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Zhang S, Zhang D, Guo Y, Zhao J, Bao Z. Rhizosphere-Associated Anammox Bacterial Diversity and Abundance of Nitrogen Cycle-Related Functional Genes of Emergent Macrophytes in Eutrophic Wetlands. Curr Microbiol 2024; 81:107. [PMID: 38427056 DOI: 10.1007/s00284-024-03620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/13/2024] [Indexed: 03/02/2024]
Abstract
Rhizospheric microbial community of emergent macrophytes plays an important role in nitrogen removal, especially in the eutrophic wetlands. The objective of this study was to identify the differences in anammox bacterial community composition among different emergent macrophytes and investigate revealed the the main factors affecting on the composition, diversity, and abundance of anammox bacterial community. Results showed that the composition, diversity, and abundance of the anammox community were significantly different between the vegetated sediments of three emergent macrophytes and unvegetated sediment. The composition of the anammox bacterial community was different in the vegetated sediments of different emergent macrophytes. Also, the abundance of nitrogen cycle-related functional genes in the vegetated sediments was found to be higher than that in the unvegetated sediment. Canonical correspondence analysis (CCA) and structural equation models analysis (SEM) showed that salinity and pH were the main environmental factors influencing the composition and diversity of the anammox bacterial community and NO2--N indirectly affected anammox bacterial community diversity by affecting TOC. nirK-type denitrifying bacteria abundance had significant effects on the bacterial community composition, diversity, and abundance of anammox bacteria. The community composition of anammox bacteria varies with emergent macrophyte species. The rhizosphere of emergent macrophytes provides a favorable environment and promotes the growth of nitrogen cycling-related microorganisms that likely accelerate nitrogen removal in eutrophic wetlands.
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Affiliation(s)
- Shaohua Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, 235 West University Street, Hohhot, 010021, China.
| | - Duo Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, 235 West University Street, Hohhot, 010021, China
| | - Ying Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, 235 West University Street, Hohhot, 010021, China
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, 235 West University Street, Hohhot, 010021, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, 010021, China
| | - Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, 235 West University Street, Hohhot, 010021, China
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, 010021, China
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Changes in Temporal Dynamics and Factors Influencing the Environment of the Bacterial Community in Mangrove Rhizosphere Sediments in Hainan. SUSTAINABILITY 2022. [DOI: 10.3390/su14127415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structural characteristics of the rhizosphere soil’s microbial community is crucial to understanding the ecological function of mangroves. However, the mechanism influencing mangrove plants in soil microbial communities has yet to be determined. Here, the mangrove ecosystem of Xinying Mangrove National Wetland Park in Hainan Province was taken as the research object. The microbial communities, external regulatory factors, and the relationship between communities were analyzed using 16S rRNA high-throughput sequencing in the rhizosphere and non-rhizosphere sediments of mangrove forests under different spatiotemporal conditions. The results showed that there was no significant difference in the α-diversity of the bacterial community between the rhizosphere and non-rhizosphere sediments. However, β-diversity was significantly different. Redundancy analysis (RDA) showed that other environmental factors besides sulfide and Fe2+ affected the bacterial community structure in sediments. The co-occurrence pattern analysis of bacteria in the mangrove ecosystem indicates that the bacteria in rhizosphere sediments were more closely related than those in non-rhizosphere sediments. The results reveal significant differences between the rhizosphere and non-rhizosphere bacterial community diversity, structure, and their interaction in the mangrove ecosystem. Therefore, the ecological system of the mangrove wetland needs to be preserved and rehabilitated, which would have a tremendous impact on the sustainable development.
