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Jiao G, Huang Y, Tang H, Chen Y, Zhou D, Yu D, Ma Z, Ni S. Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175305. [PMID: 39117200 DOI: 10.1016/j.scitotenv.2024.175305] [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: 05/18/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024]
Abstract
Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.
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Affiliation(s)
- Ganghui Jiao
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; Yunnan Earthquake Agency, Yunnan 650000, China; Observation Station for Field Scientific Research of Crustal Tectonic Activity in Northwest Yunnan, Dali 671000, China
| | - Yi Huang
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China.
| | - Hua Tang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Ying Chen
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
| | - Dan Zhou
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Daming Yu
- Pangang Group Company Limited, Sichuan 617050, China
| | - Zhongjian Ma
- Pangang Group Company Limited, Sichuan 617050, China
| | - Shijun Ni
- College of Geosciences, Chengdu University of Technology, Sichuan 610059, China
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Martinez O, Bergen SR, Gareis JB. Comparison of Yamuna (India) and Mississippi River (United States of America) bacterial communities reveals greater diversity below the Yamunotri Glacier. PLoS One 2024; 19:e0304664. [PMID: 38968225 PMCID: PMC11226128 DOI: 10.1371/journal.pone.0304664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/15/2024] [Indexed: 07/07/2024] Open
Abstract
The Yamuna River in India and the Mississippi River in the United States hold significant commercial, cultural, and ecological importance. This preliminary survey compares the bacterial communities sampled in surface waters at 11 sites (Yamuna headwaters, Mississippi headwaters, Yamuna River Yamunotri Town, Mississippi River at Winona, Tons River, Yamuna River at Paonta Sahib, Yamuna River Delhi-1, Yamuna River Delhi-2, Yamuna River before Sangam, Sangam, Ganga River before Sangam). Bacterial 16S rDNA analyses demonstrate dominance of Proteobacteria and Bacteroidetes phyla. Actinobacteria were also dominant at sites near Sangam in India and sites in Minnesota. A dominance of Epsilonbacteraeota were found in Delhi, India. Principal component analysis (PCA) using unique operational taxonomic units (OTUs) resulted in the identification of 3 groups that included the Yamuna River locations in Delhi (Delhi locations), Yamuna headwaters and Yamuna River at Yamunotri (Yamuna River locations below the Glacier) and Mississippi, Ganga, Tons, and other Yamuna River locations. Diversity indices were significantly higher at the Yamuna River locations below the Glacier (Simpson D = 0.986 and Shannon H = 5.06) as compared (p value <0.001) to the Delhi locations (D = 0.951 and H = 4.23) and as compared (p value < 0.001) to Mississippi, Ganga, Tons, and other Yamuna River locations (D = 0.943 and H = 3.96). To our knowledge, this is the first survey to compare Mississippi and Yamuna River bacterial communities. We demonstrate higher diversity in the bacterial communities below the Yamunotri glacier in India.
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Affiliation(s)
- Osvaldo Martinez
- Biology Department, Winona State University, Winona, MN, United States of America
| | - Silas R. Bergen
- Mathematics and Statistics Department, Winona State University, Winona, MN, United States of America
| | - Jacob B. Gareis
- Mathematics and Statistics Department, Winona State University, Winona, MN, United States of America
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Fontaine L, Pin L, Savio D, Friberg N, Kirschner AKT, Farnleitner AH, Eiler A. Bacterial bioindicators enable biological status classification along the continental Danube river. Commun Biol 2023; 6:862. [PMID: 37596339 PMCID: PMC10439154 DOI: 10.1038/s42003-023-05237-8] [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: 05/15/2022] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium, and Rhodoluna, and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2-3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems.
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Affiliation(s)
- Laurent Fontaine
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernv. 31, 0371, Oslo, Norway
| | - Lorenzo Pin
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernv. 31, 0371, Oslo, Norway
- Norsk Institutt for Vannforskning (NIVA) Gaustadalléen 21, 0349, Oslo, Norway
| | - Domenico Savio
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Research Group for Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Nikolai Friberg
- Norsk Institutt for Vannforskning (NIVA) Gaustadalléen 21, 0349, Oslo, Norway
- Freshwater Biological Section, University of Copenhagen, Universitetsparken 4, Third Floor, 2100, Copenhagen, Denmark
- School of Geography, University of Leeds, Leeds, LS2 9JT, UK
| | - Alexander K T Kirschner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Microbiology, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Andreas H Farnleitner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
- Research Group for Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Alexander Eiler
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernv. 31, 0371, Oslo, Norway.
