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Cruz FVDS, Barbosa da Costa N, Juneau P. Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174663. [PMID: 38992379 DOI: 10.1016/j.scitotenv.2024.174663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/22/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO2 fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.
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Affiliation(s)
- Fernanda Vieira da Silva Cruz
- Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Université du Québec à Montréal, Montréal Succ. Centre-Ville, H3C 3P8 Montréal, QC, Canada
| | - Naíla Barbosa da Costa
- Institut national de la recherche scientifique - Centre Eau Terre Environnement, 490 Couronne St, Québec City, Québec G1K 9A9, Canada
| | - Philippe Juneau
- Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Université du Québec à Montréal, Montréal Succ. Centre-Ville, H3C 3P8 Montréal, QC, Canada.
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2
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Liu X, Pan B, Wang L, Zhang Y, Zhao X, Han X, Liu X, Hu J. Water temperature and salt ions respectively drive the community assembly of bacterial generalists and specialists in diverse plateau lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175271. [PMID: 39102958 DOI: 10.1016/j.scitotenv.2024.175271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Plateau lakes (e.g., freshwater and saltwater lakes) are formed through intricate processes and harbor diverse microorganisms that mediate aquatic ecosystem functions. The adaptive mechanisms of lake microbiota to environmental changes and the ecological impacts of such changes on microbial community assembly are still poorly understood in plateau regions. This study investigated the structure and assembly of planktonic bacterial communities in 24 lakes across the Qinghai-Tibetan and Inner Mongolia Plateaus, with particular focus on habitat generalists, opportunists, and specialists. High-throughput sequencing of the 16S ribosomal RNA genes revealed that bacterial generalists had a lower species number (2196) but higher alpha diversity than the specialist and opportunist counterparts. Taxonomic dissimilarity and phylogenetic diversity analyses unraveled less pronounced difference in the community composition of bacterial generalists compared to the specialist and opportunist counterparts. Geographical scale (14.4 %) and water quality (12.6 %) emerged as major ecological variables structuring bacterial communities. Selection by water temperature and related variables, including mean annual temperature, elevation, longitude, and latitude, mainly shaped the assembly of bacterial generalists. Ecological drift coupled with selection by salt ions and related variables, including total phosphorus, chlorophyll a, and salinity, predominantly drove the assembly of bacterial specialists and opportunists. This study uncovers distinct bacterial responses to interacting ecological variables in diverse plateau lakes and the ecological processes structuring bacterial communities across various lake habitats under anthropogenic disturbance or climate change.
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Affiliation(s)
- Xing Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China.
| | - Lixin Wang
- College of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region), Hohhot 010021, China
| | - Yichi Zhang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Xiaohui Zhao
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Xu Han
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Xinyuan Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Jingxiang Hu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
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3
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Chao J, Li J, Gao J, Bai C, Tang X, Shao K. Comparing Sediment Bacterial Communities of Volcanic Lakes and Surrounding Rivers in Inner Mongolia Autonomous Region, Northeastern China. Microorganisms 2024; 12:1435. [PMID: 39065203 PMCID: PMC11278812 DOI: 10.3390/microorganisms12071435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Volcanic lakes originate from a volcanic crater or caldera, and were a crucial component of aquatic ecosystems. Sediment bacteria play an important role in the nutrient cycling of aquatic ecosystems; however, their patterns distribution in volcanic lakes and the surrounding river habitats are unknown. In this study, we compare the sediment bacterial communities and their co-occurrence networks between these two habitats in the Inner Mongolia Autonomous Region, Northeastern China (the Arxan UNESCO Global Geopark), using 16S rRNA gene amplicon sequencing. The results revealed that there were significant variations in the physicochemical parameters of the sediment between these two habitats. The bacterial α-diversity, β-diversity, and community composition of the sediment also significantly differed between these two habitats. Network analysis showed that the co-occurrence patterns and keystone taxa in the sediment differed between these two habitats. The sediment bacterial communities in the river habitats were more stable than those in the lake habitats in the face of environmental change. Canonical correspondence analysis demonstrated that both physical (pH and MC) and nutrition-related factors (TN, TP, LOI, and TOC) were the most important environmental factors shaping the variations of bacterial community composition (BCC) in the sediment between these two habitats. This work could greatly improve our understanding of the sediment BCC of the sediment from aquatic ecosystems in the UNESCO Global Geopark.
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Affiliation(s)
- Jianying Chao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; (J.C.); (J.L.); (J.G.)
| | - Jian Li
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; (J.C.); (J.L.); (J.G.)
| | - Jing Gao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; (J.C.); (J.L.); (J.G.)
| | - Chengrong Bai
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Shandong University of Aeronautics, Binzhou 256600, China;
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
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Liu X, Zhang L, Wang Y, Hu S, Zhang J, Huang X, Li R, Hu Y, Yao H, Wang Z. Microbiome analysis in Asia's largest watershed reveals inconsistent biogeographic pattern and microbial assembly mechanisms in river and lake systems. iScience 2024; 27:110053. [PMID: 38947525 PMCID: PMC11214296 DOI: 10.1016/j.isci.2024.110053] [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: 01/03/2024] [Revised: 04/02/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
Microorganisms are critical to the stability of aquatic environments, and understanding the ecological mechanisms of microbial community is essential. However, the distinctions and linkages across biogeographic patterns, ecological processes, and formation mechanisms of microbes in rivers and lakes remain unknown. Accordingly, microbiome-centric analysis was conducted in rivers and lakes in the Yangtze River watershed. Results revealed significant differences in the structure and diversity of microbial communities between rivers and lakes, with rivers showing higher diversity. Lakes exhibited lower community stability, despite higher species interactions. Although deterministic processes dominated microbial community assembly both in rivers and lakes, higher stochastic processes of rare and abundant taxa exhibited in rivers. Spatial factors influenced river microbial community, while environmental factors drove differences in the lake bacterial community. This study deepened the understanding of microbial biogeography and formation mechanisms in large watershed rivers and lakes, highlighting distinct community aggregation patterns between river and lake microorganisms.
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Affiliation(s)
- Xi Liu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingcai Wang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Sheng Hu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Jing Zhang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Xiaolong Huang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Ruiwen Li
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Yuxin Hu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, Hubei, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, Hubei, China
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Ahlinder J, Eriksson KIA, Hellmér M, Salomonsson E, Granberg M, Dacklin I, Elving J, Brindefalk B. Upstream land use with microbial downstream consequences: Iron and humic substances link to Legionella spp. WATER RESEARCH 2024; 256:121579. [PMID: 38631237 DOI: 10.1016/j.watres.2024.121579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
Intensified land use can disturb water quality, potentially increasing the abundance of bacterial pathogens, threatening public access to clean water. This threat involves both direct contamination of faecal bacteria as well as indirect factors, such as disturbed water chemistry and microbiota, which can lead to contamination. While direct contamination has been well described, the impact of indirect factors is less explored, despite the potential of severe downstream consequences on water supply. To assess direct and indirect downstream effects of buildings, farms, pastures and fields on potential water sources, we studied five Swedish lakes and their inflows. We analysed a total of 160 samples in a gradient of anthropogenic activity spanning four time points, including faecal and water-quality indicators. Through species distribution modelling, Random Forest and network analysis using 16S rRNA amplicon sequencing data, our findings highlight that land use indirectly impacts lakes via inflows. Land use impacted approximately one third of inflow microbiota taxa, in turn impacting ∼20-50 % of lake taxa. Indirect effects via inflows were also suggested by causal links between e.g. water colour and lake bacterial taxa, where this influenced the abundance of several freshwater bacteria, such as Polynucleobacter and Limnohabitans. However, it was not possible to identify direct effects on the lakes based on analysis of physiochemical- or microbial parameters. To avoid potential downstream consequences on water supply, it is thus important to consider possible indirect effects from upstream land use and inflows, even when no direct effects can be observed on lakes. Legionella (a genus containing bacterial pathogens) illustrated potential consequences, since the genus was particularly abundant in inflows and was shown to increase by the presence of pastures, fields, and farms. The approach presented here could be used to assess the suitability of lakes as alternative raw water sources or help to mitigate contaminations in important water catchments. Continued broad investigations of stressors on the microbial network can identify indirect effects, avoid enrichment of pathogens, and help secure water accessibility.
