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Liu C, Yue Y, Zheng S, Liu X, Pang L, Yang Z. Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:120930-120944. [PMID: 37945964 DOI: 10.1007/s11356-023-30818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.
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Affiliation(s)
- Caiqiong Liu
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
| | - Yao Yue
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, Wuhan University, Wuhan, 430072, China
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Shan Zheng
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
| | - Xuna Liu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Zhonghua Yang
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China.
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2
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Zhang M, Daraz U, Sun Q, Chen P, Wei X. Denitrifier abundance and community composition linked to denitrification potential in river sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:51928-51939. [PMID: 33990922 DOI: 10.1007/s11356-021-14348-w] [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: 08/10/2020] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Denitrification in river sediments plays a very important role in removing nitrogen in aquatic ecosystem. To gain insight into the key factors driving denitrification at large spatial scales, a total of 135 sediment samples were collected from Huaihe River and its branches located in the northern of Anhui province. Bacterial community composition and denitrifying functional genes (nirS, nirK, and nosZ) were measured by high-throughput sequencing and real-time PCR approaches. Potential denitrification rate (PDR) was measured by acetylene inhibition method, which varied from 0.01 to 15.69 μg N g-1 h-1. The sequencing results based on 16S rRNA gene found that the main denitrification bacterial taxa included Bacillus, Thiobacillus, Acinetobacter, Halomonas, Denitratisoma, Pseudomonas, Rhodanobacter, and Thauera. Therein, Thiobacillus might play key roles in the denitrification. Total nitrogen and N:P ratio were the only chemical factors related with all denitrification genes. Furthermore, nirS gene abundance could be more susceptible to environmental parameters compared with nirK and nosZ genes. Canonical correspondence analysis indicated that NO3-, NO2-, NH4+ and IP had the significant impacts on the nirS-encoding bacterial community and spatial distributions. There was a significantly positive correlation between Thiobacillus and nirS gene. We considered that higher numbers of nosZ appeared in nutrient rich sediments. More strikingly, PDR was positively correlated with the abundance of three functional genes. Random forest analysis showed that NH4+ was the most powerful predictor of PDR. These findings can yield practical and important reference for the bioremediation or evaluation of wetland systems.
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Affiliation(s)
- Mingzhu Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, Anhui Province, China
- Key Laboratory of Wetland Ecological Protection and Restoration, Hefei, China
- Anhui Province Engineering Laboratory for Mine Ecological Remediation, Hefei, China
| | - Umar Daraz
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, Anhui Province, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, Anhui Province, China.
- Key Laboratory of Wetland Ecological Protection and Restoration, Hefei, China.
- Anhui Province Engineering Laboratory for Mine Ecological Remediation, Hefei, China.
| | - Piaoxue Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, Anhui Province, China
- Key Laboratory of Wetland Ecological Protection and Restoration, Hefei, China
- Anhui Province Engineering Laboratory for Mine Ecological Remediation, Hefei, China
| | - Xuhao Wei
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, Anhui Province, China
- Key Laboratory of Wetland Ecological Protection and Restoration, Hefei, China
- Anhui Province Engineering Laboratory for Mine Ecological Remediation, Hefei, China
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3
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Xiao Y, Yin X, Chen L, Wang J, Wang Y, Liu G, Hua Y, Wan X, Xiao N, Zhao J, Zhu D. Effects of illumination on nirS denitrifying and anammox bacteria in the rhizosphere of submerged macrophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143420. [PMID: 33189380 DOI: 10.1016/j.scitotenv.2020.143420] [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: 08/13/2020] [Revised: 10/08/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Visibility in lakes can decrease due to increases in the amounts of suspended solids and algae, which inhibits the growth of submerged macrophytes. However, the understanding about whether illumination reduction affects the nitrogen-cycling microorganisms in the rhizosphere of submerged macrophytes, is limited. The abundance and biodiversity of nirS denitrifying and anammox bacteria in the rhizosphere of Potamogeton crispus were studied under 0% (natural light), 20%, 40%, and 60% shading treatments. The abundance of the nirS gene was highest under 60% shading treatment, while the anammox 16S rRNA gene was highest under 40% shading treatment. Moreover, the abundance of the two genes were lower under natural light than under shading conditions during most sampling periods. The quantitative ratio of the two gene (anammox 16S rRNA to nirS gene) abundance fluctuated wildly with the distance away from the roots, under natural light and 20% shading treatment. However, the ratio varied relatively little under 40% and 60% shading treatments. The diversity of nirS denitrifying bacteria was high in the rhizosphere, while the diversity of anammox bacteria was low, and Candidatus Brocadia fulgida was dominant. This study revealed that illumination reduction not only facilitated the growth of nirS denitrifying and anammox bacteria in the rhizosphere, but also weakened the competition between the two bacteria.