- eDNA Solutions AB, Kärrbogata 22, 44196, Alingsås, Sweden.
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Liu M, Graham N, Xu L, Zhang K, Yu W. Bubbleless aerated-biological activated carbon as a superior process for drinking water treatment in rural areas. WATER RESEARCH 2023; 240:120089. [PMID: 37216786 DOI: 10.1016/j.watres.2023.120089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/26/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Drinking water supply in rural areas remains a substantial challenge due to complex natural, technical and economic conditions. To provide safe and affordable drinking water to all, as targeted in the UN Sustainable Development Goals (2030 Agenda), low-cost, efficient water treatment processes suitable for rural areas need to be developed. In this study, a bubbleless aeration BAC (termed ABAC) process is proposed and evaluated, involving the incorporation of a hollow fiber membrane (HFM) assembly within a slow-rate BAC filter, to provide dissolved oxygen (DO) throughout the BAC filter and an increased DOM removal efficiency. The results showed that after a 210-day period of operation, the ABAC increased the DOC removal by 54%, and decreased the disinfection byproduct formation potential (DBPFP) by 41%, compared to a comparable BAC filter without aeration (termed NBAC). The elevated DO (> 4 mg/L) not only reduced secreted extracellular polymer, but also modified the microbial community with a stronger degradation ability. The HFM-based aeration showed comparable performance to 3 mg/L pre-ozonation, and the DOC removal efficiency was four times greater than that of a conventional coagulation process. The proposed ABAC treatment, with its various advantages (e.g., high stability, avoidance of chemicals, ease of operation and maintenance), is well-suited to be integrated as a prefabricated device, for decentralized drinking water systems in rural areas.
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Affiliation(s)
- Mengjie Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nigel Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Lei Xu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Kai Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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5
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Liu M, Graham NJD, Xu L, Zhang K, Yu W. Bubbleless Air Shapes Biofilms and Facilitates Natural Organic Matter Transformation in Biological Activated Carbon. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4543-4555. [PMID: 36877961 DOI: 10.1021/acs.est.2c08889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The biodegradation in the middle and downstream of slow-rate biological activated carbon (BAC) is limited by insufficient dissolved oxygen (DO) concentrations. In this study, a bubbleless aerated BAC (termed ABAC) process was developed by installing a hollow fiber membrane (HFM) module within a BAC filter to continuously provide aeration throughout the BAC system. The BAC filter without an HFM was termed NBAC. The laboratory-scale ABAC and NBAC systems operated continuously for 426 days using secondary sewage effluent as an influent. The DO concentrations for NBAC and ABAC were 0.78 ± 0.27 and 4.31 ± 0.44 mg/L, respectively, with the latter providing the ABAC with greater electron acceptors for biodegradation and a microbial community with better biodegradation and metabolism capacity. The biofilms in ABAC secreted 47.3% less EPS and exhibited greater electron transfer capacity than those in NBAC, resulting in enhanced contaminant degradation efficiency and long-term stability. The extra organic matter removed by ABAC included refractory substances with a low elemental ratio of oxygen to carbon (O/C) and a high elemental ratio of hydrogen to carbon (H/C). The proposed ABAC filter provides a valuable, practical example of how to modify the BAC technology to shape the microbial community, and its activity, by optimizing the ambient atmosphere.
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Affiliation(s)
- Mengjie Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Nigel J D Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Lei Xu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China
| | - Kai Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China
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Numberger D, Zoccarato L, Woodhouse J, Ganzert L, Sauer S, Márquez JRG, Domisch S, Grossart HP, Greenwood AD. Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157321. [PMID: 35839872 DOI: 10.1016/j.scitotenv.2022.157321] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urbanization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sediments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urbanization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.