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Affiliation(s)
- Jon Ahlinder
- Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden; Department of Tree Breeding, Skogforsk, Sävar, SE-91821, Sweden
| | - Karolina Ida Anna Eriksson
- Department of Ecology and Environmental Sciences, Faculty of Science and Technology, Umeå University, Sweden; Umeå Marine Sciences Centre, Umeå University, Hörnefors, 905 71, Sweden.
| | - Maria Hellmér
- Department of Biology, Science Division, Swedish Food Agency, Sweden
| | - Emelie Salomonsson
- Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden
| | - Malin Granberg
- Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden
| | - Ingrid Dacklin
- Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden
| | - Josefine Elving
- Department of Chemistry, Environment and Feed Hygiene, Swedish Veterinary Agency, Sweden
| | - Björn Brindefalk
- Division of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Sweden; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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6
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Wang B, Hu K, Li C, Zhang Y, Hu C, Liu Z, Ding J, Chen L, Zhang W, Fang J, Zhang H. Geographic distribution of bacterial communities of inland waters in China. ENVIRONMENTAL RESEARCH 2024; 249:118337. [PMID: 38325783 DOI: 10.1016/j.envres.2024.118337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.
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Affiliation(s)
- Binhao Wang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Kaiming Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chuqiao Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yinan Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chao Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhiquan Liu
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Jiafeng Ding
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Lin Chen
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Wei Zhang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Jing Fang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Hangjun Zhang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China; Hangzhou International Urbanology Research Center and Center for Zhejiang Urban Governance Studies, Hangzhou, 311121, China.
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7
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Tan Q, Wu H, Zheng L, Wang X, Xing Y, Tian Q, Zhang Y. Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum. WATER RESEARCH 2024; 255:121480. [PMID: 38518415 DOI: 10.1016/j.watres.2024.121480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/22/2024] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.
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Affiliation(s)
- Qiuyang Tan
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Haoming Wu
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Lei Zheng
- College of Water Science, Beijing Normal University, Beijing 100875, PR China.
| | - Xue Wang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yuzi Xing
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Qi Tian
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yaoxin Zhang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
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Chao J, Li J, Kong M, Shao K, Tang X. Bacterioplankton diversity and potential health risks in volcanic lakes: A study from Arxan Geopark, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123058. [PMID: 38042466 DOI: 10.1016/j.envpol.2023.123058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/29/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Bacterioplankton play a vital role in maintaining the functions and services of lake ecosystems. Understanding the diversity and distribution patterns of bacterioplankton, particularly the presence of potential pathogenic bacterial communities, is crucial for safeguarding human health. In this study, we employed 16S rRNA gene amplicon sequencing to investigate the diversity and geographic patterns of bacterioplankton communities, as well as potential pathogens, in eight volcanic lakes located in the Arxan UNESCO Global Geopark (in the Greater Khingan Mountains of China). Our results revealed that the bacterial communities primarily comprised Bacteroidota (45.3%), Proteobacteria (33.1%), and Actinobacteria (9.0%) at the phylum level. At the genus level, prominent taxa included Flavobacterium (31.5%), Acinetobacter (11.0%), Chryseobacterium (7.9%), and CL500-29 marine group (5.6%). Among the bacterioplankton, we identified 34 pathogen genera (165 amplicon sequence variants [ASVs]), with Acinetobacter (59.8%), Rahnella (18.3%), Brevundimonas (9.6%), and Pseudomonas (5.8%) being the most dominant. Our findings demonstrated distinct biogeographic patterns in the bacterial communities at the local scale, driven by a combination of dispersal limitation and environmental factors influenced by human activities. Notably, approximately 15.3% of the bacterioplankton reads in the Arxan lakes were identified as potential pathogens, underscoring the potential risks to public health in these popular tourist destinations. This study provides the first comprehensive insight into the diversity of bacterioplankton in mountain lake ecosystems affected by high tourist activity, laying the groundwork for effective control measures against bacterial pathogens.
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Affiliation(s)
- Jianying Chao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Jian Li
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Ming Kong
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Rodríguez-Gijón A, Hampel JJ, Dharamshi J, Bertilsson S, Garcia SL. Shotgun metagenomes from productive lakes in an urban region of Sweden. Sci Data 2023; 10:810. [PMID: 37978200 PMCID: PMC10656542 DOI: 10.1038/s41597-023-02722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden.
| | - Justyna J Hampel
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Jennah Dharamshi
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75651, Uppsala, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691, Stockholm, Sweden.
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, 26129, Oldenburg, Germany.
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10
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Shi J, Yang L, Liao Y, Li J, Jiao S, Shangguan Z, Deng L. Soil labile organic carbon fractions mediate microbial community assembly processes during long-term vegetation succession in a semiarid region. IMETA 2023; 2:e142. [PMID: 38868232 PMCID: PMC10989986 DOI: 10.1002/imt2.142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 06/14/2024]
Abstract
Conceptual diagram for the labile organic carbon (OC) fractions mediating microbial assembly processes during long-term vegetation succession.
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Affiliation(s)
- Jingwei Shi
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lin Yang
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Liao
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jiwei Li
- College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation)Northwest A&F UniversityYanglingShaanxiChina
| | - Shuo Jiao
- College of Life SciencesNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhouping Shangguan
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
- College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation)Northwest A&F UniversityYanglingShaanxiChina
| | - Lei Deng
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
- College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation)Northwest A&F UniversityYanglingShaanxiChina
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11
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Garner RE, Kraemer SA, Onana VE, Fradette M, Varin MP, Huot Y, Walsh DA. A genome catalogue of lake bacterial diversity and its drivers at continental scale. Nat Microbiol 2023; 8:1920-1934. [PMID: 37524802 DOI: 10.1038/s41564-023-01435-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 06/20/2023] [Indexed: 08/02/2023]
Abstract
Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km2 of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.
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Affiliation(s)
- Rebecca E Garner
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
| | | | - Vera E Onana
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
| | - Maxime Fradette
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Marie-Pierre Varin
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Yannick Huot
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada.
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada.
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12
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Akter S, Rahman MS, Ali H, Minch B, Mehzabin K, Siddique MM, Galib SM, Yesmin F, Azmuda N, Adnan N, Hasan NA, Rahman SR, Moniruzzaman M, Ahmed MF. Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast. Sci Rep 2023; 13:15976. [PMID: 37749192 PMCID: PMC10520010 DOI: 10.1038/s41598-023-43306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023] Open
Abstract
The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.