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Affiliation(s)
- Yang Xiao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingjia Yin
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Lijuan Chen
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Jing Wang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuchun Wang
- Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Institute of Water Resources and China Hydropower Research, Beijing 100038, China.
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqiong Wan
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Naidong Xiao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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4
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Chen M, Song Y, Feng X, Tang K, Jiao N, Tian J, Zhang Y. Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. Front Microbiol 2020; 11:1739. [PMID: 32793171 PMCID: PMC7393951 DOI: 10.3389/fmicb.2020.01739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022] Open
Abstract
Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.
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Affiliation(s)
- Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Xiaoyuan Feng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jiwei Tian
- Physical Oceanography Laboratory, Ocean University of China, Qingdao, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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5
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Sun W, Xia C, Xu M, Guo J, Sun G. Seasonality Affects the Diversity and Composition of Bacterioplankton Communities in Dongjiang River, a Drinking Water Source of Hong Kong. Front Microbiol 2017; 8:1644. [PMID: 28912759 PMCID: PMC5583224 DOI: 10.3389/fmicb.2017.01644] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/15/2017] [Indexed: 01/11/2023] Open
Abstract
Water quality ranks the most vital criterion for rivers serving as drinking water sources, which periodically changes over seasons. Such fluctuation is believed associated with the state shifts of bacterial community within. To date, seasonality effects on bacterioplankton community patterns in large rivers serving as drinking water sources however, are still poorly understood. Here we investigated the intra-annual bacterial community structure in the Dongjiang River, a drinking water source of Hong Kong, using high-throughput pyrosequencing in concert with geochemical property measurements during dry, and wet seasons. Our results showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla of bacterioplankton communities, which varied in composition, and distribution from dry to wet seasons, and exhibited profound seasonal changes. Actinobacteria, Bacteroidetes, and Cyanobacteria seemed to be more associated with seasonality that the relative abundances of Actinobacteria, and Bacteroidetes were significantly higher in the dry season than those in the wet season (p < 0.01), while the relative abundance of Cyanobacteria was about 10-fold higher in the wet season than in the dry season. Temperature and NO3--N concentration represented key contributing factors to the observed seasonal variations. These findings help understand the roles of various bacterioplankton and their interactions with the biogeochemical processes in the river ecosystem.
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Affiliation(s)
- Wei Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China.,School of Life Sciences, Longyan UniversityLongyan, China
| | - Chunyu Xia
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China.,School of Life Sciences, Longyan UniversityLongyan, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China.,State Key Laboratory of Applied Microbiology Southern ChinaGuangzhou, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China.,State Key Laboratory of Applied Microbiology Southern ChinaGuangzhou, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China.,State Key Laboratory of Applied Microbiology Southern ChinaGuangzhou, China
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6
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Gao M, Liu J, Qiao Y, Zhao M, Zhang XH. Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors. MICROBIAL ECOLOGY 2017; 73:602-615. [PMID: 27924403 DOI: 10.1007/s00248-016-0906-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.
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Affiliation(s)
- Minghong Gao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Meixun Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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7
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Saarenheimo J, Rissanen AJ, Arvola L, Nykänen H, Lehmann MF, Tiirola M. Genetic and environmental controls on nitrous oxide accumulation in lakes. PLoS One 2015; 10:e0121201. [PMID: 25756328 PMCID: PMC4355481 DOI: 10.1371/journal.pone.0121201] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/28/2015] [Indexed: 11/19/2022] Open
Abstract
We studied potential links between environmental factors, nitrous oxide (N2O) accumulation, and genetic indicators of nitrite and N2O reducing bacteria in 12 boreal lakes. Denitrifying bacteria were investigated by quantifying genes encoding nitrite and N2O reductases (nirS/nirK and nosZ, respectively, including the two phylogenetically distinct clades nosZI and nosZII) in lake sediments. Summertime N2O accumulation and hypolimnetic nitrate concentrations were positively correlated both at the inter-lake scale and within a depth transect of an individual lake (Lake Vanajavesi). The variability in the individual nirS, nirK, nosZI, and nosZII gene abundances was high (up to tenfold) among the lakes, which allowed us to study the expected links between the ecosystem's nir-vs-nos gene inventories and N2O accumulation. Inter-lake variation in N2O accumulation was indeed connected to the relative abundance of nitrite versus N2O reductase genes, i.e. the (nirS+nirK)/nosZI gene ratio. In addition, the ratios of (nirS+nirK)/nosZI at the inter-lake scale and (nirS+nirK)/nosZI+II within Lake Vanajavesi correlated positively with nitrate availability. The results suggest that ambient nitrate concentration can be an important modulator of the N2O accumulation in lake ecosystems, either directly by increasing the overall rate of denitrification or indirectly by controlling the balance of nitrite versus N2O reductase carrying organisms.
