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Yang W, Zhang D, Cai X, Xia L, Luo Y, Cheng X, An S. Significant alterations in soil fungal communities along a chronosequence of Spartina alterniflora invasion in a Chinese Yellow Sea coastal wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133548. [PMID: 31369894 DOI: 10.1016/j.scitotenv.2019.07.354] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 05/24/2023]
Abstract
Plant invasion typically alters the microbial communities of soils, which affects ecosystem carbon (C) and nitrogen (N) cycles. The responses of the soil fungal communities to plant invasion along its chronosequence remain poorly understood. For this study, we investigated variations in soil fungal communities through Illumina MiSeq sequencing analyses of the fungal internal transcribed spacer (ITS) region, and quantitative polymerase chain reaction (qPCR), along a chronosequence (i.e., 9-, 13-, 20- and 23-year-old) of invasive Spartina alterniflora. We compared these variations with those of bare flat in a Chinese Yellow Sea coastal wetland. Our results highlighted that the abundance of soil fungi, the number of operational taxonomic units (OTUs), species richness, and Shannon diversity indices for soil fungal communities were highest in 9-year-old S. alterniflora soil, which gradually declined along the invasion chronosequence. The relative abundance of copiotrophic Basidiomycota revealed significant decreasing trend, while the relative abundance of oligotrophic Ascomycota gradually increased along the S. alterniflora invasion chronosequence. The relative abundance of soil saprotrophic fungi (e.g., undefined saprotrophs) was gradually reduced while symbiotic fungi (e.g., ectomycorrhizal fungi) and pathotrophic fungi (e.g., plant and animal pathogens) progressively increased along the S. alterniflora invasion chronosequence. Our results suggested that S. alterniflora invasion significantly altered soil fungal abundance and diversity, community composition, trophic modes, and functional groups along a chronosequence, via substantially reduced soil litter inputs, and gradually decreased soil pH, moisture, and soil nutrient substrates along the invasion chronosequence, from 9 to 23 years. These changes in soil fungal communities, particularly their trophic modes and functional groups along the S. alterniflora invasion chronosequence could well impact the decomposition and accumulation of soil C and N, while potentially altering ecosystem C and N sinks in a Chinese Yellow Sea coastal wetland.
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Affiliation(s)
- Wen Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, PR China.
| | - Di Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, PR China
| | - Xinwen Cai
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, PR China
| | - Lu Xia
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing 210023, PR China
| | - Yiqi Luo
- Center for Ecosystem Science and Society (Ecoss), Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Xiaoli Cheng
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China.
| | - Shuqing An
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing 210023, PR China
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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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Zhang G, Bai J, Jia J, Wang W, Wang X, Zhao Q, Lu Q. Shifts of soil microbial community composition along a short-term invasion chronosequence of Spartina alterniflora in a Chinese estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:222-233. [PMID: 30543970 DOI: 10.1016/j.scitotenv.2018.12.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/21/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Exotic plant invasion can alter native soil microbial community composition, and further influence the biogeochemical processes. Little information is available about the impacts of the invasion chronosequence of Spartina alterniflora on the dynamics of soil microbial community. Soil microbial community in coastal salt marshes invaded by S. alterniflora and reference wetlands covered by Suaeda salsa were investigated using phospholipid fatty acids (PLFAs) profiling along a short-term chronosequence (i.e., 2-, 5- and 10-year) of S. alterniflora invasion in the Yellow River Estuary. Results exhibited an increase in soil moisture, soil organic matter (SOM), soil dissolved organic carbon (DOC), total nitrogen (TN) and the total of PLFAs with increasing invasion ages of S. alterniflora in these coastal salt marshes. Comparatively, soil pH and bulk density exhibited a weak decline along the invasion chronosequence. The elevated values of relative abundance of fungi and the ratios of fungi: bacteria (F/B) in all invaded salt marshes were mainly associated with the accumulation of soil available substrate (e.g., SOM, DOC and TN). S. alterniflora invasion also increased the ratios of gram-positive/gram-negative (G+/G-) bacterial PLFAs, with the highest value occurring in the 2-year invaded salt marshes. The bacterial stress indicated by ratios of cy17:0/16:1ω7c and cy19:0/18:1ω7c consistently decreased along the invasion chronosequence. In conclusion, the shifts of soil microbial community composition were tightly associated with soil variables, such as soil pH and soil nutrient supply. Our findings reflect the short-term chronological effects of S. alterniflora invasion on the soil physicochemical characteristics and microbial communities, which contributes to the linkage between the plant invasion and soil development of coastal salt marshes.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China.