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Affiliation(s)
- Daniela Numberger
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany; Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany
| | - Luca Zoccarato
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany; University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Jason Woodhouse
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany
| | - Lars Ganzert
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany; GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.7 Geomicrobiology, Telegrafenberg C-422, 14473 Potsdam, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 16775, 13125 Berlin, Germany
| | | | - Sami Domisch
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany; University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstrasse 32, 14195 Berlin, Germany.
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany; Freie Universität Berlin, Department of Veterinary Medicine, Institute for Virology, Robert von Ostertag-Strasse 7-13, 14163 Berlin, Germany
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Characterization of Bacterial Communities from the Surface and Adjacent Bottom Layers of Water in the Billings Reservoir. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081280. [PMID: 36013459 PMCID: PMC9409723 DOI: 10.3390/life12081280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]
Abstract
Here, we describe the bacterial diversity and physicochemical properties in freshwater samples from the surface and bottom layers of the Billings Reservoir, the largest open-air storage ecosystem in the São Paulo (Brazil) metropolitan area. Forty-four samples (22 from the surface and 22 from the bottom layers) were characterized based on 16S rRNA gene analysis using Illumina MiSeq. Taxonomical composition revealed an abundance of the Cyanobacteria phylum, followed by Proteobacteria, which were grouped into 1903 and 2689 different genera in the surface and the deep-water layers, respectively. Chroobacteria, Actinobacteria, Betaproteobacteria, and Alphaproteobacteria were the most dominant classes. The Shannon diversity index was in the range of 2.3–5.39 and 4.04–6.86 in the surface and bottom layers, respectively. Flavobacterium was the most predominant pathogenic genus. Temperature and phosphorus concentrations were among the most influential factors in shaping the microbial communities of both layers. Predictive functional analysis suggests that the reservoir is enriched in motility genes involved in flagellar assembly. The overall results provide new information on the diversity composition, ecological function, and health risks of the bacterial community detected in the Billings freshwater reservoir. The broad bacterial diversity indicates that the bacterioplankton communities in the reservoir were involved in multiple essential environmental processes.
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Genome Analysis of Enterobacter asburiae and Lelliottia spp. Proliferating in Oligotrophic Drinking Water Reservoirs and Lakes. Appl Environ Microbiol 2022; 88:e0047122. [PMID: 35862664 PMCID: PMC9317948 DOI: 10.1128/aem.00471-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Surface waters are one of the main sources for drinking water production, and thus microbial contamination should be as minimal as possible. However, high concentrations of coliform bacteria were detected in reservoirs and lakes used for drinking water production during summer months due to autochthonous proliferation processes. Here, we present the genomic analyses of 17 strains of Enterobacter asburiae and Lelliottia spp. proliferating in reservoirs and lakes with special focus on the hygienic relevance, antibiotic resistance, and adaptations to the oligotrophic environments. The genomes contain neither genes for the type III secretion system nor cytotoxins or hemolysins, which are considered typical virulence factors. Examination of antibiotic resistance genes revealed mainly efflux pumps and β-lactamase class C (ampC) genes. Phenotypically, single isolates of Enterobacter asburiae showed resistance to fosfomycin and ceftazidime. The genome analyses further suggest adaptations to oligotrophic and changing environmental conditions in reservoirs and lakes, e.g., genes to cope with low nitrate and phosphate levels and the ability to utilize substances released by algae, like amino acids, chitin, alginate, rhamnose, and fucose. This leads to the hypothesis that the proliferation of the coliform bacteria could occur at the end of summer due to algae die-off. IMPORTANCE Certain strains of coliform bacteria have been shown to proliferate in the oligotrophic water of drinking water reservoirs and lakes, reaching values above 104 per 100 mL. Such high concentrations challenge drinking water treatment, and occasionally the respective coliform bacteria have been detected in the treated drinking water. Thus, the question of their hygienic relevance is of high importance for water suppliers and authorities. Our genomic analyses suggest that the strains are not hygienically relevant, as typical virulence factors are absent and antibiotic resistance genes in the genomes most likely are of natural origin. Furthermore, their presence in the water is not related to fecal contamination. The proliferation in reservoirs and lakes during stable summer stratification is an autochthonic process of certain E. asburiae and Lelliottia strains that are well adapted to the surrounding oligotrophic environment.
