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Rohwer RR, Kirkpatrick M, Garcia SL, Kellom M, McMahon KD, Baker BJ. Bacterial ecology and evolution converge on seasonal and decadal scales. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579087. [PMID: 38370794 PMCID: PMC10871203 DOI: 10.1101/2024.02.06.579087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum.
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Affiliation(s)
- Robin R. Rohwer
- The University of Texas at Austin, Department of Integrative Biology, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Mark Kirkpatrick
- The University of Texas at Austin, Department of Integrative Biology, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Sarahi L. Garcia
- Carl von Ossietzky Universität Oldenburg, Institute for Chemistry and Biology of the Marine Environment (ICBM), 26129 Oldenburg, Germany
- Stockholm University, Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, 106 91 Stockholm, Sweden
| | - Matthew Kellom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Katherine D. McMahon
- University of Wisconsin-Madison, Department of Bacteriology, 1550 Linden Drive, Madison, WI, 53706, USA
- University of Wisconsin-Madison, Department of Civil and Environmental Engineering, 1550 Linden Drive, Madison, WI, 53706, USA
| | - Brett J. Baker
- The University of Texas at Austin, Department of Integrative Biology, 2415 Speedway #C0930, Austin, TX 78712, USA
- The University of Texas at Austin, Department of Marine Science, Port Aransas, Austin, TX 78373, USA
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Liu H, Dai J, Fan Z, Yang B, Wang H, Hu Y, Shao K, Gao G, Tang X. Bacterial community assembly driven by temporal succession rather than spatial heterogeneity in Lake Bosten: a large lake suffering from eutrophication and salinization. Front Microbiol 2023; 14:1261079. [PMID: 37808304 PMCID: PMC10552925 DOI: 10.3389/fmicb.2023.1261079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Oligosaline lakes in arid and semi-arid regions play a crucial role in providing essential water resources for local populations. However, limited research exists on the impact of the environment on bacterial community structure in these lakes, co-occurrence patterns and the mechanisms governing bacterial community assembly. This study aims to address this knowledge gap by examining samples collected from five areas of Lake Bosten over four seasons. Using the 16S rRNA gene sequencing method, we identified a total of 510 to 1,005 operational taxonomic units (OTUs) belonging to 37 phyla and 359 genera in Lake Bosten. The major bacterial phyla were Proteobacteria (46.5%), Actinobacteria (25.9%), Bacteroidetes (13.2%), and Cyanobacteria (5.7%), while the major genera were hgcI_clade (12.9%), Limnohabitans (6.2%), and Polynucleobacter (4.7%). Water temperature emerged as the primary driver of these community structure variations on global level. However, when considering only seasonal variations, pH and nitrate were identified as key factors influencing bacterial community structures. Summer differed from other seasons in aspects of seasonal symbiotic patterns of bacterial communities, community assembly and function are different from other seasons. There were notable variations in bacterial community structures between winter and summer. Deterministic processes dominated community assembly, but there was an increase in the proportion of stochastic processes during summer. In summer, the functions related to photosynthesis, nitrogen fixation, and decomposition of organic matter showed higher abundance. Our findings shed light on the response of bacterial communities to environmental changes and the underlying mechanisms of community assembly in oligosaline lakes in arid regions.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Taihu Basin Water Resources Management, Ministry of Water Resources, Nanjing Hydraulic Research Institute, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Jiangyu Dai
- Key Laboratory of Taihu Basin Water Resources Management, Ministry of Water Resources, Nanjing Hydraulic Research Institute, Nanjing, China
| | - Ziwu Fan
- Key Laboratory of Taihu Basin Water Resources Management, Ministry of Water Resources, Nanjing Hydraulic Research Institute, Nanjing, China
| | - Bei Yang
- Key Laboratory of Agricultural Environment of the Lower Reaches of the Yangtze River, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hang Wang
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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Rojas MVR, Alonso DP, Dropa M, Razzolini MTP, de Carvalho DP, Ribeiro KAN, Ribolla PEM, Sallum MAM. Next-Generation High-Throughput Sequencing to Evaluate Bacterial Communities in Freshwater Ecosystem in Hydroelectric Reservoirs. Microorganisms 2022; 10:microorganisms10071398. [PMID: 35889116 PMCID: PMC9322053 DOI: 10.3390/microorganisms10071398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
The quality of aquatic ecosystems is a major public health concern. The assessment and management of a freshwater system and the ecological monitoring of microorganisms that are present in it can provide indicators of the environment and water quality to protect human and animal health. with bacteria is. It is a major challenge to monitor the microbiological bacterial contamination status of surface water associated with anthropogenic activities within rivers and freshwater reservoirs. Understanding the composition of aquatic microbial communities can be beneficial for the early detection of pathogens, improving our knowledge of their ecological niches, and characterizing the assemblages of microbiota responsible for the degradation of contaminants and microbial substrates. The present study aimed to characterize the bacterial microbiota of water samples collected alongside the Madeira River and its small tributaries in rural areas near the Santo Antonio Energia hydroelectric power plant (SAE) reservoir in the municipality of Porto Velho, Rondonia state, Western Brazil. An Illumina 16s rRNA metagenomic approach was employed and the physicochemical characteristics of the water sample were assessed. We hypothesized that both water metagenomics and physicochemical parameters would vary across sampling sites. The most abundant genera found in the study were Acinetobacter, Deinococcus, and Pseudomonas. PERMANOVA and ANCOM analysis revealed that collection points sampled at the G4 location presented a significantly different microbiome compared to any other group, with the Chlamidomonadaceae family and Enhydrobacter genus being significantly more abundant. Our findings support the use of metagenomics to assess water quality standards for the protection of human and animal health in this microgeographic region.
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Affiliation(s)
- Martha Virginia R. Rojas
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil; (M.V.R.R.); (M.A.M.S.)
- FUNDUNESP—Fundação para o Desenvolvimento da UNESP, São Paulo 01009-906, Brazil
| | - Diego Peres Alonso
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil; (M.V.R.R.); (M.A.M.S.)
- Instituto de Biotecnologia da UNESP (IBTEC-Campus Botucatu), São Paulo 18607-440, Brazil;
- Correspondence:
| | - Milena Dropa
- Departamento de Saúde Ambiental, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil; (M.D.); (M.T.P.R.)
| | - Maria Tereza P. Razzolini
- Departamento de Saúde Ambiental, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil; (M.D.); (M.T.P.R.)
| | | | | | | | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil; (M.V.R.R.); (M.A.M.S.)
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Zhao YQ, Shen J, Feng JM, Wang XZ. Relative contributions of different sources to DOM in Erhai Lake as revealed by PLS-PM. CHEMOSPHERE 2022; 299:134377. [PMID: 35364075 DOI: 10.1016/j.chemosphere.2022.134377] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Dissolved organic matter (DOM) is a complex mixture of organic molecules that plays an important role in freshwater lake ecosystems. Excitation emission matrix-parallel factor analysis (EEM-PARAFAC) is an important tool for the identification and source analysis of DOM but is still inadequate for studying the differences and quantifying the contributions of different sources. Here, based on the maximum fluorescence intensities (Fmax) of the four fluorescent components (e.g., protein-like component C1, and the humic-like components C2, C3, C4) identified by EEM-PARAFAC, combined with large-scale data obtained from observations at Erhai Lake, we used partial least squares path modeling (PLS-PM) to improve the understanding of the migration and transformation mechanisms of DOM. The results showed that the phytoplankton and trophic state had greater impacts on DOM, while the impacts of sediment and inflow rivers were less significant. The results of the models that used nitrogen nutrients (N) and phosphorus nutrients (P) to separately indicate the trophic state suggested that the driving force of P on DOM was stronger than that of N in Erhai Lake. Among the four fluorescent components, the protein-like component with the largest relative proportion (41.98%) was mainly affected by phytoplankton, which was consistent with the autogenic characteristics obtained through spontaneous source index (BIX). The duality of the humic-like components was consistent with the duality of DOM through fluorescent index (FI). C3 had a higher sensitivity to the trophic state than the other components, and C2 received the greatest positive contribution from the rivers entering the lake. These results provide an improved insight into the influence of different sources on the behavior of DOM and demonstrate the potential of using PLS-PM to study the complex driving mechanism of aquatic biogeochemical parameters.