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Affiliation(s)
- Salma Akter
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hazrat Ali
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA
| | - Kaniz Mehzabin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Moradul Siddique
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Syed Md Galib
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farida Yesmin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nur A Hasan
- University of Maryland, College Park, MD, USA
| | | | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA.
| | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
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13
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Sagua MI, Nuozzi G, Sánchez ML, Huber P, Perdomo S, Schiaffino MR. Unraveling the effect of land use on the bacterioplankton community composition from highly impacted shallow lakes at a regional scale. FEMS Microbiol Ecol 2023; 99:fiad109. [PMID: 37715304 DOI: 10.1093/femsec/fiad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
Bacterioplankton communities play a crucial role in global biogeochemical processes and are highly sensitive to changes induced by natural and anthropogenic stressors in aquatic ecosystems. We assessed the influence of Land Use Land Cover (LULC), environmental, and geographic changes on the bacterioplankton structure in highly connected and impacted shallow lakes within the Salado River basin, Buenos Aires, Argentina. Additionally, we investigated how changes in LULC affected the limnological characteristics of these lakes at a regional scale. Our analysis revealed that the lakes were ordinated by sub-basins (upper and lower) depending on their LULC characteristics and limnological properties. In coincidence, the same ordination was observed when considering the Bacterioplankton Community Composition (BCC). Spatial and environmental predictors significantly explained the variation in BCC, although when combined with LULC the effect was also important. While the pure LULC effect did not explain a significant percentage of BCC variation, the presence of atrazine in water, an anthropogenic variable linked to LULC, directly influenced both the BCC and some Amplicon Sequence Variants (ASVs) in particular. Our regional-scale approach contributes to understanding the complexity of factors driving bacterioplankton structure and how LULC pervasively affect these communities in highly impacted shallow lake ecosystems from the understudied Southern Hemisphere.
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Affiliation(s)
- Mara I Sagua
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - Guillermina Nuozzi
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - María L Sánchez
- CONICET - Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires, Intendente Guiraldes 2160 (C1428EGA), Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Intendente Guiraldes 2160 (C1428EGA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Huber
- Instituto Nacional de Limnología (INALI, CONICET-UNL). Colectora RN 168 Km 0 (3000), Paraje El Pozo, Santa Fe, Argentina
- Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luis S/N - Monjolinho (13565-905), São Carlos, São Paulo, Brazil
| | - Santiago Perdomo
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - María R Schiaffino
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
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14
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Tan Q, Zhang G, Ding A, Bian Z, Wang X, Xing Y, Zheng L. Anthropogenic land-use activities within watersheds reduce comammox activity and diversity in rivers. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 338:117841. [PMID: 37003226 DOI: 10.1016/j.jenvman.2023.117841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/12/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Nitrogen cycling plays a key role in maintaining river ecological functions which are threatened by anthropogenic activities. The newly discovered complete ammonia oxidation, comammox, provides novel insights into the ecological effects of nitrogen on that it oxidizes ammonia directly to nitrate without releasing nitrite as canonical ammonia oxidization conducted by AOA or AOB which is believed to play an important role in greenhouse gas generation. Theoretically, contribution of commamox, AOA and AOB to ammonia oxidization in rivers might be impacted by anthropogenic land-use activities through alterations in flow regime and nutrient input. While how land use pattern affects comammox and other canonical ammonia oxidizers remains elusive. In this study, we examined the ecological effects of land use practices on the activity and contribution of three distinctive groups of ammonia oxidizers (AOA, AOB, comammox) as well as the composition of comammox bacterial communities from 15 subbasins covering an area of 6166 km2 in North China. The results showed that comammox dominated nitrification (55.71%-81.21%) in less disturbed basins characterized by extensive forests and grassland, while AOB became the major player (53.83%-76.43%) in highly developed basins with drastic urban and agricultural development. In addition, increasing anthropogenic land use activities within the watershed lowered the alpha diversity of comammox communities and simplified the comammox network. Additionally, the alterations of NH4+-N, pH and C/N induced by land use change were found to be crucial drivers in determining the distribution and activity of AOB and comammox. Together, our findings cast a new light on aquatic-terrestrial linkages from the view of microorganism-mediated nitrogen cycling and can further be applied to target watershed land use management.
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Affiliation(s)
- Qiuyang Tan
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Guoyu Zhang
- Department of Environmental Engineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, China
| | - Aizhong Ding
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Zhaoyong Bian
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Xue Wang
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Yuzi Xing
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Lei Zheng
- College of Water Science, Beijing Normal University, Beijing, 100875, China.
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15
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Wang Q, Li Y, Liu L, Cui S, Liu X, Chen F, Jeppesen E. Human impact on current environmental state in Chinese lakes. J Environ Sci (China) 2023; 126:297-307. [PMID: 36503758 DOI: 10.1016/j.jes.2022.05.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 06/17/2023]
Abstract
Anthropogenic and natural disturbance to inland aquatic ecosystems displays a notable spatial difference, yet data to measure these differences are scarce. This study encompasses 217 lakes distributed over five lake regions of China and elucidates the environmental factors determining the spatial variability of the water quality and trophic status. A significant correlation between human modification index in surrounding terrestrial systems (HMT) and trophic status of lake ecosystems (TSI) was found, and the regression slope in each region was similar except in the Qinghai-Tibet Plateau region. It was further noted that the pattern of environmental factor network (EF network) differed among freshwater and saline lakes. The EF network was complex for freshwater lakes in less human-influenced areas, but intensive man-made influence disrupted most relationships except for those between total nitrogen, total phosphorus, chlorophyll-a, and water turbidity. As for regions including saline lakes, correlations among water salinity and organic forms of carbon and nitrogen were apparent. Our results suggest that HMT and EF network can be useful indicators of the ecological integrity of local lake ecosystems, and integrating spatial information on a large scale provides conservation planners the option for evaluating the potential risk on inland aquatic systems.
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Affiliation(s)
- Qianhong Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Le Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suzhen Cui
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xia Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Feizhou Chen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research (SDC), Beijing 100049, China.
| | - Erik Jeppesen
- Sino-Danish Centre for Education and Research (SDC), Beijing 100049, China; Department of Ecoscience, Aarhus University, Silkeborg 8600, 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, Mersin, Turkey
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16
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Oliva A, Onana VE, Garner RE, Kraemer SA, Fradette M, Walsh DA, Huot Y. Geospatial analysis reveals a hotspot of fecal bacteria in Canadian prairie lakes linked to agricultural non-point sources. WATER RESEARCH 2023; 231:119596. [PMID: 36653256 DOI: 10.1016/j.watres.2023.119596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Lakes are sentinels of environmental changes within their watersheds including those induced by a changing climate and anthropogenic activities. In particular, contamination originating from point or non-point sources (NPS) within watersheds might be reflected in changes in the bacterial composition of lake water. We assessed the abundance of potentially pathogenic bacteria (PPB) sampled in 413 lakes within 8 southern Canadian ecozones that represent a wide diversity of lakes and watershed land use. The study objectives were (1) to explore the diversity of PPB; (2) to build a fecal multi-indicator from a cluster of co-occurring PPB; and (3) to predict the fecal multi-indicator over thousands of lakes. We identified bacterial taxa based on 16S rRNA amplicon sequencing and clustered 33 PPB matching taxa in the Canadian ePATHogen database using a Sørensen dissimilarity index on binary data across the sampled lakes. One cluster contained Erysipelothrix, Desulfovibrio, Bacteroides, Vibrio and Acholeplasma and was related to the NPS fraction of agriculture and pasture within the watershed as its main driver and thus it was determined as the fecal multi-indicator. We subsequently developed a fecal multi-indicator predictive model across 200 212 southern Canadian lakes which explained 55.1% of the deviance. Mapping the predictions showed higher fecal multi-indicator abundances in the Prairies and Boreal Plains compared to the other ecozones. These results represent the first attempt to map a potential fecal multi-indicator at the continental scale, which may be further improved in the future. Lastly, the study demonstrates the capacity of a multi-disciplinary approach leveraging both datasets derived from remote sensing and DNA sequencing to provide mapping information for public health governmental policies.