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Ou-Yang T, Yang SQ, Zhao L, Ji LL, Shi JQ, Wu ZX. Temporal heterogeneity of bacterial communities and their responses to Raphidiopsis raciborskii blooms. Microbiol Res 2022; 262:127098. [PMID: 35753182 DOI: 10.1016/j.micres.2022.127098] [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: 11/05/2021] [Revised: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022]
Abstract
To elucidate the interspecies connectivity between cyanobacteria and other bacteria (noncyanobacteria), microbial diversity and composition were investigated through high-throughput sequencing (HTS) in a drinking water reservoir in Chongqing city, Southwest China, during Raphidiopsis raciborskii blooms. Significant temporal changes were observed in microbial community composition during the sampling period, primarily reflected by variations in relative bacterial abundance. The modularity analysis of the network demonstrated that the bacterial community forms co-occurrence/exclusion patterns in response to variations in environmental factors. Moreover, five modules involved in the dynamic phases of the R. raciborskii bloom were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups. The reservoir was eutrophic (i.e., the average concentrations of total nitrogen (TN) and total phosphorus (TP) were 2.32 and 0.07 mg L-1, respectively) during the investigation; however, Pearson's correlation coefficient showed that R. raciborskii was not significantly correlated with nitrogen and phosphorus. However, other environmental factors, such as water temperature, pH, and the permanganate index, were positively correlated with R. raciborskii. Importantly, Proteobacteria (α-, γ-Proteobacteria), Acidobacteria, Chloroflexi, and Firmicutes were preferentially associated with increased R. raciborskii blooms. These results suggested that the transition of R. raciborskii bloom-related microbial modules and their keystone species could be crucial in the development and collapse of R. raciborskii blooms and could provide a fundamental basis for understanding the linkage between the structure and function of the microbial community during bloom dynamics.
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Affiliation(s)
- Tian Ou-Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Song-Qi Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Lu Zhao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Lu-Lu Ji
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Jun-Qiong Shi
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China
| | - Zhong-Xing Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, PR China.
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10
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Yu C, Wang Q, Zhang S, Zeng H, Chen W, Chen W, Lou H, Yu W, Wu J. Effects of Strigolactone on Torreya grandis Gene Expression and Soil Microbial Community Structure Under Simulated Nitrogen Deposition. FRONTIERS IN PLANT SCIENCE 2022; 13:908129. [PMID: 35720604 PMCID: PMC9201785 DOI: 10.3389/fpls.2022.908129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Nitrogen enters the terrestrial ecosystem through deposition. High nitrogen levels can affect physical and chemical properties of soil and inhibit normal growth and reproduction of forest plants. Nitrogen modulates the composition of soil microorganisms. Strigolactones inhibits plant branching, promotes root growth, nutrient absorption, and promotes arbuscular fungal mycelia branching. Plants are subjected to increasing atmospheric nitrogen deposition. Therefore, it is imperative to explore the relationship between strigolactone and nitrogen deposition of plants and abundance of soil microorganisms. In the present study, the effects of strigolactone on genetic responses and soil microorganisms of Torreya grandis, under simulated nitrogen deposition were explored using high-throughput sequencing techniques. T. grandis is a subtropical economic tree species in China. A total of 4,008 differentially expressed genes were identified in additional N deposition and GR24 treatment. These genes were associated with multiple GO terms and metabolic pathways. GO enrichment analysis showed that several DEGs were associated with enrichment of the transporter activity term. Both additional nitrogen deposition and GR24 treatment modulated the content of nutrient elements. The content of K reduced in leaves after additional N deposition treatment. The content of P increased in leaves after GR24 treatment. A total of 20 families and 29 DEGs associated with transporters were identified. These transporters may be regulated by transcription factors. A total of 1,402,819 clean reads and 1,778 amplicon sequence variants (ASVs) were generated through Bacterial 16S rRNA sequencing. Random forest classification revealed that Legionella, Lacunisphaera, Klebsiella, Bryobacter, and Janthinobacterium were significantly enriched in the soil in the additional N deposition group and the GR24 treatment group. Co-occurrence network analysis showed significant differences in composition of soil microbial community under different treatments. These results indicate a relationship between N deposition and strigolactones effect. The results provide new insights on the role of strigolactones in plants and composition of soil microorganisms under nitrogen deposition.