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Ding LJ, Cui HL, Nie SA, Long XE, Duan GL, Zhu YG. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol Ecol 2020; 95:5420819. [PMID: 30916760 DOI: 10.1093/femsec/fiz040] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/26/2019] [Indexed: 11/12/2022] Open
Abstract
Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - San-An Nie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Xi-En Long
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
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Zhou X, Wang M, Wen C, Liu D. Nitrogen release and its influence on anammox bacteria during the decay of Potamogeton crispus with different values of initial debris biomass. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:604-615. [PMID: 30208346 DOI: 10.1016/j.scitotenv.2018.08.358] [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: 01/28/2018] [Revised: 07/03/2018] [Accepted: 08/25/2018] [Indexed: 06/08/2023]
Abstract
Aquatic macrophytes play a significant role in the nutrient cycle of freshwater ecosystems. However, nutrients from plant debris release into both sediments and overlying water if not timely harvested. To date, minimal information is available regarding nutrient release and its subsequent influences on bacterial communities with decaying debris. In this study, Potamogeton crispus was used as a model plant. Debris biomass levels of 0 g (control, J-CK), 10 g dry weight (DW) (100 g DW/m2, J-10 g), 40 g DW (400 g DW/m2, J-40 g) and 80 g DW (800 g DW/m2, J-80 g) were used to simulate the different biomass densities of P. crispus in field. The physicochemical parameters of overlying water and sediment samples were analysed. The community composition of anammox bacteria in the sediment was also analysed using 16S rRNA genes as markers. The results showed that dissolved oxygen and pH dramatically decreased, whereas total nitrogen (TN) and NH4+-N concentrations increased in the overlying water in the initial stage of P. crispus decomposition. However, NO3--N concentration changes in the overlying water were more complicated. The concentrations of organic matter, TN and NH4+-N in the sediment all increased, but the rate of increase varied among the groups with different initial biomass levels, indicating that these physicochemical properties in sediment are significantly affected by debris biomass level and decay time. In addition, the order of anammox bacteria abundance was J-40 g > J-CK > J-80 g > J-10 g. Moreover, the community structure of anammox bacteria were simpler compared to that of J-CK as debris biomass level increased. The results demonstrate that P. crispus debris decomposition could affect the ecological distribution of anammox bacteria. Such influence clearly varies with varying amounts of P. crispus biomass debris. This information could be useful for the management of aquatic macrophytes in freshwater ecosystems.
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Affiliation(s)
- Xiaohong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Mingyuan Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chunzi Wen
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dan Liu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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Wang B, Huang S, Zhang L, Zhao J, Liu G, Hua Y, Zhou W, Zhu D. Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae). PeerJ 2018; 6:e6041. [PMID: 30533317 PMCID: PMC6284450 DOI: 10.7717/peerj.6041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/30/2018] [Indexed: 12/15/2022] Open
Abstract
Background The nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum. M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity of M. oxyfera in the rhizosphere of aquatic plants has not been widely reported. Method In order to simulate the rhizosphere microenvironment of submerged plants, Potamogeton crispus was cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity of M. oxyfera-like bacteria in these sediments. Results Methylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10. Discussion Our results confirmed the existence of M. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plant P. crispus. Group b of M. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology of M. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.
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Affiliation(s)
- Binghan Wang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Shanshan Huang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Liangmao Zhang
- Laboratory of Environmental Planning and Management, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Wenbing Zhou
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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Zhou X, Zhang J, Wen C. Community Composition and Abundance of Anammox Bacteria in Cattail Rhizosphere Sediments at Three Phenological Stages. Curr Microbiol 2017; 74:1349-1357. [DOI: 10.1007/s00284-017-1324-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
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Yang Y, Dai Y, Li N, Li B, Xie S, Liu Y. Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes. MICROBIAL ECOLOGY 2017; 73:285-295. [PMID: 27726034 DOI: 10.1007/s00248-016-0872-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 09/29/2016] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yu Dai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Zheng Y, Hou L, Liu M, Yin G, Gao J, Jiang X, Lin X, Li X, Yu C, Wang R. Community composition and activity of anaerobic ammonium oxidation bacteria in the rhizosphere of salt-marsh grass Spartina alterniflora. Appl Microbiol Biotechnol 2016; 100:8203-12. [DOI: 10.1007/s00253-016-7625-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/03/2016] [Accepted: 05/07/2016] [Indexed: 11/28/2022]
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