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Affiliation(s)
- Anaïs Oliva
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Géomatique Appliquée, CARTEL - Centre d'Applications et de Recherche en TELédétection, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada.
| | - Vera E Onana
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Rebecca E Garner
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Susanne A Kraemer
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada; Environment and Climate Change Canada, Montréal, Canada; Department of Microbiology & Immunology, Genome Center, McGill University, Montreal, Canada
| | - Maxime Fradette
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Géomatique Appliquée, CARTEL - Centre d'Applications et de Recherche en TELédétection, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada
| | - David A Walsh
- Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Yannick Huot
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Géomatique Appliquée, CARTEL - Centre d'Applications et de Recherche en TELédétection, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Sciences Biologiques, GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada
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17
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Rheinheimer Dos Santos D, Camotti Bastos M, Monteiro De Castro Lima JA, Le Guet T, Vargas Brunet J, Fernandes G, Zanella R, Damian Prestes O, Mondamert L, Labanowski J. Epilithic biofilms, POCIS, and water samples as complementary sources of information for a more comprehensive view of aquatic contamination by pesticides and pharmaceuticals in southern Brazil. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2023; 58:273-284. [PMID: 36861268 DOI: 10.1080/03601234.2023.2182583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Spatial-temporal monitoring of the presence of pesticides and pharmaceuticals in water requires rigor in the choice of matrix to be analyzed. The use of matrices, isolated or combined, may better represent the real state of contamination. In this sense, the present work contrasted the effectiveness of using epilithic biofilms with active water sampling and with a passive sampler-POCIS. A watershed representative of South American agriculture was monitored. Nine sites with different rural anthropic pressures (natural forest, intensive use of pesticides, and animal waste), and urban areas without sewage treatment, were monitored. Water and epilithic biofilms were collected during periods of intensive pesticide and animal waste application. After the harvest of the spring/summer crop, a period of low agrochemical input, the presence of pesticides and pharmaceuticals was monitored using the POCIS and epilithic biofilms. The spot water sampling leads to underestimation of the level of contamination of water resources as it does not allow discrimination of different anthropic pressures in rural areas. The use of endogenous epilithic biofilms as a matrix for the analysis of pesticides and pharmaceuticals is a viable and highly recommended alternative to diagnose the health of water sources, especially if associated with the use of POCIS.
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Affiliation(s)
| | - Marília Camotti Bastos
- Departamento de Solos, Centro de Ciências Rurais, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Laboratoire E2Lim - Eau et Environnement Limoges, Université de Limoges, Limoges, France
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers, Poitiers, France
| | | | - Thibaut Le Guet
- Laboratoire E2Lim - Eau et Environnement Limoges, Université de Limoges, Limoges, France
| | - Jocelina Vargas Brunet
- Departamento de Solos, Centro de Ciências Rurais, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers, Poitiers, France
| | - Gracieli Fernandes
- Departamento de Solos, Centro de Ciências Rurais, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Renato Zanella
- Departamento de Solos, Centro de Ciências Rurais, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Osmar Damian Prestes
- Departamento de Solos, Centro de Ciências Rurais, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Leslie Mondamert
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers, Poitiers, France
| | - Jérôme Labanowski
- Institut de Chimie des Milieux et Matériaux de Poitiers, Université de Poitiers, Poitiers, France
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18
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Wang B, Ma B, Stirling E, He Z, Zhang H, Yan Q. Freshwater trophic status mediates microbial community assembly and interdomain network complexity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120690. [PMID: 36403871 DOI: 10.1016/j.envpol.2022.120690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/18/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Freshwater microorganisms and their interactions are important drivers of nutrient cycling that are in turn affected by nutrient status, causing shifts in microbial community diversity, composition, and interactions. However, the impact of water trophic status on bacterial-archaeal interdomain interactions remains poorly understood. This study focused on the impact of trophic status, as characterized by trophic state index (TSI), on the interdomain interactions of freshwater microbial communities from 45 ponds in Hangzhou. Our results showed that the mesotrophic wetland bordering on lightly eutrophic (Hemu: TSI of 49; lightly eutrophic is defined as 50 ≤ TSI <60) harbored a much more complex bacterial-archaeal interdomain network, which showed significantly (P < 0.05) higher connectivity than the wetlands with lower (TSI of 38) or higher (TSI of 57) trophic levels. Notably, light eutrophication strengthened the network modules' negative associations with organic carbon through some network hubs, which could trigger carbon loss in wetlands. We also detected a non-linear response of interdomain network complexity to the increasing of nutrients with a turning point of approximately TSI 50. Quantitative estimates of community assembly processes and structural equation modelling analysis indicated that chlorophyll-a, total nitrogen, and total phosphorus could regulate interdomain network complexity (50% of the variation explanation rate) by driving microbial community assembly. This study demonstrates that microbial interdomain network complexity could be used as a bioindicator for ecological changes, which would helpful for improving ecological assessment of the freshwater eutrophication.
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Affiliation(s)
- Binhao Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China; Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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19
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Pearman JK, Thomson-Laing G, Thompson L, Waters S, Vandergoes MJ, Howarth JD, Duggan IC, Hogg ID, Wood SA. Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes. PeerJ 2022; 10:e14378. [PMID: 36389411 PMCID: PMC9661969 DOI: 10.7717/peerj.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.
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Affiliation(s)
| | | | | | | | | | | | | | - Ian D. Hogg
- University of Waikato, Hamilton, New Zealand,Canadian High Arctic Research Station, Nunavut, Canada
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20
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Kraemer SA, Barbosa da Costa N, Oliva A, Huot Y, Walsh DA. A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use. Front Microbiol 2022; 13:995418. [PMID: 36338036 PMCID: PMC9629221 DOI: 10.3389/fmicb.2022.995418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome – the diversity of ARGs – under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.
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Affiliation(s)
- Susanne A. Kraemer
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Biology, Concordia University, Montreal, QC, Canada
- *Correspondence: Susanne A. Kraemer,
| | | | - Anais Oliva
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Yannick Huot
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - David A. Walsh
- Department of Biology, Concordia University, Montreal, QC, Canada
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21
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Sheridan EA, Fonvielle JA, Cottingham S, Zhang Y, Dittmar T, Aldridge DC, Tanentzap AJ. Plastic pollution fosters more microbial growth in lakes than natural organic matter. Nat Commun 2022; 13:4175. [PMID: 35882837 PMCID: PMC9325981 DOI: 10.1038/s41467-022-31691-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/29/2022] [Indexed: 01/04/2023] Open
Abstract
Plastic debris widely pollutes freshwaters. Abiotic and biotic degradation of plastics releases carbon-based substrates that are available for heterotrophic growth, but little is known about how these novel organic compounds influence microbial metabolism. Here we found leachate from plastic shopping bags was chemically distinct and more bioavailable than natural organic matter from 29 Scandinavian lakes. Consequently, plastic leachate increased bacterial biomass acquisition by 2.29-times when added at an environmentally-relevant concentration to lake surface waters. These results were not solely attributable to the amount of dissolved organic carbon provided by the leachate. Bacterial growth was 1.72-times more efficient with plastic leachate because the added carbon was more accessible than natural organic matter. These effects varied with both the availability of alternate, especially labile, carbon sources and bacterial diversity. Together, our results suggest that plastic pollution may stimulate aquatic food webs and highlight where pollution mitigation strategies could be most effective. Ultra-high resolution mass spectrometry revealed that plastic bags leach labile compounds. Bioassays performed in Scandinavian lakes indicated that these compounds are incorporated into biomass faster and more efficiently than natural organic matter.