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Affiliation(s)
- Chenliang Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Qi Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Shouke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Hao Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Weijie Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Weiwu Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
- NFGA Engineering Research Center for Torreya grandis ‘Merrillii’, Zhejiang A&F University, Hangzhou, China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
- NFGA Engineering Research Center for Torreya grandis ‘Merrillii’, Zhejiang A&F University, Hangzhou, China
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11
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Blakney AJC, Bainard LD, St-Arnaud M, Hijri M. Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought. Environ Microbiol 2022; 24:3529-3548. [PMID: 35590462 DOI: 10.1111/1462-2920.16046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew J C Blakney
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada
| | - Luke D Bainard
- Agassiz Research and Development Centre, AgricuSlture and Agri-Food Canada, Agassiz, BC, V0M 1A2, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada.,African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir, 43150, Morocco
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12
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Sanseverino I, Pretto P, António DC, Lahm A, Facca C, Loos R, Skejo H, Beghi A, Pandolfi F, Genoni P, Lettieri T. Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese. MICROBIAL ECOLOGY 2022; 83:850-868. [PMID: 34766210 PMCID: PMC9016052 DOI: 10.1007/s00248-021-01914-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/26/2021] [Indexed: 05/09/2023]
Abstract
Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.
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Affiliation(s)
- Isabella Sanseverino
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Patrizia Pretto
- Biosearch Ambiente Srl, Via Tetti Gai 59, 10091, Alpignano, TO, Italy
| | - Diana Conduto António
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Armin Lahm
- Bioinformatics Project Support, P.za S.M. Liberatrice 18, 00153, Roma, Italy
| | - Chiara Facca
- Department of Environmental Science, Informatics and Statistics, University Ca' Foscari Venezia, Via Torino 155, 301702, Mestre, VE, Italy
| | - Robert Loos
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Helle Skejo
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Andrea Beghi
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Franca Pandolfi
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Pietro Genoni
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Teresa Lettieri
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy.
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13
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Horii T, Suzuki S, Takano C, Shibuya H, Ichijima R, Kusano C, Ikehara H, Gotoda T. Lower impact of vonoprazan-amoxicillin dual therapy on gut microbiota for Helicobacter pylori eradication. J Gastroenterol Hepatol 2021; 36:3314-3321. [PMID: 34107551 DOI: 10.1111/jgh.15572] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 05/11/2021] [Accepted: 06/05/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM Helicobacter pylori eradication can disrupt the gut microbiome. Here, we investigated the short-term impact of minimum antibiotic treatment-a 7-day vonoprazan and low-dose amoxicillin regimen (VA-dual therapy)-on gut microbiota and compared it with that of vonoprazan-based triple therapy (VAC-triple therapy). METHODS Fifty-nine patients with H. pylori infection were recruited (UMIN000034140) from March to May 2019 and randomly assigned to the VAC-triple therapy or VA-dual therapy groups, according to the first-line H. pylori treatment received. Fecal samples were collected before treatment initiation and 1 and 8 weeks after eradication therapy completion. The composition ratios of the bacterial taxa and the alpha and beta diversities were evaluated in both groups via polymerase chain reaction amplification of the V3-V4 region of the 16S rRNA gene and sequencing using the MiSeq system. RESULTS Nineteen patients were assigned to the VA-dual group and 24 to the VAC-triple group. Compared with baseline, the alpha diversity reduced significantly 1 and 8 weeks after VAC-triple therapy. However, for VA-dual therapy, the alpha diversities at 1 and 8 weeks after the treatment did not change significantly compared with those at baseline. Additionally, the beta diversity differed significantly between baseline and 1 and 8 weeks after VAC-triple therapy. VAC-triple therapy led to significant alteration in the relative abundance of Actinobacteria at the phylum level and Collinsella, Blautia, and Streptococcus at the genus level. CONCLUSIONS Compared with VAC-triple therapy, VA-dual therapy induced minimal changes in the diversity and relative abundance of gut microbiota.