| | - Jia Jia
- State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Qingqing Zhao
- State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Qiongqiong Lu
- State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
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Gao GF, Li PF, Zhong JX, Shen ZJ, Chen J, Li YT, Isabwe A, Zhu XY, Ding QS, Zhang S, Gao CH, Zheng HL. Spartina alterniflora invasion alters soil bacterial communities and enhances soil N 2O emissions by stimulating soil denitrification in mangrove wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:231-240. [PMID: 30412868 DOI: 10.1016/j.scitotenv.2018.10.277] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 05/13/2023]
Abstract
Chinese mangrove, an important ecosystem in coastal wetlands, is sensitive to the invasive alien species Spartina alterniflora. However, the effects of the S. alterniflora invasion on mangrove soil N2O emissions and the underlying mechanisms by which emissions are affected have not been well studied. In this study, the N2O emitted from soils dominated by two typical native mangroves (i.e. Kandelia obovata: KO; Avicennia marina: AM), one invaded by S. alterniflora (SA), and one bare mudflat (Mud) were monitored at Zhangjiang Mangrove Estuary (where S. alterniflora is exotic). Together with soil biogeochemical properties, the potential denitrification rate and the composition of soil bacterial communities were determined simultaneously by 15NO3- tracer and high-throughput sequencing techniques, respectively. Our results showed that S. alterniflora invasion significantly (p < 0.05) increases soil N2O emissions by 15-28-fold. In addition, isotope results revealed that the soil potential denitrification rate was significantly (p < 0.05) enhanced after S. alterniflora invasion. Moreover, the S. alterniflora invasion significantly (p < 0.05) decreased soil bacterial α-diversity and strongly modified soil bacterial communities. Indicator groups strongly associated with S. alterniflora were Chloroflexia, Alphaproteobacteria, and Bacilli, each of which was abundant and acts as connector in the co-occurrence network. FAPROTAX analysis implied that the S. alterniflora invasion stimulated soil denitrification and nitrification while depressing anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA). Redundancy analysis (RDA) found that soil organic matter (SOM) and pH were the most important environmental factors in altering soil bacterial communities. Taken together, our results imply that the S. alterniflora invasion in mangrove wetlands significantly stimulates soil denitrification and N2O emissions, thereby contributing N2O to the atmosphere and contributing to global climate change.
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Affiliation(s)
- Gui-Feng Gao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Peng-Fei Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Jia-Xin Zhong
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen, Fujian 361102, China
| | - Zhi-Jun Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu 210098, China
| | - Yun-Tao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361102, China
| | - Xue-Yi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Qian-Su Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Shan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Chang-Hao Gao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.
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Lin L, Liu W, Zhang M, Lin X, Zhang Y, Tian Y. Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China. MICROBIAL ECOLOGY 2019; 77:124-135. [PMID: 29948019 DOI: 10.1007/s00248-018-1208-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
In the southernmost part of coast of China, two height forms of Spartina alterniflora, tall and short, have invaded Leizhou Peninsula within the last decade. However, the effect of different height forms of Spartina alterniflora on plant-microbe interaction has not been clarified. Here, the community structures of rhizosphere bacteria and the abundance of N- and S-cycling functional genes associated with selected S. alterniflora were investigated in the field and a common garden. The community structure of tall-form S. alterniflora was distinct from short-form S. alterniflora at OTU level in the field, even after transplantation into a common garden. The abundance of bacterial amoA, nirS, and nosZ in tall S. alterniflora was significantly greater than those in short S. alterniflora in the field; however, this difference disappeared in a 1-year common garden experiment. These results suggested that compared with the tall-form S. alterniflora, the rhizosphere of short-form S. alterniflora harbored fewer nitrification-denitrification related microorganisms, which might benefit from conserving N in an N limited habitat. Together, our results suggested that tall- and short-form S. alterniflora can host their specific rhizosphere microbial communities and had different strategies of N usage via selecting the composition of rhizosphere bacterial assemblages, which in turn might determine the growth and invasiveness of S. alterniflora in its introduced range.
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Affiliation(s)
- Li'an Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Wenwen Liu
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Manping Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Yihui Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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Li B, Yang Y, Chen J, Wu Z, Liu Y, Xie S. Nitrifying activity and ammonia-oxidizing microorganisms in a constructed wetland treating polluted surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:310-318. [PMID: 29444483 DOI: 10.1016/j.scitotenv.2018.02.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/03/2018] [Accepted: 02/03/2018] [Indexed: 06/08/2023]
Abstract
Ammonia oxidation, performed by both ammonia oxidizing bacteria (AOB) and archaea (AOA), is an important step for nitrogen removal in constructed wetlands (CWs). However, little is known about the distribution of these ammonia oxidizing organisms in CWs and the associated wetland environmental variables. Their relative importance to nitrification in CWs remains still controversial. The present study investigated the seasonal dynamics of AOA and AOB communities in a free water surface flow CW (FWSF-CW) used to ameliorate the quality of polluted river water. Strong seasonality effects on potential nitrification rate (PNR) and the abundance, richness, diversity and structure of AOA and AOB communities were observed in the river water treatment FWSF-CW. PNR was positively correlated to AOB abundance. AOB (6.76×105-6.01×107 bacterial amoA gene copies per gram dry sediment/soil) tended to be much more abundant than AOA (from below quantitative PCR detection limit to 9.62×106 archaeal amoA gene copies per gram dry sediment/soil). Both AOA and AOB abundance were regulated by the levels of nitrogen, phosphorus and organic carbon. Different wetland environmental variables determined the diversity and structure of AOA and AOB communities. Wetland AOA communities were mainly composed of unknown species and Nitrosopumilus-like organisms, while AOB communities were mainly represented by both Nitrosospira and Nitrosomonas.
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Affiliation(s)
- Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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10
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Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China. J Microbiol 2018; 56:507-515. [PMID: 29948827 DOI: 10.1007/s12275-018-8062-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 10/14/2022]
Abstract
Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China's wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.
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11
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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: 38] [Impact Index Per Article: 6.3] [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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Rodriguez D, Guerra TM, Forstner MR, Hahn D. Diversity of Frankia in soil assessed by Illumina sequencing of nifH gene fragments. Syst Appl Microbiol 2016; 39:391-7. [DOI: 10.1016/j.syapm.2016.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 02/02/2023]
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13
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Song H, Che Z, Cao W, Huang T, Wang J, Dong Z. Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:11964-11974. [PMID: 26961528 DOI: 10.1007/s11356-016-6396-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.
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Affiliation(s)
- He Song
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Zhao Che
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenchao Cao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Ting Huang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jingguo Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Dong
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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