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Affiliation(s)
- Eleanor A Sheridan
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom. .,Department of Zoology, University of Cambridge, The David Attenborough Building, Cambridge, CB2 3QZ, United Kingdom.
| | - Jérémy A Fonvielle
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Samuel Cottingham
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Yi Zhang
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, 26129, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
| | - David C Aldridge
- Department of Zoology, University of Cambridge, The David Attenborough Building, Cambridge, CB2 3QZ, United Kingdom
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.
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22
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Obieze CC, Wani GA, Shah MA, Reshi ZA, Comeau AM, Khasa DP. Anthropogenic activities and geographic locations regulate microbial diversity, community assembly and species sorting in Canadian and Indian freshwater lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154292. [PMID: 35248630 DOI: 10.1016/j.scitotenv.2022.154292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Freshwater lakes are important reservoirs and sources of drinking water globally. However, the microbiota, which supports the functionality of these ecosystems is threatened by the influx of nutrients, heavy metals and other toxic chemical substances from anthropogenic activities. The influence of these factors on the diversity, assembly mechanisms and co-occurrence patterns of bacterial communities in freshwater lakes is not clearly understood. Hence, samples were collected from six different impacted lakes in Canada and India and examined by 454-pyrosequencing technology. The trophic status of these lakes was determined using specific chemical parameters. Our results revealed that bacterial diversity and community composition was altered by both the lake water chemistry and geographic distance. Anthropogenic activities pervasively influenced species distribution. Dispersal limitation (32.3%), homogenous selection (31.8%) and drift (20%) accounted for the largest proportions of the bacterial community assembly mechanisms. Homogenous selection increased in lakes with higher nutrient concentration, while stochasticity reduced. Community functional profiles revealed that deterministic processes dominated the assembly mechanisms of phylotypes with higher potential for biodegradation, while stochasticity dominated the assembly of phylotypes with potential for antimicrobial resistance. Bacteroidota (44%) and Proteobacteria (34%) were the most abundant phyla. Co-occurrence network analysis revealed that complexity increased in more impacted lakes, while competition and the nature of anthropogenic activity contributed to species sorting. Overall, this study demonstrates that bacterial community changes in freshwater lakes are linked to anthropogenic activities, with corresponding consequences on the distribution of phylotypes of environmental and human health interest.
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Affiliation(s)
- Chinedu C Obieze
- Centre for Forest Research, Institute of Integrative Biology and Systems, Université Laval, Quebec, QC G1V0A6, Canada.
| | - Gowher A Wani
- Centre for Forest Research, Institute of Integrative Biology and Systems, Université Laval, Quebec, QC G1V0A6, Canada; Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - André M Comeau
- Integrated Microbiome Resource, Dalhousie University, Halifax, NS, Canada
| | - Damase P Khasa
- Centre for Forest Research, Institute of Integrative Biology and Systems and Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC G1V0A6, Canada
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23
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Sperlea T, Schenk JP, Dreßler H, Beisser D, Hattab G, Boenigk J, Heider D. The relationship between land cover and microbial community composition in European lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153732. [PMID: 35157872 DOI: 10.1016/j.scitotenv.2022.153732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.
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Affiliation(s)
- Theodor Sperlea
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032 Marburg, Lahn, Germany; Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Jan Philip Schenk
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032 Marburg, Lahn, Germany
| | - Hagen Dreßler
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032 Marburg, Lahn, Germany
| | - Daniela Beisser
- Department of Biodiversity, Center for Water and Environmental Research, University of Duisburg-Essen, D-45141 Essen, Germany
| | - Georges Hattab
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032 Marburg, Lahn, Germany
| | - Jens Boenigk
- Department of Biodiversity, Center for Water and Environmental Research, University of Duisburg-Essen, D-45141 Essen, Germany
| | - Dominik Heider
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032 Marburg, Lahn, Germany.
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24
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Luo J, Zeng H, Zhou Q, Hu X, Qu Q, Ouyang S, Wang Y. Anthropogenic impacts on the biodiversity and anti-interference ability of microbial communities in lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153264. [PMID: 35065108 DOI: 10.1016/j.scitotenv.2022.153264] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Lakes are critical for biogeochemical and ecological processes and are sensitive and vulnerable to anthropogenic disturbances, but how and to what extent human activities disturb the biodiversity in lakes remain unknown. Here, we showed the microbial diversity in 46 lakes and assessed the influence of 27 anthropogenic factors. We found that the economic level (e.g., per capita gross domestic product) was strongly negatively correlated (r = -0.97) with bacterial diversity but positively correlated (r = 0.17) with fungal diversity in lakes. The composition of the microbial community significantly changed with increasing economic level. Bacteria are more sensitive than fungi to anthropogenic impacts. Expanding the population size and increasing the economic level may promote the development of fungal diversity but inhibit bacterial diversity. Air quality, urbanization and ozone were negatively correlated with bacterial diversity, and fisheries had a negative correlation with fungal diversity. The anti-interference ability of lake microorganisms in the middle economic level zones (45,000-90,000 yuan/person) was stronger than that in high-level (> 90,000 yuan/person) and low-level (> 45,000 yuan/person) economic zones. Overall, our investigation provides national-scale evidence that changes in the microbial diversity in lakes were related to economic levels.
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Affiliation(s)
- Jiwei Luo
- 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 300350, China
| | - Hui Zeng
- 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 300350, China
| | - Qixing Zhou
- 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 300350, China
| | - Xiangang Hu
- 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 300350, China.
| | - Qian Qu
- 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 300350, China
| | - Shaohu Ouyang
- 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 300350, 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 300350, China
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25
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Gautam A, Lear G, Lewis GD. Time after time: Detecting annual patterns in stream bacterial biofilm communities. Environ Microbiol 2022; 24:2502-2515. [PMID: 35466520 PMCID: PMC9324112 DOI: 10.1111/1462-2920.16017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/03/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022]
Abstract
To quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.
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Affiliation(s)
- Anju Gautam
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Gillian D Lewis
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
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26
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Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
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27
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Sauer HM, Hamilton TL, Anderson RE, Umbanhowar CE, Heathcote AJ. Diversity and distribution of sediment bacteria across an ecological and trophic gradient. PLoS One 2022; 17:e0258079. [PMID: 35312685 PMCID: PMC8936460 DOI: 10.1371/journal.pone.0258079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/04/2022] [Indexed: 11/18/2022] Open
Abstract
The microbial communities of lake sediments have the potential to serve as valuable bioindicators and integrators of watershed land-use and water quality; however, the relative sensitivity of these communities to physio-chemical and geographical parameters must be demonstrated at taxonomic resolutions that are feasible by current sequencing and bioinformatic approaches. The geologically diverse and lake-rich state of Minnesota (USA) is uniquely situated to address this potential because of its variability in ecological region, lake type, and watershed land-use. In this study, we selected twenty lakes with varying physio-chemical properties across four ecological regions of Minnesota. Our objectives were to (i) evaluate the diversity and composition of the bacterial community at the sediment-water interface and (ii) determine how lake location and watershed land-use impact aqueous chemistry and influence bacterial community structure. Our 16S rRNA amplicon data from lake sediment cores, at two depth intervals, data indicate that sediment communities are more likely to cluster by ecological region rather than any individual lake properties (e.g., trophic status, total phosphorous concentration, lake depth). However, composition is tied to a given lake, wherein samples from the same core were more alike than samples collected at similar depths across lakes. Our results illustrate the diversity within lake sediment microbial communities and provide insight into relationships between taxonomy, physicochemical, and geographic properties of north temperate lakes.