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Affiliation(s)
- Yu-Quan Zhao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China; National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali, China
| | - Jian Shen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China; National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali, China; Yunnan Dali Research Institute of Shanghai Jiao Tong University, Dali, China.
| | - Ji-Meng Feng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China; National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali, China; Yunnan Dali Research Institute of Shanghai Jiao Tong University, Dali, China
| | - Xin-Ze Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China; National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali, China; Yunnan Dali Research Institute of Shanghai Jiao Tong University, Dali, China.
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5
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Bi S, Lai H, Guo D, Liu X, Wang G, Chen X, Liu S, Yi H, Su Y, Li G. Spatio-temporal variation of bacterioplankton community structure in the Pearl River: impacts of artificial fishery habitat and physicochemical factors. BMC Ecol Evol 2022; 22:10. [PMID: 35114951 PMCID: PMC8812236 DOI: 10.1186/s12862-022-01965-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/22/2022] [Indexed: 11/30/2022] Open
Abstract
Background Artificial fishery habitat has been widely used in fishery resource protection and water habitat restoration. Although the bacterioplankton plays an important ecological role in fisheries ecosystems, the effect of artificial fishery habitat on bacterioplankton is not clear. In this study, high-throughput sequencing based on the 16S rRNA gene was carried out to study the characteristics of bacterioplankton community structure in artificial fishery habitat and to determine the principal environmental factors that shaped the composition, structure and function of bacterioplankton communities in an unfed aquaculture system. Results The results indicated that the most dominant phyla were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Actinobacteria, Cyanobacteria, and Bacteroidetes, which accounted for 28.61%, 28.37%, 19.79%, and 10.25% of the total abundance, respectively. The factors that cause the differences in bacterioplankton community were mainly manifested in three aspects, including the diversity of the community, the role of artificial fishery habitat, and the change of environmental factors. The alpha diversity analysis showed that the diversity and richness index of the bacterioplankton communities were the highest in summer, which indicated that the seasonal variation characteristics had a great influence on it. The CCA analysis identified that the dissolved oxygen, temperature, and ammonium salt were the dominant environmental factors in an unfed aquaculture system. The LEfSe analysis founded 37 indicator species in artificial structure areas (AS group), only 9 kinds existing in the control areas of the open-water group (CW group). Meanwhile, the KEGG function prediction analysis showed that the genes which were related to metabolism in group AS were significantly enhanced. Conclusions This study can provide reference value for the effect of artificial habitat on bacterioplankton community and provide fundamental information for the follow-up study of ecological benefits of artificial fishery habitat. It may be contributed to apply artificial fishery habitat in more rivers. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01965-3.
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Affiliation(s)
- Sheng Bi
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,School of Agriculture, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Han Lai
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Dingli Guo
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Xuange Liu
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Gongpei Wang
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China.,Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Xiaoli Chen
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Shuang Liu
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Huadong Yi
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Yuqin Su
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China
| | - Guifeng Li
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China. .,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, 510006, China. .,School of Life Sciences, Institute of Aquatic Economic Animals, Sun Yat-Sen University, No. 132, East Outer Ring Road, Guangzhou, 510006, China.
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FERMANI PAULINA, LAGOMARSINO LEONARDO, TORREMORRELL ANA, ESCARAY ROBERTO, BUSTINGORRY JOSÉ, LLAMES MARÍA, PÉREZ GONZALO, ZAGARESE HORACIO, MATALONI GABRIELA. Divergent dynamics of microbial components in two temperate shallow lakes with contrasting steady states in the Southern Hemisphere. AN ACAD BRAS CIENC 2022; 94:e20191545. [DOI: 10.1590/0001-3765202220191545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 08/21/2020] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | | | | | - MARÍA LLAMES
- Universidad Nacional de San Martín/UNSAM, Argentina
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7
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Bacterioplankton Community as a Biological Element for Reservoirs Water Quality Assessment. WATER 2021. [DOI: 10.3390/w13202836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Water Framework Directive (WFD) is used to evaluate the water quality of aquatic ecosystems. Phytoplankton is the only biological element considered in the reservoirs water quality assessment. In this study, we aimed to assess the use of the bacterioplankton community as an indicator of water quality, using a culture-independent assay (denaturing gradient gel electrophoresis, DGGE). Four Portuguese reservoirs (Miranda, Pocinho, Aguieira and Alqueva) were analysed in four periods (autumn 2018, spring and autumn 2019, and spring 2020). Bacterial total abundance had similar values for Miranda, Pocinho and Aguieira, and generally lower values for Alqueva. Diversity and richness values did not show a clear trend. Negative correlations were observed between some nutrients and the bacterial community. Overall, members of Actinobacteria, Bacteroidetes, Cyanobacteria, Nitrospirae and Proteobacteria were identified in all sampling sites. In Alqueva, no spatial, temporal or water body quality relationships with bacterial community were observed, which may be due to its higher size, low water velocity rate and higher residence times. However, in Miranda, Pocinho and Aguieira, a strong spatial and temporal bacterial community dynamic was observed. Furthermore, the presence of some species (e.g., Acinetobacter sp.) may reflect the poor water quality that was not detected by the WFD approach.
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8
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Zhang J, Chen Y, Huo Y, Guo J, Wan L, Lu Z, Wu QL, Jeppesen E, Han BP, Ren L. Eutrophication increases deterministic processes and heterogeneity of co-occurrence networks of bacterioplankton metacommunity assembly at a regional scale in tropical coastal reservoirs. WATER RESEARCH 2021; 202:117460. [PMID: 34343871 DOI: 10.1016/j.watres.2021.117460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Understanding microbial metacommunity assembly and the underlying methanisms are fundamental objectives of aquatic ecology. However, little is known about how eutrophication, the primary water quality issue of aquatic ecosystems, regulates bacterioplankton metacommunity assembly at a regional scale in reservoirs. In this study, we applied a metacommunity framework to study bacterioplankton communities in 210 samples collected from 42 tropical coastal reservoirs in the wet summer season. We found that the spatial pattern of bacterioplankton community compositions (BCCs) at a regional scale was shaped mainly by species sorting. The reservoir trophic state index (TSI) was the key determinant of bacterioplankton metacommunity assembly. BCC turnover increased significantly with the TSI differences between sites (∆TSI) when ∆TSI was < 20, but remained at a level of about 80% when ∆TSI was > 20. Compared to oligo-mesotrophic and mesotrophic reservoirs, increased heterogeneity of co-occurrence bacterioplankton networks and bacterioplankton β-diversity were observed across eutrophic reservoirs. We propose that larger variation in phytoplankton community assembly may play directly or indirectly deterministic processes in controlling the bacterioplankton metacommunity assembly and became the potential mechanisms behind the observed higher BCC heterogeneity across the eutrophic reservoirs. Our research contributes to a broader understanding of the ecological effects of eutrophication on reservoir ecosystems and provides clues to the management of the tropical coastal reservoirs.
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Affiliation(s)
- Jiexiang Zhang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Ye Chen
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Yong Huo
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Jia Guo
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Linglin Wan
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Zhe Lu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China.
| | - Erik Jeppesen
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China; Department of Bioscience, Aarhus University, Silkeborg, Denmark; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Turkey; Institute of Marine Sciences, Middle East Technical University, Erdemli-Mersin, Turkey.
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
| | - Lijuan Ren
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China.