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Affiliation(s)
- Toshiki Horii
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan.,Department of Gastroenterology, Yuri Kumiai General Hospital, Akita, Japan
| | - Sho Suzuki
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Shibuya
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Ryoji Ichijima
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Chika Kusano
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Hisatomo Ikehara
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Takuji Gotoda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
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14
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Suzuki S, Gotoda T, Takano C, Horii T, Sugita T, Ogura K, Ichijima R, Kusano C, Ikehara H. Long term impact of vonoprazan-based Helicobacter pylori treatment on gut microbiota and its relation to post-treatment body weight changes. Helicobacter 2021; 26:e12851. [PMID: 34486195 DOI: 10.1111/hel.12851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Vonoprazan-based Helicobacter pylori (H. pylori) treatment is highly effective in eradicating the target bacteria; however, its post-1-year impact on gut microbiota is unknown. This study evaluated the impact of vonoprazan-based H. pylori therapy on gut microbiota 1-year post-therapy and investigated the relationship between body weight changes and post-therapy gut microbiota perturbations. MATERIALS AND METHODS Between March and May 2019, 43 patients with H. pylori infections received either vonoprazan/amoxicillin (VA) or vonoprazan/amoxicillin/clarithromycin (VAC) therapy. Fecal samples were collected prior to treatment and 1 year after treatment. The alpha and beta diversities and the bacterial taxa composition ratios were determined using polymerase chain reaction amplification of the V3-V4 region of the 16S ribosomal RNA gene. The correlation between body weight changes and relative abundances of genera post-therapy was also analyzed. RESULTS Among the 43 patients, 18 received VA therapy and 21 received VAC therapy. One year after treatment, the alpha diversity was significantly higher in both the treatment groups (p < .001, using observed operational taxonomic units and Chao1 index), and beta diversity was significantly different in both the groups (p = .001, using unweighted UniFrac distance) compared with baseline findings. Significant positive correlations were found between body weight changes and the relative abundances of Coprococcus spp. (p = .037) and Odoribacter spp. (p = .022) post-therapy. CONCLUSION Vonoprazan-based H. pylori therapies are associated with long-term impacts on gut microbiota, including effects on bacterial species richness, and potentially affect metabolism by altering the microbiota. TRIAL REGISTRATION NUMBER UMIN000040025.
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Affiliation(s)
- Sho Suzuki
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan.,Department of Gastroenterology, Yuri Kumiai General Hospital, Akita, Japan
| | - Takuji Gotoda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Chika Takano
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Toshiki Horii
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Tomomi Sugita
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Kanako Ogura
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Ryoji Ichijima
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Chika Kusano
- Department of Gastroenterology, Internal Medicine, Kitasato University School of Medicine, Sagamihara, Japan
| | - Hisatomo Ikehara
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
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15
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Moradinejad S, Trigui H, Maldonado JFG, Shapiro BJ, Terrat Y, Sauvé S, Fortin N, Zamyadi A, Dorner S, Prévost M. Metagenomic study to evaluate functional capacity of a cyanobacterial bloom during oxidation. CHEMICAL ENGINEERING JOURNAL ADVANCES 2021. [DOI: 10.1016/j.ceja.2021.100151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Akbari A, Kasprzyk A, Galvez R, Ghoshal S. A rhamnolipid biosurfactant increased bacterial population size but hindered hydrocarbon biodegradation in weathered contaminated soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:145441. [PMID: 33725602 DOI: 10.1016/j.scitotenv.2021.145441] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Surfactants are used to enhance the bioavailability of recalcitrant residual petroleum contamination during bioremediation. However, surfactants in some cases inhibit biodegradation, which is often attributed to their toxicity. Herein, we show that a rhamnolipid biosurfactant likely served as a carbon source and exhibited physiological inhibition on petroleum biodegradation. The addition of biosurfactants in mixed, batch, slurry bioreactors with soils from a petroleum-contaminated site led to a dose-dependent shift in the microbial community with a decrease in diversity and increase in population size and delayed biodegradation. Microbial community analysis indicated the enrichment of Alphaproteobacteria affiliated taxa such as Sphingomonadaceae in systems amended with biosurfactant. The diversity was significantly lower in systems with higher doses of biosurfactants compared to systems without biosurfactant. Droplet Digital PCR indicated a 30-90 fold increase in 16S rRNA copy numbers in systems with higher doses of biosurfactant than control systems without surfactant and nutrients, whereas the nutrient amendment alone led to a two-fold increase in population size. Total petroleum hydrocarbon analysis showed that the biodegradation extent was negatively impacted by rhamnolipid at the highest dose compared to lower doses (23% vs. 40%) or without the biosurfactant. Indigenous isolates cultivated from the oil-amended soil exhibited growth on rhamnolipid as a sole carbon source. A novel insight gained is how dose-dependent responses of microbial communities to biosurfactants alter the biodegradation time profile of hydrocarbons. The study highlights the significance of microbial assessment prior to surfactant-mediated bioremediation practices.