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Affiliation(s)
- Jatta Saarenheimo
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
- * E-mail:
| | - Antti J. Rissanen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Lauri Arvola
- Lammi Biological Station, University of Helsinki, 16900, Lammi, Finland
| | - Hannu Nykänen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Moritz F. Lehmann
- Department for Environmental Science, University of Basel, CH-4058, Basel, Switzerland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
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8
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Du J, Xiao K, Li L, Ding X, Liu H, Lu Y, Zhou S. Temporal and spatial diversity of bacterial communities in coastal waters of the South china sea. PLoS One 2013; 8:e66968. [PMID: 23785512 PMCID: PMC3681761 DOI: 10.1371/journal.pone.0066968] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/14/2013] [Indexed: 01/09/2023] Open
Abstract
Bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems. Temporal and geographical patterns in ocean bacterial communities have been observed in many studies, but the temporal and spatial patterns in the bacterial communities from the South China Sea remained unexplored. To determine the spatiotemporal patterns, we generated 16S rRNA datasets for 15 samples collected from the five regularly distributed sites of the South China Sea in three seasons (spring, summer, winter). A total of 491 representative sequences were analyzed by MOTHUR, yielding 282 operational taxonomic units (OTUs) grouped at 97% stringency. Significant temporal variations of bacterial diversity were observed. Richness and diversity indices indicated that summer samples were the most diverse. The main bacterial group in spring and summer samples was Alphaproteobacteria, followed by Cyanobacteria and Gammaproteobacteria, whereas Cyanobacteria dominated the winter samples. Spatial patterns in the samples were observed that samples collected from the coastal (D151, D221) waters and offshore (D157, D1512, D224) waters clustered separately, the coastal samples harbored more diverse bacterial communities. However, the temporal pattern of the coastal site D151 was contrary to that of the coastal site D221. The LIBSHUFF statistics revealed noticeable differences among the spring, summer and winter libraries collected at five sites. The UPGMA tree showed there were temporal and spatial heterogeneity of bacterial community composition in coastal waters of the South China Sea. The water salinity (P=0.001) contributed significantly to the bacteria-environment relationship. Our results revealed that bacterial community structures were influenced by environmental factors and community-level changes in 16S-based diversity were better explained by spatial patterns than by temporal patterns.
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Affiliation(s)
- Jikun Du
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Department of Clinical Laboratory, Shenzhen Shajing Affiliated Hospital of Guangzhou Medical University, Shenzhen, China
| | - Kai Xiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Li Li
- Department of Pharmacology, Guangdong Medical College, Dongguan, China
- * E-mail: (LL); (SZ)
| | - Xian Ding
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Helu Liu
- Department of Clinical Laboratory, Shenzhen Shajing Affiliated Hospital of Guangzhou Medical University, Shenzhen, China
| | - Yongjun Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shining Zhou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (LL); (SZ)
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9
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Wang C, Zhu G, Wang Y, Wang S, Yin C. Nitrous oxide reductase gene (nosZ) and N2O reduction along the littoral gradient of a eutrophic freshwater lake. J Environ Sci (China) 2013; 25:44-52. [PMID: 23586298 DOI: 10.1016/s1001-0742(12)60005-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Lake littoral zones are characterized by heterogeneity in the biogeochemistry of nutrient elements. This study aimed to explore the relationship between the nitrous oxide reductase gene (nosZ)-encoding denitrifier community composition/abundance and N2O reduction. Five samples (deep sediment, near-transition sediment, transition site, near-transition land and land soil) were collected along a littoral gradient of eutrophic Baiyangdian Lake, North China. To investigate the relationship between the nosZ-encoding denitrifier community structure and N2O reduction, the nosZ-encoding denitrifier community composition/abundance, potential denitrification rate (DNR) and potential N2O production rate (pN2O) were investigated using molecular biological technologies and laboratory incubation experiments. The results showed that the average DNR of sediments was about 25 times higher than that of land soils, reaching 282.5 nmol N/(g dry weight (dw) x hr) and that the average pN2O of sediments was about 3.5 times higher than that of land soils, reaching 15.7 nmol N/(g dw x hr). In the land area, the nosZ gene abundance showed a negative correlation with the N2O/(N2O + N2) ratio, indicating that nosZ gene abundance dominated N2O reduction both in the surface soils of the land area and in the soil core of the transition site. Phylogenetic analysis showed that all the nosZ sequences recovered from sediment clustered closely with the isolates Azospirillum largimobile and Azospirillum irakense affiliated to Rhodospirillaceae in alpha-Proteobacteria, while about 92.3% (12/13) of the nosZ sequences recovered from land soil affiliated to Rhizobiaceae and Bradyrhizobiaceae in alpha-Proteobacteria. The community composition of nosZ gene-encoding denitrifiers appeared to be coupled with N2O reduction along the littoral gradient.