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Wang J, Fan H, He X, Zhang F, Xiao J, Yan Z, Feng J, Li R. Response of bacterial communities to variation in water quality and physicochemical conditions in a river-reservoir system. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01541] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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10
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Walke JB, Becker MH, Krinos A, Chang EAB, Santiago C, Umile TP, Minbiole KPC, Belden LK. Seasonal changes and the unexpected impact of environmental disturbance on skin bacteria of individual amphibians in a natural habitat. FEMS Microbiol Ecol 2021; 97:6024676. [PMID: 33278302 DOI: 10.1093/femsec/fiaa248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/02/2020] [Indexed: 01/16/2023] Open
Abstract
Amphibians host diverse skin bacteria that have a role in pathogen defense, but these skin communities could change over time and impact this function. Here, we monitored individual Eastern red-spotted newts (Notophthalmus viridescens; N = 17) for 2 years in a field pond enclosure and assessed the effects of season and disturbance on skin bacterial community dynamics. We created disturbances by adding additional pond substrate to the enclosure at two timepoints. We planned to sample the skin bacterial community and metabolite profiles of each newt every 6 weeks; we ultimately sampled eight individuals at least six times. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities and HPLC-MS for metabolite profiling. We found that disturbance had a dramatic effect on skin bacterial communities and metabolite profiles, while season had an effect only using select metrics. There were seven core bacterial taxa (97% OTUs) that were found on all newts in all seasons, pre- and post-disturbance. Lastly, there was a correlation between bacterial and metabolite profiles post-disturbance, which was not observed pre-disturbance. This longitudinal study suggests that environmental disturbances can have lasting effects on skin bacterial communities that overwhelm seasonal changes, although the core bacteria remain relatively consistent over time.
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Affiliation(s)
- Jenifer B Walke
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Matthew H Becker
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Arianna Krinos
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Celina Santiago
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
| | - Thomas P Umile
- Department of Chemistry, Villanova University, Villanova, PA 19085, USA
| | | | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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11
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Ahmad T, Gupta G, Sharma A, Kaur B, El-Sheikh MA, Alyemeni MN. Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake. PLoS One 2021; 16:e0248116. [PMID: 33764980 PMCID: PMC7993826 DOI: 10.1371/journal.pone.0248116] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/21/2021] [Indexed: 11/23/2022] Open
Abstract
Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).
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Affiliation(s)
- Tawseef Ahmad
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Anshula Sharma
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Baljinder Kaur
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
- * E-mail: (BK); (MNA)
| | - Mohamed A. El-Sheikh
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Nasser Alyemeni
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail: (BK); (MNA)
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12
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Ozbayram EG, Koker L, Akçaalan R, Aydın F, Ertürk A, Ince O, Albay M. Contrasting the Water Quality and Bacterial Community Patterns in Shallow and Deep Lakes: Manyas vs. Iznik. ENVIRONMENTAL MANAGEMENT 2021; 67:506-512. [PMID: 32889606 DOI: 10.1007/s00267-020-01357-7] [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: 05/12/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
The objectives of this study are to monitor the physicochemical properties of two freshwater lakes with different chemical characteristics and trophic status over a year (2019) and assess the bacterial diversity by a high-throughput sequencing method for a certain time. Carlson Trophic Index analysis revealed that, whereas the deep lake, Iznik Lake, (TSImean = 48.9) has mesotrophic characteristics, the shallow lake Manyas Lake (TSImean = 74.2) was found at a hypertrophic status. The most important parameters controlling water qualities in the lakes were temperature, alkalinity, and phosphate levels. Although the bacterial communities were dominated by the same phyla (Cyanobacteria, Bacteroidetes, Actinomicrobia, Proteobacteria, and Verrucomicrobia) in both lakes, the communities differed distinctly at the lower levels. Whereas Sporichthyaceae in Manyas Lake accounted for 10% of the total reads, the major share of the sequences was assigned to Cyanobacteria Family I (8%) in Iznik Lake. The hypertrophic Manyas Lake had a more diverse bacterial community rather than Iznik Lake and contained higher numbers of unique Operational Taxonomic Units.
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Affiliation(s)
- E Gozde Ozbayram
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey.
| | - Latife Koker
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Reyhan Akçaalan
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Fatih Aydın
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Ali Ertürk
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Faculty of Civil Engineering, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
| | - Meriç Albay
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
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13
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Baker SS, Alhassan MS, Asenov KZ, Choi JJ, Craig GE, Dastidar ZA, Karim SJ, Sheardy EE, Sloulin SZ, Aggarwal N, Al-Habib ZM, Camaj V, Cleminte DD, Hamady MH, Jaafar M, Jones ML, Khan ZM, Khoshaba ES, Khoshaba R, Ko SS, Mashrah AT, Patel PA, Rajab R, Tandon S. Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples. Front Microbiol 2021; 12:579325. [PMID: 33679627 PMCID: PMC7929996 DOI: 10.3389/fmicb.2021.579325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Course-based undergraduate research experience (CURE) courses incorporate high-impact pedagogies that have been shown to increase undergraduate retention among underrepresented minorities and women. As part of the Building Infrastructure Leading to Diversity program at the University of Detroit Mercy, a CURE metagenomics course was established in the winter of 2019. Students investigated the bacterial community composition in a eutrophic cove in Lake Saint Clair (Harrison Township, MI, United States) from water samples taken in the summer and winter. The students created 16S rRNA libraries that were sequenced using next-generation sequencing technology. They used a public web-based supercomputing resource to process their raw sequencing data and web-based tools to perform advanced statistical analysis. The students discovered that the most common operational taxonomic unit, representing 31% of the prokaryotic sequences in both summer and winter samples, corresponded to an organism that belongs to a previously unidentified phylum. This result showed the students the power of metagenomics because the approach was able to detect unclassified organisms. Principal Coordinates Analysis of Bray-Curtis dissimilarity index data showed that the winter community was distinct from the summer community [Analysis of Similarities (ANOSIM) r = 0.59829, n = 18, and p < 0.001]. Dendrograms based on hierarchically clustered Pearson correlation coefficients of phyla were divided into a winter clade and a summer clade. The conclusion is that the winter bacterial population was fundamentally different from the summer population, even though the samples were taken from the same locations in a protected cove. Because of the small class sizes, qualitative as well as statistical methods were used to evaluate the course's impact on student attitudes. Results from the Laboratory Course Assessment Survey showed that most of the respondents felt they were contributing to scientific knowledge and the course fostered student collaboration. The majority of respondents agreed or strongly agreed that the course incorporated iteration aspects of scientific investigations, such as repeating procedures to fix problems. In summary, the metagenomics CURE course was able to add to scientific knowledge and allowed students to participate in authentic research.
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Affiliation(s)
- Stokes S Baker
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Mohamed S Alhassan
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Kristian Z Asenov
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Joyce J Choi
- Biology Department, University of Detroit Mercy, Detroit, MI, United States.,School of Environment and Sustainability, University of Michigan, Ann Arbor, MI, United States
| | - Griffin E Craig
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Zayn A Dastidar
- Biology Department, University of Detroit Mercy, Detroit, MI, United States.,Mike Ilitch School of Business, Wayne State University, Detroit, MI, United States
| | - Saleh J Karim
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Erin E Sheardy
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Salameh Z Sloulin
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Nitish Aggarwal
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Zahraa M Al-Habib
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Valentina Camaj
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Dennis D Cleminte
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Mira H Hamady
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Mike Jaafar
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Marcel L Jones
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Zayan M Khan
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Evileen S Khoshaba
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Rita Khoshaba
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Sarah S Ko
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | | | - Pujan A Patel
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Rabeeh Rajab
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Sahil Tandon
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
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14
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Jones EF, Griffin N, Kelso JE, Carling GT, Baker MA, Aanderud ZT. Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems. Front Microbiol 2020; 11:491425. [PMID: 33324353 PMCID: PMC7726219 DOI: 10.3389/fmicb.2020.491425] [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: 08/13/2019] [Accepted: 11/04/2020] [Indexed: 01/09/2023] Open
Abstract
Stream bacterioplankton communities, a crucial component of aquatic ecosystems and surface water quality, are shaped by environmental selection (i.e., changes in taxa abundance associated with more or less favorable abiotic conditions) and passive dispersal (i.e., organisms' abundance and distribution is a function of the movement of the water). These processes are a function of hydrologic conditions such as residence time and water chemistry, which are mediated by human infrastructure. To quantify the role of environmental conditions, dispersal, and human infrastructure (dams) on stream bacterioplankton, we measured bacterioplankton community composition in rivers from sub-alpine to urban environments in three watersheds (Utah, United States) across three seasons. Of the 53 environmental parameters measured (including physicochemical parameters, solute concentrations, and catchment characteristics), trace element concentrations explained the most variability in bacterioplankton community composition using Redundancy Analysis ordination. Trace elements may correlate with bacterioplankton due to the commonality in source of water and microorganisms, and/or environmental selection creating more or less favorable conditions for bacteria. Bacterioplankton community diversity decreased downstream along parts of the stream continuum but was disrupted where large reservoirs increased water residence time by orders of magnitude, potentially indicating a shift in the relative importance of environmental selection and dispersal at these sites. Reservoirs also had substantial effects on community composition, dissimilarity (Bray-Curtis distance) and species interactions as indicated by co-occurrence networks. Communities downstream of reservoirs were enriched with anaerobic Sporichthyaceae, methanotrophic Methylococcaceae, and iron-transforming Acidimicrobiales, suggesting alternative metabolic pathways became active in the hypolimnion of large reservoirs. Our results identify that human activity affects river microbial communities, with potential impacts on water quality through modified biogeochemical cycling.