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Affiliation(s)
- Ali Akbari
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada.
| | - Aleksandra Kasprzyk
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Rosa Galvez
- Department of Civil and Water Engineering, Laval University, Quebec, Quebec G1V 0A6, Canada
| | - Subhasis Ghoshal
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 0C3, Canada
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17
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Dungan AM, Bulach D, Lin H, van Oppen MJH, Blackall LL. Development of a free radical scavenging bacterial consortium to mitigate oxidative stress in cnidarians. Microb Biotechnol 2021; 14:2025-2040. [PMID: 34259383 PMCID: PMC8449677 DOI: 10.1111/1751-7915.13877] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Corals are colonized by symbiotic microorganisms that profoundly influence the animal’s health. One noted symbiont is a single‐celled alga (in the dinoflagellate family Symbiodiniaceae), which provides the coral with most of its fixed carbon. Thermal stress increases the production of reactive oxygen species (ROS) by Symbiodiniaceae during photosynthesis. ROS can both damage the algal symbiont’s photosynthetic machinery and inhibit its repair, causing a positive feedback loop for the toxic accumulation of ROS. If not scavenged by the antioxidant network, excess ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating in a process known as bleaching. We use Exaiptasia diaphana as a model for corals and constructed a consortium comprised of E. diaphana–associated bacteria capable of neutralizing ROS. We identified six strains with high free radical scavenging (FRS) ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae and Micrococcaceae. In parallel, we established a consortium of low FRS isolates consisting of genetically related strains. Bacterial whole genome sequences were used to identify key pathways that are known to influence ROS.
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Affiliation(s)
- Ashley M Dungan
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia
| | - Dieter Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Vic., Australia
| | - Heyu Lin
- School of Earth Sciences, The University of Melbourne, Melbourne, Vic., Australia
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Linda L Blackall
- School of Biosciences, The University of Melbourne, Melbourne, Vic., Australia
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18
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Ramos-Barbero MD, Viver T, Zabaleta A, Senel E, Gomariz M, Antigüedad I, Santos F, Martínez-García M, Rosselló-Móra R, Antón J. Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface. Environ Microbiol 2021; 23:3477-3498. [PMID: 34110059 DOI: 10.1111/1462-2920.15630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 11/28/2022]
Abstract
Microbial communities in hypersaline underground waters derive from ancient organisms trapped within the evaporitic salt crystals and are part of the poorly known subterranean biosphere. Here, we characterized the viral and prokaryotic assemblages present in the hypersaline springs that dissolve Triassic-Keuper evaporite rocks and feed the Añana Salt Valley (Araba/Alava, Basque Country, Spain). Four underground water samples (around 23% total salinity) with different levels of exposure to the open air were analysed by means of microscopy and metagenomics. Cells and viruses in the spring water had lower concentrations than what are normally found in hypersaline environments and seemed to be mostly inactive. Upon exposure to the open air, there was an increase in activity of both cells and viruses as well as a selection of phylotypes. The underground water was inhabited by a rich community harbouring a diverse set of genes coding for retinal binding proteins. A total of 35 viral contigs from 15 to 104 kb, representing partial or total viral genomes, were assembled and their evolutionary changes through the spring system were followed by SNP analysis and metagenomic island tracking. Overall, both the viral and the prokaryotic assemblages changed quickly upon exposure to the open air conditions.
