101
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Tse TJ, Doig LE, Tang S, Zhang X, Sun W, Wiseman SB, Feng CX, Liu H, Giesy JP, Hecker M, Jones PD. Combining High-Throughput Sequencing of sedaDNA and Traditional Paleolimnological Techniques To Infer Historical Trends in Cyanobacterial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6842-6853. [PMID: 29782156 DOI: 10.1021/acs.est.7b06386] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Freshwaters worldwide are under increasing pressure from anthropogenic activities and changing climate. Unfortunately, many inland waters lack sufficient long-term monitoring to assess environmental trends. Analysis of sedimentary ancient DNA ( sedaDNA) is emerging as a means to reconstruct the past occurrence of microbial communities of inland waters. The purpose of this study was to assess a combination of high-throughput sequencing (16S rRNA) of sedaDNA and traditional paleolimnological analyses to explore multidecadal relationships among cyanobacterial community composition, the potential for cyanotoxin production, and paleoenvironmental proxies. DNA was extracted from two sediment cores collected from a northern Canadian Great Plains reservoir. Diversity indices illustrated significant community-level changes since reservoir formation. Furthermore, higher relative abundances in more recent years were observed for potentially toxic cyanobacterial genera including Dolichospermum. Correlation-based network analysis revealed this trend significantly and positively correlated to abundances of the microcystin synthetase gene ( mcyA) and other paleoproxies (nutrients, pigments, stanols, sterols, and certain diatom species), demonstrating synchrony between molecular and more standard proxies. These findings demonstrate a novel approach to infer long-term dynamics of cyanobacterial diversity in inland waters and highlight the power of high-throughput sequencing to reconstruct trends in environmental quality and inform lake and reservoir management and monitoring program design.
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Affiliation(s)
- Timothy J Tse
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
| | - Lorne E Doig
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
| | - Song Tang
- School of Environment and Sustainability , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5C3 , Canada
- National Institute of Environmental Health , Chinese Center for Disease Control and Prevention , No. 7 Panjiayuan Nanli , Chaoyang District, Beijing 100021 , China
| | - Xiaohui Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , Jiangsu 210023 , China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management , Guangdong Institute of Eco-environment Science & Technology , Guangzhou , Guangdong 510650 , China
| | - Steve B Wiseman
- Department of Biological Sciences , University of Lethbridge , Lethbridge , AB T1K 3M4 , Canada
| | - Cindy Xin Feng
- School of Public Health , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5E5 , Canada
| | - Hongling Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , Jiangsu 210023 , China
| | - John P Giesy
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , Jiangsu 210023 , China
- Zoology Department, Center for Integrative Toxicology , Michigan State University , East Lansing , Michigan 48824 , United States
- School of Biological Sciences , University of Hong Kong , Hong Kong , SAR 999077 , China
| | - Markus Hecker
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
- School of Environment and Sustainability , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5C3 , Canada
| | - Paul D Jones
- Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5B3 , Canada
- Global Institute for Water Security , University of Saskatchewan , Saskatoon , Saskatchewan S7N 3H5 , Canada
- School of Environment and Sustainability , University of Saskatchewan , Saskatoon , Saskatchewan S7N 5C3 , Canada
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102
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Ruuskanen MO, St Pierre KA, St Louis VL, Aris-Brosou S, Poulain AJ. Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada. Front Microbiol 2018; 9:1138. [PMID: 29922252 PMCID: PMC5996194 DOI: 10.3389/fmicb.2018.01138] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.
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Affiliation(s)
| | - Kyra A St Pierre
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Vincent L St Louis
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada
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103
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Zhang H, Jia J, Chen S, Huang T, Wang Y, Zhao Z, Feng J, Hao H, Li S, Ma X. Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15020361. [PMID: 29463021 PMCID: PMC5858430 DOI: 10.3390/ijerph15020361] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 11/24/2022]
Abstract
The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.
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Affiliation(s)
- Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Jingyu Jia
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Shengnan Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Tinglin Huang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Zhenfang Zhao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Ji Feng
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Huiyan Hao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Sulin Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
| | - Xinxin Ma
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, Shaanxi Province, China.
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104
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Wang L, Ye L, Yu Y, Jing C. Antimony Redox Biotransformation in the Subsurface: Effect of Indigenous Sb(V) Respiring Microbiota. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1200-1207. [PMID: 29313683 DOI: 10.1021/acs.est.7b04624] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Anaerobic microbiological antimonate [Sb(V)] respiration is a newly discovered process regulating the Sb redox transformation in soils. However, little is known about the role microbiological Sb(V) respiration plays in the fate of Sb in the subsurface, especially in the presence of sulfate and electron shuttles. Herein, we successfully enriched a Sb(V) reducing microbiota (SbRM) from the subsurface near an active Sb mine. SbRM was dominated by genus Alkaliphilus (18-36%), Clostridiaceae (17-18%), Tissierella (24-27%), and Lysinibacillus (16-37%). The incubation results showed that SbRM reduced 88% of dissolved Sb(V) to Sb(III), but the total Sb mobility remained the same as in the abiotic control, indicating that SbRM alone did not increase the total Sb release but regulated the Sb speciation in the subsurface. Micro X-ray fluorescence (μ-XRF) analysis suggested the association of Sb and Fe, and electron shuttles such as anthraquinone-2,6-disulfonic disodium salt (AQDS) markedly enhanced the Sb release due to its ability to facilitate Fe mineral dissolution. Sb L-edge and S K-edge X-ray absorption near edge structure (XANES) results demonstrated that indigenous SbRM immobilized Sb via Sb2S3 formation, especially in a sulfur-rich environment. The insights gained from this study shed new light on Sb mobilization and its risk assessment in the subsurface environment.
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Affiliation(s)
- Liying Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Li Ye
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yaqin Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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105
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Sun W, Xiao E, Pu Z, Krumins V, Dong Y, Li B, Hu M. Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:884-893. [PMID: 28886540 DOI: 10.1016/j.scitotenv.2017.08.275] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/22/2017] [Accepted: 08/28/2017] [Indexed: 05/21/2023]
Abstract
UNLABELLED Rice paddies are a significant source of the greenhouse gas methane, which mainly originates from microbial activity. Methane generation in anaerobic systems involves complex interactions of multiple functional microbial groups. Rice paddies installed in hilly terrain are often terraced, providing multiple quasi-independent plots differing primarily in their elevation up a hillside. This represents an excellent study site to explore the influence of environmental factors on microbial communities and interactions among microbial populations. In this study, we used a combination of geochemical analyses, high-throughput amplicon sequencing, and statistical methods to elucidate these interactions. Sulfate, total nitrogen, total iron, and total organic carbon were determined to be critical factors in steering the ecosystem composition and function. Sulfate-reducing bacteria predominated in the rice terrace microbial communities, and Fe(III)-reducing and methane-oxidizing bacteria were abundant as well. Biotic interactions indicated by co-occurrence network analysis suggest mutualistic interactions among these three functional groups. Paddy-scale methane production may be affected by competition among methanogens and sulfate- and Fe(III)-reducing bacteria, or by direct methane oxidation by methane-oxidizing bacteria. CAPSULE Microbial communities were characterized in rice terrace. The environment- and microbe-microbe interactions indicated the mitigation of sulfate and Fe on methane production.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China.
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zilun Pu
- Yingrui Biotechnology Ltd., Guangzhou 510006, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Yiran Dong
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Baoqin Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Min Hu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
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