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Affiliation(s)
- Chaoxu Wang
- State Key Laboratory of Environmental Aquatic Quality, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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10
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Correa-Galeote D, Tortosa G, Bedmar EJ. Determination of Denitrification Genes Abundance in Environmental Samples. ACTA ACUST UNITED AC 2013. [DOI: 10.4303/mg/235702] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Bai Y, Sun Q, Sun R, Wen D, Tang X. Comparison of denitrifier communities in the biofilms of bioaugmented and non-augmented zeolite-biological aerated filters. ENVIRONMENTAL TECHNOLOGY 2012; 33:1993-1998. [PMID: 23240192 DOI: 10.1080/09593330.2012.655319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The denitrifier communities of a bioaugmented and non-augmented zeolite-biological aerated filter (Z-BAFs) were investigated and compared because the bioaugmented Z-BAF provided better and more stable treatment efficiency for nitrate and nitrite removal. Terminal restriction fragment length polymorphism (T-RFLP) and reverse transcription T-RFLP (RT-T-RFLP) were applied to analyse the denitrifier community diversity in the biofilm collected from each Z-BAF. The results showed that the bioaugmentation technology favourably changed the indigenous denitrifier community and enhanced denitrification under nitrogen loading shocks. The cDNA clone libraries were developed to explore the active denitrifier community structures of both filters. The results showed that the active denitrifiers in both the bioaugmented and non-bioaugmented Z-BAF belonged to alpha-, beta- and gamma-proteobacteria. However, the sequence of the introduced denitrifier (Paracoccus sp. BW001) was not found in the clone library of the bioaugmented filter, which implied that the removal of nitrate and nitrite was attributed mainly to the indigenous denitrifiers in the adjusted bacterial community in the bioaugmented Z-BAF.
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Affiliation(s)
- Yaohui Bai
- Research Centre for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
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12
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Srinandan CS, Shah M, Patel B, Nerurkar AS. Assessment of denitrifying bacterial composition in activated sludge. BIORESOURCE TECHNOLOGY 2011; 102:9481-9489. [PMID: 21868215 DOI: 10.1016/j.biortech.2011.07.094] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/23/2011] [Accepted: 07/25/2011] [Indexed: 05/31/2023]
Abstract
The abundance and structure of denitrifying bacterial community in different activated sludge samples were assessed, where the abundance of denitrifying functional genes showed nirS in the range of 10(4)-10(5), nosZ with 10(4)-10(6) and 16S rRNA gene in the range 10(9)-10(10) copy number per ml of sludge. The culturable approach revealed Pseudomonas sp. and Alcaligenes sp. to be numerically high, whereas culture independent method showed betaproteobacteria to dominate the sludge samples. Comamonas sp. and Pseudomonas fluorescens isolates showed efficient denitrification, while Pseudomonas mendocina, Pseudomonas stutzeri and Brevundimonas diminuta accumulated nitrite during denitrification. Numerically dominant RFLP OTUs of the nosZ gene from the fertilizer factory sludge samples clustered with the known isolates of betaproteobacteria. The data also suggests the presence of different truncated denitrifiers with high numbers in sludge habitat.
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Affiliation(s)
- C S Srinandan
- Department of Microbiology and Biotechnology Centre, Faculty of Science, M.S. University of Baroda, Vadodara, Gujarat, India
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The community composition of soil-denitrifying bacteria from a turfgrass environment. Res Microbiol 2010; 161:315-25. [DOI: 10.1016/j.resmic.2010.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 11/22/2022]
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Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China. Appl Environ Microbiol 2010; 76:4691-702. [PMID: 20511433 DOI: 10.1128/aem.02563-09] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments.