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Affiliation(s)
- Erin Fleming Jones
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Natasha Griffin
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Julia E. Kelso
- Department of Biology and the Ecology Center, Utah State University, Logan, UT, United States
| | - Gregory T. Carling
- Department of Geological Sciences, Brigham Young University, Provo, UT, United States
| | - Michelle A. Baker
- Department of Biology and the Ecology Center, Utah State University, Logan, UT, United States
| | - Zachary T. Aanderud
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
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15
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Schiaffino MR, Huber P, Sagua M, Sabio Y García CA, Reissig M. Covariation patterns of phytoplankton and bacterioplankton in hypertrophic shallow lakes. FEMS Microbiol Ecol 2020; 96:5894912. [PMID: 32816009 DOI: 10.1093/femsec/fiaa161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/12/2020] [Indexed: 11/14/2022] Open
Abstract
The aim of this work was to assess the temporal patterns in the community composition of phytoplankton (PCC) and bacterioplankton (BCC) in two interconnected and hypertrophic Pampean shallow lakes in Argentina. Factors shaping their community dynamics and community temporal covariations were also analysed. We performed 4 years of seasonal samplings (2012-2016) and communities were studied by the Utermöhl approach (PCC) and Illumina MiSeq sequencing (BCC). We found marked seasonal variations in both communities and inter-annual variations with decreasing microbial community similarities during the study. We also observed covariation in community-level dynamics among PCC and BCC within and between shallow lakes. The within-lake covariations remained positive and significant, while controlling for the effects of intrinsic (environmental) and extrinsic (temporal and meteorological) factors, suggesting a community coupling mediated by intrinsic biotic interactions. Algal-bacterial associations between different taxa of phytoplankton and bacterioplankton within each lake were also found. PCC was mainly explained by pure regional extrinsic (17-21%) and intrinsic environmental (8-9%) factors, while BCC was explained by environmental (8-10%) and biotic interactions with phytoplankton (7-8%). Our results reveal that the influence of extrinsic regional factors can be channeled to bacterioplankton through both environmental (i.e. water temperature) and phytoplankton effects.
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Affiliation(s)
- M R Schiaffino
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Sáenz Peña 456, 6000, Junín, Argentina.,Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) - UNNOBA-UNSAdA-CONICET, Jorge Newbery 355, 6000, Junín, Argentina
| | - P Huber
- Instituto Nacional de Limnología (INALI, CONICET-UNL), Colectora Ruta Nac. 168, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - M Sagua
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Sáenz Peña 456, 6000, Junín, Argentina.,Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) - UNNOBA-UNSAdA-CONICET, Jorge Newbery 355, 6000, Junín, Argentina
| | - C A Sabio Y García
- CONICET - Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Intendente Güiraldes 2160, Ciudad Universitaria - C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Depto. Ecología, Genética y Evolución, Intendente Güiraldes 2160, Ciudad Universitaria - C1428EGA, Buenos Aires, Argentina
| | - M Reissig
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue - CONICET, Quintral 1250, 8400, San Carlos de Bariloche, Argentina
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16
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Zhang L, Fang W, Li X, Lu W, Li J. Strong linkages between dissolved organic matter and the aquatic bacterial community in an urban river. WATER RESEARCH 2020; 184:116089. [PMID: 32693265 DOI: 10.1016/j.watres.2020.116089] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Aquatic bacterial communities play an important role in biogeochemical cycling in river ecosystems; however, knowledge of the linkages between bacterial communities and dissolved organic matter (DOM) in urban rivers is limited. Here, 16S rRNA amplicon sequencing and parallel factor (PARAFAC) modeling of excitation-emission fluorescence spectroscopy were used to analyze the compositions, co-occurrence patterns, and interactions with chromophoric DOM (CDOM) of bacterial communities in urban river water samples influenced by different human activities. The results revealed that two protein-like components accounted for 65.2 ± 9.56% of the total variability in all three fluorescence components, which suggests that CDOM in urban rivers is mainly a microbial source. In addition to pH and DO, CDOM is also an important factor affecting bacterial community structure, and the main classes (Gammaproteobacteria and Clostridia) and genera (Limnohabitans and Alpinimonas) showed strong positive correlations with terrestrial humic-like C1 and tryptophan-like C2, respectively. When autotrophic and heterotrophic bacteria coexist in urban rivers, the production and degradation of CDOM will occur simultaneously. Furthermore, the riverine bacterial co-occurrence network had a nonrandom modular structure, which was mainly driven by classification correlation and bacterial function. The high abundance of genes related to xenobiotic metabolism, carbon metabolism and nitrogen metabolism in the urban river indicated that anthropogenic activity may be the dominant selective force altering the bacterial communities. Overall, our results provide a novel view for the assembly of bacterial communities in urban river ecosystems under the influence of different human activities.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China.
| | - Wangkai Fang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jing Li
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
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17
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Aguilar P, Sommaruga R. The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time. Mol Ecol 2020; 29:3117-3130. [PMID: 32628343 PMCID: PMC7540538 DOI: 10.1111/mec.15538] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023]
Abstract
One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short‐term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
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18
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Zhang J, Zhang H, Li L, Wang Q, Yu J, Chen Y. Microbial community analysis and correlation with 2-methylisoborneol occurrence in landscape lakes of Beijing. ENVIRONMENTAL RESEARCH 2020; 183:109217. [PMID: 32065914 DOI: 10.1016/j.envres.2020.109217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 06/10/2023]
Abstract
The microbial community is an important factor influencing the health of the water ecosystem in landscape lakes; in particular, proliferation of some cyanobacteria could cause odor problems. Exploring the microbial community is important for water quality management. In this study, focusing on seven landscape lakes in Beijing, the microbial communities were investigated based on 16S rRNA gene amplicon sequencing, and typical odor-causing compounds and interfering factors were identified. The results showed that 2-methylisoborneol (MIB) was the major odor-causing compound responsible for the earthy/musty odor in landscape lakes. For algal communities, Chlorella and Diatoms were the main eukaryote algae in the water. The bacterial community was dominated by Proteobacteria at the phylum level, and then Cyanobacteria, Actinobacteria, and Firmicutes, etc., most of which were the major phyla of the heterotrophic bacterial population. The richness and diversity of bacteria in natural-water-source lakes were higher than those in reclaimed-water-source lakes. Synechococcus (Cyanobacteria) and GKS98 (Proteobacteria) in reclaimed-water-source lakes were higher than those in natural-water-source lakes, however, CL500-29 (Actinobacteria) in natural-water-source lakes was higher than that in reclaimed-water-source lakes. These bacteria also had significantly positive correlations with MIB. Cyanobacteria and Actinobacteria were the main MIB compound contributors to the variability of MIB in the landscape lakes in Beijing.