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Affiliation(s)
- Hailey M. Sauer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, Minnesota, United States of America
| | - Trinity L. Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- The Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
| | - Rika E. Anderson
- Biology Department, Carleton College, Northfield, Minnesota, United States of America
| | - Charles E. Umbanhowar
- Department of Biology and Environmental Studies, St. Olaf College, Northfield, Minnesota, United States of America
| | - Adam J. Heathcote
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, Minnesota, United States of America
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28
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Pearman JK, Wood SA, Vandergoes MJ, Atalah J, Waters S, Adamson J, Thomson-Laing G, Thompson L, Howarth JD, Hamilton DP, Pochon X, Biessy L, Brasell KA, Dahl J, Ellison R, Fitzsimons SJ, Gard H, Gerrard T, Gregersen R, Holloway M, Li X, Kelly DJ, Martin R, McFarlane K, McKay NP, Moody A, Moy CM, Naeher S, Newnham R, Parai R, Picard M, Puddick J, Rees ABH, Reyes L, Schallenberg M, Shepherd C, Short J, Simon KS, Steiner K, Šunde C, Terezow M, Tibby J. A bacterial index to estimate lake trophic level: National scale validation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152385. [PMID: 34942258 DOI: 10.1016/j.scitotenv.2021.152385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Lakes and their catchments have been subjected to centuries to millennia of exploitation by humans. Efficient monitoring methods are required to promote proactive protection and management. Traditional monitoring is time consuming and expensive, which limits the number of lakes monitored. Lake surface sediments provide a temporally integrated representation of environmental conditions and contain high microbial biomass. Based on these attributes, we hypothesized that bacteria associated with lake trophic states could be identified and used to develop an index that would not be confounded by non-nutrient stressor gradients. Metabarcoding (16S rRNA gene) was used to assess bacterial communities present in surface sediments from 259 non-saline lakes in New Zealand encompassing a range of trophic states from alpine microtrophic lakes to lowland hypertrophic lakes. A subset of lakes (n = 96) with monitoring data was used to identify indicator amplicon sequence variants (ASVs) associated with different trophic states. A total of 10,888 indicator taxa were identified and used to develop a Sediment Bacterial Trophic Index (SBTI), which signficantly correlated (r2 = 0.842, P < 0.001) with the Trophic Lake Index. The SBTI was then derived for the remaining 163 lakes, providing new knowledge of the trophic state of these unmonitored lakes. This new, robust DNA-based tool provides a rapid and cost-effective method that will allow a greater number of lakes to be monitored and more effectively managed in New Zealand and globally. The SBTI could also be applied in a paleolimnological context to investigate changes in trophic status over centuries to millennia.
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Affiliation(s)
- John K Pearman
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand.
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Javier Atalah
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Sean Waters
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Janet Adamson
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Lucy Thompson
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Jamie D Howarth
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, Qld 4111, Australia
| | - Xavier Pochon
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Laura Biessy
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Jenny Dahl
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - Riki Ellison
- Waka Taurua Consulting, Lower Hutt 5040, New Zealand
| | | | - Henry Gard
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - Tania Gerrard
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - Rose Gregersen
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | | | - Xun Li
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | - David J Kelly
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | | | - Nicholas P McKay
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ 86011, United States
| | - Adelaine Moody
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Chris M Moy
- University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | | | - Rewi Newnham
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Russleigh Parai
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Maïlys Picard
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | | | - Andrew B H Rees
- Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Lizette Reyes
- GNS Science, PO, Box 30-368, Lower Hutt 5040, New Zealand
| | | | | | - Julia Short
- Adelaide University, Adelaide, South Australia 5005, Australia
| | - Kevin S Simon
- Auckland University, Private Bag 92019, Auckland 1142, New Zealand
| | | | | | | | - John Tibby
- Adelaide University, Adelaide, South Australia 5005, Australia
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29
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Pearman JK, Thomson-Laing G, Thomson-Laing J, Thompson L, Waters S, Reyes L, Howarth JD, Vandergoes MJ, Wood SA. The Role of Environmental Processes and Geographic Distance in Regulating Local and Regionally Abundant and Rare Bacterioplankton in Lakes. Front Microbiol 2022; 12:793441. [PMID: 35250905 PMCID: PMC8888906 DOI: 10.3389/fmicb.2021.793441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.
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Affiliation(s)
- John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Lucy Thompson
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Sean Waters
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, University of Victoria, Wellington, New Zealand
| | | | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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30
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MacKeigan PW, Garner RE, Monchamp MÈ, Walsh DA, Onana VE, Kraemer SA, Pick FR, Beisner BE, Agbeti MD, da Costa NB, Shapiro BJ, Gregory-Eaves I. Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes. HARMFUL ALGAE 2022; 113:102187. [PMID: 35287928 DOI: 10.1016/j.hal.2022.102187] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Accurately identifying the species present in an ecosystem is vital to lake managers and successful bioassessment programs. This is particularly important when monitoring cyanobacteria, as numerous taxa produce toxins and can have major negative impacts on aquatic ecosystems. Increasingly, DNA-based techniques such as metabarcoding are being used for measuring aquatic biodiversity, as they could accelerate processing time, decrease costs and reduce some of the biases associated with traditional light microscopy. Despite the continuing use of traditional microscopy and the growing use of DNA metabarcoding to identify cyanobacteria assemblages, methodological comparisons between the two approaches have rarely been reported from a wide suite of lake types. Here, we compare planktonic cyanobacteria assemblages generated by inverted light microscopy and DNA metabarcoding from a 379-lake dataset spanning a longitudinal and trophic gradient. We found moderate levels of congruence between methods at the broadest taxonomic levels (i.e., Order, RV=0.40, p < 0.0001). This comparison revealed distinct cyanobacteria communities from lakes of different trophic states, with Microcystis, Aphanizomenon and Dolichospermum dominating with both methods in eutrophic and hypereutrophic sites. This finding supports the use of either method when monitoring eutrophication in lake surface waters. The biggest difference between the two methods was the detection of picocyanobacteria, which are typically underestimated by light microscopy. This reveals that the communities generated by each method currently are complementary as opposed to identical and promotes a combined-method strategy when monitoring a range of trophic systems. For example, microscopy can provide measures of cyanobacteria biomass, which are critical data in managing lakes. Going forward, we believe that molecular genetic methods will be increasingly adopted as reference databases are routinely updated with more representative sequences and will improve as cyanobacteria taxonomy is resolved with the increase in available genetic information.
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Affiliation(s)
- Paul W MacKeigan
- Department of Biology, McGill University, Montreal, Quebec, Canada; Interuniversity Research Group in Limnology (GRIL), Quebec, Canada.
| | - Rebecca E Garner
- Interuniversity Research Group in Limnology (GRIL), Quebec, Canada; Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Marie-Ève Monchamp
- Department of Biology, McGill University, Montreal, Quebec, Canada; Interuniversity Research Group in Limnology (GRIL), Quebec, Canada
| | - David A Walsh
- Interuniversity Research Group in Limnology (GRIL), Quebec, Canada; Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Vera E Onana
- Interuniversity Research Group in Limnology (GRIL), Quebec, Canada; Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Susanne A Kraemer
- Interuniversity Research Group in Limnology (GRIL), Quebec, Canada; Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Frances R Pick
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Beatrix E Beisner
- Interuniversity Research Group in Limnology (GRIL), Quebec, Canada; Department of Biological Sciences, University of Quebec at Montreal, Montreal, Quebec, Canada
| | | | - Naíla Barbosa da Costa
- Interuniversity Research Group in Limnology (GRIL), Quebec, Canada; Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Irene Gregory-Eaves
- Department of Biology, McGill University, Montreal, Quebec, Canada; Interuniversity Research Group in Limnology (GRIL), Quebec, Canada.