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Pei Y, Wang J, Wang Z, Yang Z. Characteristics of Ammonia-oxidizing and Denitrifying Bacteria at the River-sediment Interface. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.proenv.2010.10.214] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Dang H, Wang C, Li J, Li T, Tian F, Jin W, Ding Y, Zhang Z. Diversity and distribution of sediment nirS-encoding bacterial assemblages in response to environmental gradients in the eutrophied Jiaozhou Bay, China. MICROBIAL ECOLOGY 2009; 58:161-169. [PMID: 19018587 DOI: 10.1007/s00248-008-9469-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 10/29/2008] [Indexed: 05/27/2023]
Abstract
A gene-clone-library-based molecular approach was used to study the nirS-encoding bacteria-environment relationship in the sediments of the eutrophic Jiaozhou Bay. Diverse nirS sequences were recovered and most of them were related to the marine cluster I group, ubiquitous in estuarine, coastal, and marine environments. Some NirS sequences were unique to the Jiaozhou Bay, such as the marine subcluster VIIg sequences. Most of the Jiaozhou Bay NirS sequences had their closest matches originally detected in estuarine and marine sediments, especially from the Chesapeake Bay, indicating similarity of the denitrifying bacterial communities in similar coastal environments in spite of geographical distance. Multivariate statistical analyses indicated that the spatial distribution of the nirS-encoding bacterial assemblages is highly correlated with environmental factors, such as sediment silt content, NH4+ concentration, and OrgC/OrgN. The nirS-encoding bacterial assemblages in the most hypernutrified stations could be easily distinguished from that of the least eutrophic station. For the first time, the sedimentological condition was found to influence the structure and distribution of the sediment denitrifying bacterial community.
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Affiliation(s)
- Hongyue Dang
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266555, China.
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Dang H, Li J, Zhang X, Li T, Tian F, Jin W. Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin. J Appl Microbiol 2009; 106:1482-93. [PMID: 19187134 DOI: 10.1111/j.1365-2672.2008.04109.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved. Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment. METHODS AND RESULTS Archaeal amoA clone libraries were constructed. Diverse and novel amoA sequences were identified, with the Bohol Sea, Bashi Strait and Sibuyan Sea harbouring the highest and the Bicol Shelf the lowest AEA diversity. Phylogenetic and statistical analyses illustrate a heterogeneous distribution of the AEA community, probably caused by the differential distribution of the terrestrial or estuarine AEA in the various sampling sites. CONCLUSIONS The deep-sea sedimentary environments potentially harbour diverse and novel AEA in the tropical West Pacific Continental Margin. The stations in the Philippine inland seas (including station 3043) may represent AEA assemblages with various terrestrial influences and the stations connected directly to the open Philippine Sea may represent marine environment-dominant AEA assemblages. SIGNIFICANCE AND IMPACT OF STUDY Our study indicates the potential importance of geological and climatic events in the transport of terrestrial micro-organisms to the deep-sea sedimentary environments, almost totally neglected previously.
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Affiliation(s)
- H Dang
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
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Dang H, Li J, Chen M, Li T, Zeng Z, Yin X. Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9877-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Dang H, Zhang X, Sun J, Li T, Zhang Z, Yang G. Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. MICROBIOLOGY-SGM 2008; 154:2084-2095. [PMID: 18599836 DOI: 10.1099/mic.0.2007/013581-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ammonia-oxidizing archaea (AOA) have recently been found to be potentially important in nitrogen cycling in a variety of environments, such as terrestrial soils, wastewater treatment reactors, marine waters and sediments, and especially in estuaries, where high input of anthropogenic nitrogen is often experienced. The sedimentary AOA diversity, community structure and spatial distribution in the Changjiang Estuary and the adjacent East China Sea were studied. Multivariate statistical analysis indicated that the archaeal amoA genotype communities could be clustered according to sampling transects, and the station located in an estuarine mixing zone harboured a distinct AOA community. The distribution of AOA communities correlated significantly with the gradients of surface-water salinity and sediment sorting coefficient. The spatial distribution of putative soil-related AOA in certain sampling stations indicated a strong impact of the Changjiang freshwater discharge on the marine benthic microbial ecosystem. Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path.
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Affiliation(s)
- Hongyue Dang
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266555, China
| | - Xiaoxia Zhang
- Life Sciences and Technology College, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266555, China
| | - Jin Sun
- Life Sciences and Technology College, Ocean University of China, Qingdao 266003, China.,Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266555, China
| | - Tiegang Li
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhinan Zhang
- Life Sciences and Technology College, Ocean University of China, Qingdao 266003, China
| | - Guanpin Yang
- Life Sciences and Technology College, Ocean University of China, Qingdao 266003, China
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Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol 2008; 80:365-80. [PMID: 18648804 DOI: 10.1007/s00253-008-1565-4] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 05/29/2008] [Accepted: 06/01/2008] [Indexed: 10/21/2022]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.
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