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Affiliation(s)
- Junzhi Zhang
- Beijing Climate Change Response Research and Education Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Huixin Zhang
- Beijing Climate Change Response Research and Education Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Luwei Li
- Beijing Climate Change Response Research and Education Center, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Qi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100019, China
| | - Jianwei Yu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100019, China.
| | - Yongsheng Chen
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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19
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Hermans SM, Buckley HL, Case BS, Lear G. Connecting through space and time: catchment‐scale distributions of bacteria in soil, stream water and sediment. Environ Microbiol 2019; 22:1000-1010. [DOI: 10.1111/1462-2920.14792] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Syrie M. Hermans
- School of Biological SciencesUniversity of Auckland 3A Symonds Street Auckland New Zealand
| | - Hannah L. Buckley
- School of ScienceAuckland University of Technology Private Bag 92006 Auckland 1142 New Zealand
| | - Bradley S. Case
- School of ScienceAuckland University of Technology Private Bag 92006 Auckland 1142 New Zealand
| | - Gavin Lear
- School of Biological SciencesUniversity of Auckland 3A Symonds Street Auckland New Zealand
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20
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Limberger R, Pitt A, Hahn MW, Wickham SA. Spatial insurance in multi-trophic metacommunities. Ecol Lett 2019; 22:1828-1837. [PMID: 31392829 PMCID: PMC6852594 DOI: 10.1111/ele.13365] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/26/2019] [Accepted: 07/16/2019] [Indexed: 01/21/2023]
Abstract
Metacommunity theory suggests that dispersal is a key driver of diversity and ecosystem functioning in changing environments. The capacity of dispersal to mitigate effects of environmental change might vary among trophic groups, potentially resulting in changes in trophic interactions and food web structure. In a mesocosm experiment, we compared the compositional response of bacteria, phyto‐ and zooplankton to a factorial manipulation of acidification and dispersal. We found that the buffering capacity of dispersal varied among trophic groups: dispersal alleviated the negative effect of acidification on phytoplankton diversity mid‐experiment, but had no effect on the diversity of zooplankton and bacteria. Likewise, trophic groups differed in whether dispersal facilitated compositional change. Dispersal accelerated changes in phytoplankton composition under acidification, possibly mediated by changes in trophic interactions, but had no effect on the composition of zooplankton and bacteria. Overall, our results suggest that the potential for spatial insurance can vary among trophic groups.
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Affiliation(s)
- Romana Limberger
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.,Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Alexandra Pitt
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Stephen A Wickham
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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21
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Luo Z, Li S, Hou K, Ji G. Spatial and seasonal bacterioplankton community dynamics in the main channel of the Middle Route of South-to-North Water Diversion Project. Res Microbiol 2019; 170:24-34. [DOI: 10.1016/j.resmic.2018.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/30/2018] [Accepted: 08/22/2018] [Indexed: 12/01/2022]
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22
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Obertegger U, Bertilsson S, Pindo M, Larger S, Flaim G. Temporal variability of bacterioplankton is habitat driven. Mol Ecol 2018; 27:4322-4335. [PMID: 30176079 DOI: 10.1111/mec.14855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 11/27/2022]
Abstract
Temporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, nonmetric multidimensional scaling and source-sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to meltwater inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats.
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Affiliation(s)
- Ulrike Obertegger
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Simone Larger
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giovanna Flaim
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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23
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Roberto AA, Van Gray JB, Leff LG. Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition. WATER RESEARCH 2018; 134:353-369. [PMID: 29454907 DOI: 10.1016/j.watres.2018.01.045] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/04/2018] [Accepted: 01/20/2018] [Indexed: 05/25/2023]
Abstract
Sediment bacterial communities play a critical role in biogeochemical cycling in lotic ecosystems. Despite their ecological significance, the effects of urban discharge on spatiotemporal distribution of bacterial communities are understudied. In this study, we examined the effect of urban discharge on the spatiotemporal distribution of stream sediment bacteria in a northeast Ohio stream. Water and sediment samples were collected after large storm events (discharge > 100 m) from sites along a highly impacted stream (Tinkers Creek, Cuyahoga River watershed, Ohio, USA) and two reference streams. Although alpha (α) diversity was relatively constant spatially, multivariate analysis of bacterial community 16S rDNA profiles revealed significant spatial and temporal effects on beta (β) diversity and community composition and identified a number of significant correlative abiotic parameters. Clustering of upstream and reference sites from downstream sites of Tinkers Creek combined with the dominant families observed in specific locales suggests that environmentally-induced species sorting had a strong impact on the composition of sediment bacterial communities. Distinct groupings of bacterial families that are often associated with nutrient pollution (i.e., Comamonadaceae, Rhodobacteraceae, and Pirellulaceae) and other contaminants (i.e., Sphingomonadaceae and Phyllobacteriaceae) were more prominent at sites experiencing higher degrees of discharge associated with urbanization. Additionally, there were marked seasonal changes in community composition, with individual taxa exhibiting different seasonal abundance patterns. However, spatiotemporal variation in stream conditions did not affect bacterial community functional profiles. Together, these results suggest that local environmental drivers and niche filtering from discharge events associated with urbanization shape the bacterial community structure. However, dispersal limitations and interactions among other species likely play a role as well.
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Affiliation(s)
- Alescia A Roberto
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.
| | - Jonathon B Van Gray
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.
| | - Laura G Leff
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.
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24
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Chopyk J, Allard S, Nasko DJ, Bui A, Mongodin EF, Sapkota AR. Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations. Front Microbiol 2018; 9:792. [PMID: 29740420 PMCID: PMC5928236 DOI: 10.3389/fmicb.2018.00792] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/09/2018] [Indexed: 12/26/2022] Open
Abstract
Agricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of this project was to characterize the bacterial and viral communities of pond water in the Mid-Atlantic United States with a focus on the late season (October-December), where decreasing temperature and nutrient levels can affect the composition of microbial communities. Ten liters of freshwater from an agricultural pond were sampled monthly, and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, and the bacterial communities were characterized using 16S rRNA gene sequencing. The remaining filtrate was chemically concentrated for viruses, DNA-extracted, and shotgun sequenced. Bacterial community profiling showed significant fluctuations over the sampling period, corresponding to changes in the condition of the pond freshwater (e.g., pH, nutrient load). In addition, there were significant differences in the alpha-diversity and core bacterial operational taxonomic units (OTUs) between water fractions filtered through different pore sizes. The viral fraction was dominated by tailed bacteriophage of the order Caudovirales, largely those of the Siphoviridae family. Moreover, while present, genes involved in virulence/antimicrobial resistance were not enriched within the viral fraction during the study period. Instead, the viral functional profile was dominated by phage associated proteins, as well as those related to nucleotide production. Overall, these data suggest that agricultural pond water harbors a diverse core of bacterial and bacteriophage species whose abundance and composition are influenced by environmental variables characteristic of pond topology and the late season.
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Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Sarah Allard
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Daniel J. Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, United States
| | - Anthony Bui
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
| | - Emmanuel F. Mongodin
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Amy R. Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United States
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25
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Prokaryotic Community Composition Affected by Seasonal Changes in Physicochemical Properties of Water in Peat Bog Lakes. WATER 2018. [DOI: 10.3390/w10040485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Hu A, Ju F, Hou L, Li J, Yang X, Wang H, Mulla SI, Sun Q, Bürgmann H, Yu CP. Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environ Microbiol 2017; 19:4993-5009. [DOI: 10.1111/1462-2920.13942] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Feng Ju
- Department of Surface Waters-Research and Management; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum 6047 Switzerland
| | - Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Xiaoyong Yang
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Sikandar I. Mulla
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Helmut Bürgmann
- Department of Surface Waters-Research and Management; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum 6047 Switzerland
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- Graduate Institute of Environmental Engineering; National Taiwan University; Taipei 106 Taiwan
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27
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Tiede J, Scherber C, Mutschler J, McMahon KD, Gratton C. Gut microbiomes of mobile predators vary with landscape context and species identity. Ecol Evol 2017; 7:8545-8557. [PMID: 29075470 PMCID: PMC5648672 DOI: 10.1002/ece3.3390] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/19/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023] Open
Abstract
Landscape context affects predator–prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.