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31
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Oliva A, Garner RE, Walsh D, Huot Y. The occurrence of potentially pathogenic fungi and protists in Canadian lakes predicted using geomatics, in situ and satellite-derived variables: Towards a tele-epidemiological approach. WATER RESEARCH 2022; 209:117935. [PMID: 34915335 DOI: 10.1016/j.watres.2021.117935] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Eukaryotic pathogens including fungi and enteroparasites infect humans, animals and plants. As integrators of landscape catchment, lakes can reflect and record biological and geochemical events or anthropogenic changes and provide useful knowledge to formulate public health, food security and water policies to manage and prevent diseases. In this context, potentially pathogenic fungi and parasites were sampled using 18S rRNA gene amplicon sequencing in 382 lakes displaying a broad range of sizes and human impact on the watershed in 10 ecozones across Canada. Based on pathogen classifications from the ePATHogen database published by the Public Health Agency of Canada, we identified 23 health-relevant genera for human and animal hosts, including Cryptococcus and Cryptosporidium. Our study investigated the potential of remote sensing and geomatics to predict microbial contamination in a tele-epidemiological approach. We used boosted regression tree modeling to evaluate the probability of occurrence of the most common genera found in our dataset based on 10 satellite-derivable, geomatics and field survey variables which could be potential sources or transport mechanisms through the watershed or survival factors in the water. We found that southern ecozones that possess the highest agricultural and pasture activities tend to contain lakes with the largest number of potential pathogens including several fungi associated with plant diseases. Bio-optical factors, such as colored dissolved organic matter, were highly related to the occurrence of the genera, potentially by protecting against damage from ultraviolet light. Our results demonstrate the capability of tele-epidemiology to provide useful information to develop government policies for recreational and drinking water regulations as well as for food security.
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Affiliation(s)
- Anaïs Oliva
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; CARTEL - Centre d'applications et de recherche en télédétection, Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Département de Sciences Biologiques, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada.
| | - Rebecca E Garner
- GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Département de Sciences Biologiques, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal QC H4B 1R6, Canada
| | - David Walsh
- GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Département de Sciences Biologiques, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada; Department of Biology, Concordia University, Montréal QC H4B 1R6, Canada
| | - Yannick Huot
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; CARTEL - Centre d'applications et de recherche en télédétection, Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; GRIL - Groupement de Recherche Interuniversitaire en Limnologie, Département de Sciences Biologiques, Université de Montréal, Campus MIL, Montréal, QC H3C 3J7, Canada
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32
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Vincent K, Holland-Moritz H, Solon AJ, Gendron EMS, Schmidt SK. Crossing Treeline: Bacterioplankton Communities of Alpine and Subalpine Rocky Mountain Lakes. Front Microbiol 2022; 12:533121. [PMID: 35046907 PMCID: PMC8762171 DOI: 10.3389/fmicb.2021.533121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 09/23/2021] [Indexed: 01/04/2023] Open
Abstract
From the aboveground vegetation to the belowground microbes, terrestrial communities differ between the highly divergent alpine (above treeline) and subalpine (below treeline) ecosystems. Yet, much less is known about the partitioning of microbial communities between alpine and subalpine lakes. Our goal was to determine whether the composition of bacterioplankton communities of high-elevation mountain lakes differed across treeline, identify key players in driving the community composition, and identify potential environmental factors that may be driving differences. To do so, we compared bacterial community composition (using 16S rDNA sequencing) of alpine and subalpine lakes in the Southern Rocky Mountain ecoregion at two time points: once in the early summer and once in the late summer. In the early summer (July), shortly after peak runoff, bacterial communities of alpine lakes were distinct from subalpine lakes. Interestingly, by the end of the summer (approximately 5 weeks after the first visit in August), bacterial communities of alpine and subalpine lakes were no longer distinct. Several bacterial amplicon sequence variants (ASVs) were also identified as key players by significantly contributing to the community dissimilarity. The community divergence across treeline found in the early summer was correlated with several environmental factors, including dissolved organic carbon (DOC), pH, chlorophyll-a (chl-a), and total dissolved nitrogen (TDN). In this paper, we offer several potential scenarios driven by both biotic and abiotic factors that could lead to the observed patterns. While the mechanisms for these patterns are yet to be determined, the community dissimilarity in the early summer correlates with the timing of increased hydrologic connections with the terrestrial environment. Springtime snowmelt brings the flushing of mountain watersheds that connects terrestrial and aquatic ecosystems. This connectivity declines precipitously throughout the summer after snowmelt is complete. Regional climate change is predicted to bring alterations to precipitation and snowpack, which can modify the flushing of solutes, nutrients, and terrestrial microbes into lakes. Future preservation of the unique alpine lake ecosystem is dependent on a better understanding of ecosystem partitioning across treeline and careful consideration of terrestrial-aquatic connections in mountain watersheds.
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Affiliation(s)
- Kim Vincent
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Hannah Holland-Moritz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Eli M S Gendron
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, United States
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
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33
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Quiroga MV, Valverde A, Mataloni G, Casa V, Stegen JC, Cowan D. The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution. Environ Microbiol 2022; 24:3486-3499. [PMID: 35049116 PMCID: PMC9541017 DOI: 10.1111/1462-2920.15912] [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: 09/22/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%–97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco‐evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.
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Affiliation(s)
- María V Quiroga
- Instituto Tecnológico de Chascomús (INTECH, UNSAM - CONICET), Chascomús, Argentina
| | - Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Consejo Superior de Investigaciones Científicas, Salamanca, Spain
| | - Gabriela Mataloni
- Instituto de Investigación e Ingeniería Ambiental (IIIA, UNSAM-CONICET), San Martín, Buenos Aires, Argentina
| | - Valeria Casa
- Instituto de Investigación e Ingeniería Ambiental (IIIA, UNSAM-CONICET), San Martín, Buenos Aires, Argentina
| | - James C Stegen
- Pacific Northwest National Laboratory, Ecosystem Science Team, Richland, WA, USA
| | - Don Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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34
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Relating Land Use/Cover and Landscape Pattern to the Water Quality under the Simulation of SWAT in a Reservoir Basin, Southeast China. SUSTAINABILITY 2021. [DOI: 10.3390/su131911067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding the relationship between land use/cover pattern and water quality could provide guidelines for non-point source pollution and facilitate sustainable development. The previous studies mainly relate the land use/cover of the entire region to the water quality at the monitoring sites, but the water quality at monitoring sites did not totally reflect the water environment of the entire basin. In this study, the land use/cover was monitored on Google Earth Engine in Tang-Pu Reservoir basin, China. In order to reflect the water quality of the whole study area, the spatial distribution of the determinants for water quality there, i.e., the total nitrogen and total phosphorus (TN&TP), were simulated by the Soil and Water Assessment Tool (SWAT). The redundancy analysis explored the correlations between land use/cover pattern and simulated TN&TP. The results showed that: (1) From 2009 to 2019, forest was the dominant land cover, and there was little land use/cover change. The landscape fragmentation increased, and the connectivity decreased. (2) About 25% TP concentrations and nearly all the TN concentrations at the monitoring points did not reach drinking water standard, which means nitrogen and phosphorus pollution were the most serious problems. The highest output per unit TN&TP simulated by SWAT were 44.50 kg/hm2 and 9.51 kg/hm2 and occurred in areas with highly fragile landscape patterns. (3) TN&TP correlated positively with cultivated and construction land but negatively with forest. The correlation between forest and TN&TP summited at 500–700-m buffer and construction land at 100-m buffer. As the buffer size increased, the correlation between the cultivated land, and the TN weakened, while the correlation with the TP increased. TN&TP correlated positively with the Shannon’s Diversity Index and negatively with the Contagion Index. This study provides a new perspective for exporting the impact of land use/cover pattern on water quality.