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Affiliation(s)
- Julia Tiede
- Institute of Landscape Ecology University of Muenster Muenster Germany.,Department of Crop Sciences University of Goettingen Goettingen Germany.,Department of Entomology University of Wisconsin-Madison Madison WI USA
| | - Christoph Scherber
- Institute of Landscape Ecology University of Muenster Muenster Germany.,Department of Crop Sciences University of Goettingen Goettingen Germany
| | - James Mutschler
- Departments of Civil and Environmental Engineering and Bacteriology University of Wisconsin-Madison Madison WI USA
| | - Katherine D McMahon
- Departments of Civil and Environmental Engineering and Bacteriology University of Wisconsin-Madison Madison WI USA
| | - Claudio Gratton
- Department of Entomology University of Wisconsin-Madison Madison WI USA
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28
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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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29
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Rigonato J, Kent AD, Gumiere T, Branco LHZ, Andreote FD, Fiore MF. Temporal assessment of microbial communities in soils of two contrasting mangroves. Braz J Microbiol 2017; 49:87-96. [PMID: 28827029 PMCID: PMC5790579 DOI: 10.1016/j.bjm.2017.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/29/2017] [Accepted: 04/11/2017] [Indexed: 12/04/2022] Open
Abstract
Variations in microbial communities promoted by alterations in environmental conditions are reflected in similarities/differences both at taxonomic and functional levels. Here we used a natural gradient within mangroves from seashore to upland, to contrast the natural variability in bacteria, cyanobacteria and diazotroph assemblages in a pristine area compared to an oil polluted area along a timespan of three years, based on ARISA (bacteria and cyanobacteria) and nifH T-RFLP (diazotrophs) fingerprinting. The data presented herein indicated that changes in all the communities evaluated were mainly driven by the temporal effect in the contaminated area, while local effects were dominant on the pristine mangrove. A positive correlation of community structure between diazotrophs and cyanobacteria was observed, suggesting the functional importance of this phylum as nitrogen fixers in mangroves soils. Different ecological patterns explained the microbial behavior in the pristine and polluted mangroves. Stochastic models in the pristine mangrove indicate that there is not a specific environmental factor that determines the bacterial distribution, while cyanobacteria and diazotrophs better fitted in deterministic model in the same area. For the contaminated mangrove site, deterministic models better represented the variations in the communities, suggesting that the presence of oil might change the microbial ecological structures over time. Mangroves represent a unique environment threatened by global change, and this study contributed to the knowledge of the microbial distribution in such areas and its response on persistent contamination historic events.
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Affiliation(s)
- Janaina Rigonato
- University of São Paulo, Center for Nuclear Energy in Agriculture, Piracicaba, SP, Brazil; São Paulo State University, Instituto de Biociências, Letras e Ciências Exatas, Department of Zoology and Botany, São José do Rio Preto, SP, Brazil
| | - Angela D Kent
- University of Illinois at Urbana-Champaign, Department of Natural Resources and Environmental Sciences, Champaign, Illinois, USA
| | - Thiago Gumiere
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Soil Science, Piracicaba, São Paulo, Brazil
| | - Luiz Henrique Zanini Branco
- São Paulo State University, Instituto de Biociências, Letras e Ciências Exatas, Department of Zoology and Botany, São José do Rio Preto, SP, Brazil
| | - Fernando Dini Andreote
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Soil Science, Piracicaba, São Paulo, Brazil
| | - Marli Fátima Fiore
- University of São Paulo, Center for Nuclear Energy in Agriculture, Piracicaba, SP, Brazil.
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30
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Hu A, Wang H, Yang X, Hou L, Li J, Li S, Yu CP. Seasonal and spatial variations of prokaryoplankton communities in a salinity-influenced watershed, China. FEMS Microbiol Ecol 2017; 93:3966710. [DOI: 10.1093/femsec/fix093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/11/2017] [Indexed: 12/17/2022] Open
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31
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Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes. mSphere 2017; 2:mSphere00169-17. [PMID: 28680968 PMCID: PMC5489657 DOI: 10.1128/msphere.00169-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/09/2017] [Indexed: 01/01/2023] Open
Abstract
Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series. Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “Candidatus Omnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.
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32
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Yan Q, Stegen JC, Yu Y, Deng Y, Li X, Wu S, Dai L, Zhang X, Li J, Wang C, Ni J, Li X, Hu H, Xiao F, Feng W, Ning D, He Z, Van Nostrand JD, Wu L, Zhou J. Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China). Mol Ecol 2017; 26:3839-3850. [PMID: 28437572 DOI: 10.1111/mec.14151] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
Abstract
Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance >1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche-based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas.
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Affiliation(s)
- Qingyun Yan
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - James C Stegen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xinghao Li
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shu Wu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lili Dai
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiang Zhang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jinjin Li
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chun Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jiajia Ni
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xuemei Li
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hongjuan Hu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fanshu Xiao
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Weisong Feng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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33
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Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). PLoS One 2017; 12:e0177488. [PMID: 28493994 PMCID: PMC5426677 DOI: 10.1371/journal.pone.0177488] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.
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Affiliation(s)
- Jessica M. Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Kristina D. Baker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Richard M. Zamor
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Steve Nikolai
- Grand River Dam Authority (GRDA), Vinita, OK, United States of America
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States of America
- * E-mail:
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34
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Aquatic bacterial diversity: Magnitude, dynamics, and controlling factors. Microb Pathog 2017; 104:39-47. [DOI: 10.1016/j.micpath.2017.01.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 11/22/2022]
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35
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Bacterial abundance and diversity in pond water supplied with different feeds. Sci Rep 2016; 6:35232. [PMID: 27759010 PMCID: PMC5069485 DOI: 10.1038/srep35232] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/22/2016] [Indexed: 01/17/2023] Open
Abstract
The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.
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Lew S, Lew M, Koblížek M. Influence of selected environmental factors on the abundance of aerobic anoxygenic phototrophs in peat-bog lakes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:13853-13863. [PMID: 27032635 PMCID: PMC4943989 DOI: 10.1007/s11356-016-6521-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
Aerobic anoxygenic phototrophs (AAPs) are photoheterotrophic prokaryotes that are widespread in many limnic and marine environments. So far, little is known about their distribution in peat-bog lakes. Seventeen peat-bog lakes were sampled during three summer seasons 2009, 2011, and 2012, and the vertical distribution of AAPs was determined by infrared epifluorescence microscopy. The analysis demonstrated that in the surface layers of the studied lakes, AAP abundance ranged from 0.3 to 12.04 × 10(5) cells mL(-1), which represents <1 to 18.3 % of the total bacteria. The vertical distribution of AAPs confirmed their presence in the upper parts of the water column with minimum numbers in the anoxic bottom waters. We have shown that the AAP abundance was significantly positively correlated with the water pH, and the highest proportion of photoheterotrophs was found in peat-bog lakes with a pH between 6.7 and 7.6. Our results demonstrated an influence of water acidity on the abundance of AAPs, which may reflect a fundamental difference in the microbial composition between acidic and pH neutral peat-bog lakes.
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Affiliation(s)
- Sylwia Lew
- />Faculty of Biology and Biotechnology, University of Warmia and Mazury in Poland, Oczapowskiego 1a, 10-957 Olsztyn, Poland
| | - Marcin Lew
- />Faculty of Veterinary Medicine, University of Warmia and Mazury in Poland, Oczapowskiego 2, 10-957 Olsztyn, Poland
| | - Michal Koblížek
- />Institute of Microbiology CAS, Center Algatech, 37981 Třeboň, Czech Republic
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Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13060599. [PMID: 27322295 PMCID: PMC4924056 DOI: 10.3390/ijerph13060599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/03/2016] [Accepted: 06/08/2016] [Indexed: 11/16/2022]
Abstract
The bacterioplankton community composition's (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao'an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria.