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35
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Lehosmaa K, Muotka T, Pirttilä AM, Jaakola I, Rossi PM, Jyväsjärvi J. Bacterial communities at a groundwater-surface water ecotone: gradual change or abrupt transition points along a contamination gradient? Environ Microbiol 2021; 23:6694-6706. [PMID: 34382316 DOI: 10.1111/1462-2920.15708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/11/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Microbial communities contribute greatly to groundwater quality, but the impacts of land-use practices on bacteria in groundwaters and groundwater-dependent ecosystems remain poorly known. With 16S rRNA gene amplicon sequencing, we assessed bacterial community composition at the groundwater-surface water ecotone of boreal springs impacted by urbanization and agriculture, using spring water nitrate-N as a surrogate of contamination. We also measured the rate of a key ecosystem process, organic matter decomposition. We documented a recurrent pattern across all major bacterial phyla where diversity started to decrease at unexpectedly low nitrate-N concentrations (100-300 μg L-1 ). At 400 NO3 - -N μg L-1 , 25 bacterial exact sequence variants showed a negative response, resulting in a distinct threshold in bacterial community composition. Chthonomonas, Acetobacterales and Hyphomicrobium were the most sensitive taxa, while only three taxa (Duganella, Undibacterium and Thermoanaerobaculaceae) were enriched due to increased contamination. Decomposition rate responded unimodally to increasing nitrate-N concentration, with a peak rate at ~400 NO3 - -N μg L-1 , parallelly with a major shift in bacterial community composition. Our results emphasize the utility of bacterial communities in the assessment of groundwater-dependent ecosystems. They also call for a careful reconsideration of threshold nitrate values for defining groundwater ecosystem health and protecting their microbial biodiversity.
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Affiliation(s)
- Kaisa Lehosmaa
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Timo Muotka
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Iikka Jaakola
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Pekka M Rossi
- Water, Energy and Environmental Engineering Research Group, University of Oulu, Oulu, FI-90014, Finland
| | - Jussi Jyväsjärvi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
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36
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Barbosa da Costa N, Fugère V, Hébert MP, Xu CCY, Barrett RDH, Beisner BE, Bell G, Yargeau V, Fussmann GF, Gonzalez A, Shapiro BJ. Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment. Mol Ecol 2021; 30:4771-4788. [PMID: 34324752 DOI: 10.1111/mec.16100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/30/2021] [Accepted: 07/23/2021] [Indexed: 01/04/2023]
Abstract
Agricultural pollution with fertilizers and pesticides is a common disturbance to freshwater biodiversity. Bacterioplankton communities are at the base of aquatic food webs, but their responses to these potentially interacting stressors are rarely explored. To test the extent of resistance and resilience in bacterioplankton communities faced with agricultural stressors, we exposed freshwater mesocosms to single and combined gradients of two commonly used pesticides: the herbicide glyphosate (0-15 mg/L) and the neonicotinoid insecticide imidacloprid (0-60 μg/L), in high or low nutrient backgrounds. Over the 43-day experiment, we tracked variation in bacterial density with flow cytometry, carbon substrate use with Biolog EcoPlates, and taxonomic diversity and composition with environmental 16S rRNA gene amplicon sequencing. We show that only glyphosate (at the highest dose, 15 mg/L), but not imidacloprid, nutrients, or their interactions measurably changed community structure, favouring members of the Proteobacteria including the genus Agrobacterium. However, no change in carbon substrate use was detected throughout, suggesting functional redundancy despite taxonomic changes. We further show that communities are resilient at broad, but not fine taxonomic levels: 24 days after glyphosate application the precise amplicon sequence variants do not return, and tend to be replaced by phylogenetically close taxa. We conclude that high doses of glyphosate - but still within commonly acceptable regulatory guidelines - alter freshwater bacterioplankton by favouring a subset of higher taxonomic units (i.e., genus to phylum) that transiently thrive in the presence of glyphosate. Longer-term impacts of glyphosate at finer taxonomic resolution merit further investigation.
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Affiliation(s)
- Naíla Barbosa da Costa
- Département des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada.,Groupe de Recherche Interuniversitaire en Limnologie et environnement aquatique (GRIL), Montreal, QC, Canada
| | - Vincent Fugère
- Groupe de Recherche Interuniversitaire en Limnologie et environnement aquatique (GRIL), Montreal, QC, Canada.,Québec Centre for Biodiversity Science (QCBS), Montreal, QC, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada.,Département des Sciences de l'environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Marie-Pier Hébert
- Groupe de Recherche Interuniversitaire en Limnologie et environnement aquatique (GRIL), Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Charles C Y Xu
- Québec Centre for Biodiversity Science (QCBS), Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada.,Redpath Museum, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Québec Centre for Biodiversity Science (QCBS), Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada.,Redpath Museum, McGill University, Montreal, QC, Canada
| | - Beatrix E Beisner
- Groupe de Recherche Interuniversitaire en Limnologie et environnement aquatique (GRIL), Montreal, QC, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada
| | - Graham Bell
- Québec Centre for Biodiversity Science (QCBS), Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Viviane Yargeau
- Department of Chemical Engineering, McGill University, Montreal, QC, Canada
| | - Gregor F Fussmann
- Groupe de Recherche Interuniversitaire en Limnologie et environnement aquatique (GRIL), Montreal, QC, Canada.,Québec Centre for Biodiversity Science (QCBS), Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Andrew Gonzalez
- Québec Centre for Biodiversity Science (QCBS), Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - B Jesse Shapiro
- Département des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada.,Groupe de Recherche Interuniversitaire en Limnologie et environnement aquatique (GRIL), Montreal, QC, Canada.,Québec Centre for Biodiversity Science (QCBS), Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill Genome Centre, McGill University, Montreal, QC, Canada
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37
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Marmen S, Fadeev E, Al Ashhab A, Benet-Perelberg A, Naor A, Patil HJ, Cytryn E, Viner-Mozzini Y, Sukenik A, Lalzar M, Sher D. Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture. Front Microbiol 2021; 12:679743. [PMID: 34248892 PMCID: PMC8264503 DOI: 10.3389/fmicb.2021.679743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over 3 years. The system comprised two fishponds, where fish are grown, and an operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been affected by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects of aquaculture-related factors.
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Affiliation(s)
- Sophi Marmen
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Ashraf Al Ashhab
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Microbial Metagenomics Division, The Dead Sea and Arava Science Center, Masada, Israel
| | - Ayana Benet-Perelberg
- Dor Aquaculture Research Station, Fisheries Department, Israel Ministry of Agriculture and Rural Development, Dor, Israel
| | - Alon Naor
- Dor Aquaculture Research Station, Fisheries Department, Israel Ministry of Agriculture and Rural Development, Dor, Israel
| | - Hemant J. Patil
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
| | - Yehudit Viner-Mozzini
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Assaf Sukenik
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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Hahn MW, Huemer A, Pitt A, Hoetzinger M. Opening a next-generation black box: Ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit. Mol Ecol Resour 2021; 21:2471-2485. [PMID: 34101998 DOI: 10.1111/1755-0998.13444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolving protein-encoding gene priB was used to reveal ecological patterns hidden within a single operational taxonomic unit (OTU) defined by >99% 16S rRNA sequence similarity. The studied subcluster PnecC of the genus Polynucleobacter represents a ubiquitous group of abundant freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. In addition to the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. An unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca2+ -rich and Ca2+ -poor habitats. This compositional pattern strongly resembled the vicariance of plant species on silicate and limestone soils. The new cultivation-independent approach presented opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.
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Affiliation(s)
- Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Andrea Huemer
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Matthias Hoetzinger
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
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