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Ma L, Mao G, Liu J, Gao G, Zou C, Bartlam MG, Wang Y. Spatial-Temporal Changes of Bacterioplankton Community along an Exhorheic River. Front Microbiol 2016; 7:250. [PMID: 26973627 PMCID: PMC4776164 DOI: 10.3389/fmicb.2016.00250] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
To date, few aquatic microbial ecology studies have discussed the variability of the microbial community in exorheic river ecosystems on both the spatial and seasonal scales. In this study, we examined the spatio-temporal variation of bacterioplankton community composition in an anthropogenically influenced exorheic river, the Haihe River in Tianjin, China, using pyrosequencing analysis of 16S rRNA genes. It was verified by one-way ANOVA that the spatial variability of the bacterioplankton community composition over the whole river was stronger than the seasonal variation. Salinity was a major factor leading to spatial differentiation of the microbial community structure into riverine and estuarial parts. A high temperature influence on the seasonal bacterial community variation was only apparent within certain kinds of environments (e.g., the riverine part). Bacterial community richness and diversity both exhibited significant spatial changes, and their seasonal variations were completely different in the two environments studied here. Furthermore, riverine bacterial community assemblages were subdivided into urban and rural groups due to changes in the nutritional state of the river. In addition, the nutrient-loving group including Limnohabitans, Hydrogenophaga, and Polynucleobacter were abundant in the urbanized Haihe River, indicating the environmental factors in these anthropogenic waterbodies heavily influence the core freshwater community composition.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China; Department of Environmental Engineering and Safety Engineering, College of Chemistry and Chemical Engineering, Southwest Petroleum UniversityChengdu, China
| | - Guannan Mao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
| | - Jie Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
| | - Guanghai Gao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
| | - Changliang Zou
- LPMC and Institute of Statistics, Nankai University Tianjin, China
| | - Mark G Bartlam
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University Tianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
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Schmidt ML, White JD, Denef VJ. Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla. Environ Microbiol 2016; 18:1212-26. [DOI: 10.1111/1462-2920.13143] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Marian L. Schmidt
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
| | - Jeffrey D. White
- Department of Biology; Framingham State University; Framingham MA 01701 USA
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
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Cai W, Li Y, Wang P, Niu L, Zhang W, Wang C. Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River basin, Yangtze River Delta. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:1163-1176. [PMID: 27642836 DOI: 10.2166/wst.2016.224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
River pollution is one of the most challenging environmental issues, but the effect of river pollution levels on the biofilm communities has not been well-studied. Spatial and temporal distribution characteristics of environmental parameters and the biofilm communities were investigated in the Qinhuai River basin, Nanjing, China. Water samples were grouped into three clusters reflecting their varying pollution levels of relatively slight pollution, moderated pollution, and high pollution by hierarchical cluster analysis. In different clusters, the biofilm communities mainly differed in the proportion of Actinobacteria, Firmicutes, and Proteobacteria. As the dominant classes of Proteobacteria, Alpha-, Beta- and Gammaproteobacteria seemed to show an upward trend followed by a small fluctuation in the abundance with the escalation of water pollution level. Results of redundancy analysis demonstrated that temperature, total nitrogen to total phosphorus ratios (TN/TP) and concentrations of ammonia nitrogen (NH3-N) and TN were mainly responsible for the variation in bacterial community structure. The occurrences of Alpha-, Beta- and Gammaproteobacteria were closely associated with higher temperature, higher concentrations of NH3-N and TN and a lower TN/TP ratio. This study may provide a theoretical basis for the water pollution control and ecological restoration in urban rivers under different pollution levels.
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Affiliation(s)
- Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
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Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status. Appl Microbiol Biotechnol 2015; 100:4161-75. [PMID: 26711281 DOI: 10.1007/s00253-015-7253-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 12/12/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Both planktonic and sediment bacterial assemblages are the important components of freshwater lake ecosystems. However, their spatiotemporal shift and the driving forces remain still elusive. Eutrotrophic Dianchi Lake and mesotrophic Erhai Lake are the largest two freshwater lakes on the Yunnan Plateau (southwestern China). The present study investigated the spatiotemporal shift in both planktonic and sediment bacterial populations in these two plateau freshwater lakes at different trophic status. For either lake, both water and sediment samples were collected from six sampling locations in spring and summer. Bacterioplankton community abundance in Dianchi Lake generally far outnumbered that in Erhai Lake. Sediment bacterial communities in Erhai Lake were found to have higher richness and diversity than those in Dianchi Lake. Sediments had higher bacterial community richness and diversity than waters. The change patterns for both planktonic and sediment bacterial communities were lake-specific and season-specific. Either planktonic or sediment bacterial community structure showed a distinct difference between in Dianchi Lake and in Erhai Lake, and an evident structure difference was also found between planktonic and sediment bacterial communities in either of these two lakes. Planktonic bacterial communities in both Dianchi Lake and Erhai Lake mainly included Proteobacteria (mainly Alpha-, Beta-, and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Cyanobacteria, and Firmicutes, while sediment bacterial communities were mainly represented by Proteobacteria (mainly Beta- and Deltaproteobacteria), Bacteroidetes, Chlorobi, Nitrospirae, Acidobacteria, and Chloroflexi. Trophic status could play important roles in shaping both planktonic and sediment bacterial communities in freshwater lakes.
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Freimann R, Bürgmann H, Findlay SEG, Robinson CT. Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains. Front Microbiol 2015; 6:1221. [PMID: 26579113 PMCID: PMC4630579 DOI: 10.3389/fmicb.2015.01221] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 10/19/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial community assembly and microbial functions are affected by a number of different but coupled drivers such as local habitat characteristics, dispersal rates, and species interactions. In groundwater systems, hydrological flow can introduce spatial structure and directional dependencies among these drivers. We examined the importance of hydrology in structuring bacterial communities and their function within two alpine floodplains during different hydrological states. Piezometers were installed in stream sediments and surrounding riparian zones to assess hydrological flows and also were used as incubation chambers to examine bacterial community structures and enzymatic functions along hydrological flow paths. Spatial eigenvector models in conjunction with models based on physico-chemical groundwater characteristics were used to evaluate the importance of hydrologically-driven processes influencing bacterial assemblages and their enzymatic activities. Our results suggest a strong influence (up to 40% explained variation) of hydrological connectivity on enzymatic activities. The effect of hydrology on bacterial community structure was considerably less strong, suggesting that assemblages demonstrate large functional plasticity/redundancy. Effect size varied between hydrological periods but flow-related mechanisms always had the most power in explaining both bacterial structure and functioning. Changes in hydrology should be considered in models predicting ecosystem functioning and integrated into ecosystem management strategies for floodplains.
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Affiliation(s)
- Remo Freimann
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology ETH Zurich, Dübendorf, Switzerland ; Institute of Integrative Biology ETH Zurich, Zürich, Switzerland ; Department of Biology, Institute of Molecular Health Sciences, Epigenetic Regulation and Cell Identity Control ETH Zurich, Zürich, Switzerland
| | - Helmut Bürgmann
- Department of Surface Waters - Research and Management, Eawag: Swiss Federal Institute of Aquatic Science and Technology ETH Zurich, Kastanienbaum, Switzerland
| | | | - Christopher T Robinson
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology ETH Zurich, Dübendorf, Switzerland ; Institute of Integrative Biology ETH Zurich, Zürich, Switzerland
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Roguet A, Laigle GS, Therial C, Bressy A, Soulignac F, Catherine A, Lacroix G, Jardillier L, Bonhomme C, Lerch TZ, Lucas FS. Neutral community model explains the bacterial community assembly in freshwater lakes. FEMS Microbiol Ecol 2015; 91:fiv125. [PMID: 26472576 DOI: 10.1093/femsec/fiv125] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2015] [Indexed: 11/14/2022] Open
Abstract
Over the past decade, neutral theory has gained attention and recognition for its capacity to explain bacterial community structure (BCS) in addition to deterministic processes. However, no clear consensus has been drawn so far on their relative importance. In a metacommunity analysis, we explored at the regional and local scale the effects of these processes on the bacterial community assembly within the water column of 49 freshwater lakes. The BCS was assessed using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA genes. At the regional scales, results indicated that the neutral community model well predicted the spatial community structure (R(2) mean = 76%) compared with the deterministic factors - which explained only a small fraction of the BCS total variance (less than 14%). This suggests that the bacterial compartment was notably driven by stochastic processes, through loss and gain of taxa. At the local scale, the bacterial community appeared to be spatially structured by stochastic processes (R(2) mean = 65%) and temporally governed by the water temperature, a deterministic factor, even if some bacterial taxa were driven by neutral dynamics. Therefore, at both regional and local scales the neutral community model appeared to be relevant in explaining the bacterial assemblage structure.
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Affiliation(s)
- Adélaïde Roguet
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Grégory S Laigle
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Claire Therial
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Adèle Bressy
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Frédéric Soulignac
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Arnaud Catherine
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, Case 39, 57 rue Cuvier, FR 75005 Paris, France
| | - Gérard Lacroix
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618 [UPMC, UPEC, Paris Diderot, CNRS, IRD, INRA]), Université Pierre et Marie Curie, Bâtiment A, 7 quai St Bernard, FR 75005 Paris, France CEREEP-Ecotron Ile De France (UMS 3194 [CNRS, ENS]), Ecole Normale Supérieure, 78 rue du Château, 77140 St-Pierre-lès-Nemours, France
| | - Ludwig Jardillier
- Écologie Systématique Évolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Céline Bonhomme
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Thomas Z Lerch
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618 [UPMC, UPEC, Paris Diderot, CNRS, IRD, INRA]), Université Paris-Est Créteil, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Françoise S Lucas
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
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Czekalski N, Sigdel R, Birtel J, Matthews B, Bürgmann H. Does human activity impact the natural antibiotic resistance background? Abundance of antibiotic resistance genes in 21 Swiss lakes. ENVIRONMENT INTERNATIONAL 2015; 81:45-55. [PMID: 25913323 DOI: 10.1016/j.envint.2015.04.005] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 03/30/2015] [Accepted: 04/10/2015] [Indexed: 05/06/2023]
Abstract
Antibiotic resistance genes (ARGs) are emerging environmental contaminants, known to be continuously discharged into the aquatic environment via human and animal waste. Freshwater aquatic environments represent potential reservoirs for ARG and potentially allow sewage-derived ARG to persist and spread in the environment. This may create increased opportunities for an eventual contact with, and gene transfer to, human and animal pathogens via the food chain or drinking water. However, assessment of this risk requires a better understanding of the level and variability of the natural resistance background and the extent of the human impact. We have analyzed water samples from 21 Swiss lakes, taken at sampling points that were not under the direct influence of local contamination sources and analyzed the relative abundance of ARG using quantitative real-time PCR. Copy numbers of genes mediating resistance to three different broad-spectrum antibiotic classes (sulfonamides: sul1, sul2, tetracyclines: tet(B), tet(M), tet(W) and fluoroquinolones: qnrA) were normalized to copy numbers of bacterial 16S rRNA genes. We used multiple linear regression to assess if ARG abundance is related to human activities in the catchment, microbial community composition and the eutrophication status of the lakes. Sul genes were detected in all sampled lakes, whereas only four lakes contained quantifiable numbers of tet genes, and qnrA remained below detection in all lakes. Our data indicate higher abundance of sul1 in lakes with increasing number and capacity of wastewater treatment plants (WWTPs) in the catchment. sul2 abundance was rather related to long water residence times and eutrophication status. Our study demonstrates the potential of freshwater lakes to preserve antibiotic resistance genes, and provides a reference for ARG abundance from lake systems with low human impact as a baseline for assessing ARG contamination in lake water.
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Affiliation(s)
- Nadine Czekalski
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - Radhika Sigdel
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - Julia Birtel
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, 6047 Kastanienbaum, Switzerland
| | - Blake Matthews
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, 6047 Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland.
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Influence of commonly used primer systems on automated ribosomal intergenic spacer analysis of bacterial communities in environmental samples. PLoS One 2015; 10:e0118967. [PMID: 25749323 PMCID: PMC4351999 DOI: 10.1371/journal.pone.0118967] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/08/2015] [Indexed: 11/19/2022] Open
Abstract
Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA) is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub). Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify (in silico) sequences of some important crop species such as Sorghum bicolor and Zea mays. Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected.
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46
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Kraemer SA, Kassen R. Patterns of Local Adaptation in Space and Time among Soil Bacteria. Am Nat 2015; 185:317-31. [DOI: 10.1086/679585] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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47
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Dai J, Chen D, Wu S, Wu X, Zhou J, Tang X, Shao K, Gao G. Comparative analysis of alkaline phosphatase-encoding genes (phoX) in two contrasting zones of Lake Taihu. Can J Microbiol 2015; 61:227-36. [DOI: 10.1139/cjm-2014-0446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Limnetic habitats that are dominated by either algae or macrophytes represent the 2 dominant ecosystems in shallow lakes. We assessed seasonal variations in the diversity and abundance of alkaline phosphate-encoding genes (phoX) in these 2 zones of Lake Taihu, which is a large, shallow, eutrophic lake in China. There was no significant difference in seasonal mean phoX diversity between the 2 zones, whereas the seasonal mean phoX abundance in the macrophyte-dominated region was higher than that in the algae-dominated region. The bulk of the genotypes in the 2 regions were most similar to the alphaproteobacterial and betaproteobacterial phoX. Genotypes most similar to phoX affiliated with Betaproteobacteria were present with greater diversity in the macrophyte-dominated zone than in the algae-dominated zone. In the algae-dominated zone, the relative proportion of genotypes most similar to cyanobacterial phoX was highest (38.8%) in summer. In addition to the different genotype structures and environmental factors between the 2 stable states, the lower gene abundances and higher alkaline phosphatase activities in Meiliang Bay in summer than those in Xukou Bay reveals different organophosphate-mineralizing modes in these 2 contrasting habitats.
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Affiliation(s)
- Jiangyu Dai
- State Key Laboratory of Hydrology – Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, People’s Republic of China
| | - Dan Chen
- Nanjing Institute of Environmental Sciences, MEP, Nanjing 210042, People’s Republic of China
| | - Shiqiang Wu
- State Key Laboratory of Hydrology – Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, People’s Republic of China
| | - Xiufeng Wu
- State Key Laboratory of Hydrology – Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, People’s Republic of China
| | - Jie Zhou
- State Key Laboratory of Hydrology – Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, People’s Republic of China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China
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Llirós M, Inceoğlu Ö, García-Armisen T, Anzil A, Leporcq B, Pigneur LM, Viroux L, Darchambeau F, Descy JP, Servais P. Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status. PLoS One 2014; 9:e116145. [PMID: 25541975 PMCID: PMC4277477 DOI: 10.1371/journal.pone.0116145] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/03/2014] [Indexed: 11/21/2022] Open
Abstract
In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga–Flavobacteria–Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions.
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Affiliation(s)
- Marc Llirós
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | - Özgül Inceoğlu
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Adriana Anzil
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Bruno Leporcq
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | | | - Laurent Viroux
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | | | - Jean-Pierre Descy
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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Huang Q, Briggs BR, Dong H, Jiang H, Wu G, Edwardson C, De Vlaminck I, Quake S. Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China. PLoS One 2014; 9:e111681. [PMID: 25365331 PMCID: PMC4218802 DOI: 10.1371/journal.pone.0111681] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 09/29/2014] [Indexed: 11/19/2022] Open
Abstract
Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.
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Affiliation(s)
- Qiuyuan Huang
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, United States of America
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Brandon R. Briggs
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, United States of America
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, United States of America
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Christian Edwardson
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Iwijn De Vlaminck
- Departments of Bioengineering and Applied Physics, Stanford University and the Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Stephen Quake
- Departments of Bioengineering and Applied Physics, Stanford University and the Howard Hughes Medical Institute, Stanford, California, United States of America
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50
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Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One 2014; 9:e93827. [PMID: 24714158 PMCID: PMC3979728 DOI: 10.1371/journal.pone.0093827] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 02/19/2014] [Indexed: 12/12/2022] Open
Abstract
This study explored the short-term planktonic microbial community structure and resilience in Lake Lanier (GA, USA) while simultaneously evaluating the technical aspects of identifying taxa via 16S rRNA gene amplicon and metagenomic sequence data. 16S rRNA gene amplicons generated from four temporally discrete samples were sequenced with 454 GS-FLX-Ti yielding ∼40,000 rRNA gene sequences from each sample and representing ∼300 observed OTUs. Replicates obtained from the same biological sample clustered together but several biases were observed, linked to either the PCR or sequencing-preparation steps. In comparisons with companion whole-community shotgun metagenome datasets, the estimated number of OTUs at each timepoint was concordant, but 1.5 times and ∼10 times as many phyla and genera, respectively, were identified in the metagenomes. Our analyses showed that the 16S rRNA gene captures broad shifts in community diversity over time, but with limited resolution and lower sensitivity compared to metagenomic data. We also identified OTUs that showed marked shifts in abundance over four close timepoints separated by perturbations and tracked these taxa in the metagenome vs. 16S rRNA amplicon data. A strong summer storm had less of an effect on community composition than did seasonal mixing, which revealed a distinct succession of organisms. This study provides insights into freshwater microbial communities and advances the approaches for assessing community diversity and dynamics in situ.
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