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Affiliation(s)
- Mª Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Ane Zabaleta
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Ece Senel
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain.,Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey
| | - María Gomariz
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Iñaki Antigüedad
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Manuel Martínez-García
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
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19
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Huby TJC, Clark DR, McKew BA, McGenity TJ. Extremely halophilic archaeal communities are resilient to short-term entombment in halite. Environ Microbiol 2021; 23:3370-3383. [PMID: 31919959 PMCID: PMC8359394 DOI: 10.1111/1462-2920.14913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite-entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory-grown halite over 21 weeks, using high-throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite-entombed communities. These results show that halite-entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of 'halite specialists' observed in ancient halite must occur over periods of years, rather than months, hinting at long-term successional dynamics in this environment.
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Affiliation(s)
- Tom J. C. Huby
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Dave R. Clark
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Boyd A. McKew
- School of Life SciencesUniversity of EssexColchesterEssexUK
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20
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Din G, Farooqi A, Sajjad W, Irfan M, Gul S, Ali Shah A. Cadmium and antibiotic-resistant Acinetobacter calcoaceticus strain STP14 reported from sewage treatment plant. J Basic Microbiol 2021; 61:230-240. [PMID: 33491793 DOI: 10.1002/jobm.202000538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/14/2020] [Accepted: 01/10/2021] [Indexed: 11/07/2022]
Abstract
A bacterium designated as strain STP14 was isolated from a sewage treatment plant and identified as Acinetobacter calcoaceticus based on 16S ribosomal RNA gene sequencing. Strain STP14 exhibited resistance to several metals such as mercury, cobalt, copper, nickel, lead, and cadmium. Among these metals, the bacterium showed maximum resistance to cadmium in concentration up to 1200 mg/L. The antimicrobial susceptibility test of A. calcoaceticus strain STP14 showed coresistance to all tested antibiotics except tigecycline and chloramphenicol for which 16 ± 1- and 15 ± 1-mm zone of inhibition was observed, respectively. The protein pattern of the crude cellular extract revealed substantial differences in protein bands of untreated control and cadmium treated A. calcoaceticus strain STP14 suggesting variable protein expression under cadmium stress. Metals and antibiotic resistance are increasing phenomenon and universal concern of public health. This study improves our understanding regarding the bacterial coresistance against metals and antibiotics and the possible emergence of multidrug resistance due to selective pressure and coselection in the metal polluted sewage sludge.
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Affiliation(s)
- Ghufranud Din
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asifa Farooqi
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Sarah Gul
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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21
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Gweon HS, Bowes MJ, Moorhouse HL, Oliver AE, Bailey MJ, Acreman MC, Read DS. Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum. Environ Microbiol 2021; 23:484-498. [PMID: 33258525 PMCID: PMC7898806 DOI: 10.1111/1462-2920.15337] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/03/2020] [Accepted: 11/24/2020] [Indexed: 01/26/2023]
Abstract
The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.
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Affiliation(s)
- Hyun S. Gweon
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
- School of Biological SciencesUniversity of ReadingReadingRG6 6EXUK
| | - Michael J. Bowes
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | - Heather L. Moorhouse
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
- Lancaster Environment CentreLancaster UniversityLibrary Avenue, LancasterLA1 4YQUK
| | - Anna E. Oliver
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | - Mark J. Bailey
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | | | - Daniel S. Read
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
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Tang H, Li C, Cheng K, Shi L, Wen L, Li W, Xiao X. Effect of different short-term tillage management on nitrogen-fixing bacteria community in a double-cropping paddy field of southern China. J Basic Microbiol 2020; 61:241-252. [PMID: 33351219 DOI: 10.1002/jobm.202000608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Accepted: 12/11/2020] [Indexed: 11/07/2022]
Abstract
Soil nitrogen (N)-fixing bacteria community plays an important role in the N cycling process in soil, but there is still limited information about how the soil microbes that drive this process to respond to combined application of tillage and crop residue management under the double-cropping rice (Oryza sativa L.) paddy field in southern of China. Therefore, the effects of 6-years short-term tillage treatment on soil N-fixing bacteria community under the double-cropping rice paddy field in southern China were studied by using the polymerase chain reaction-denaturing gradient gel electrophoresis method. The field experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), rotary tillage with crop residue removed as control (RTO). The results showed that the diversity index and richness index of cbbLR and nifH genes with CT, RT, and NT treatments were increased, compared with RTO treatment. Compared with RTO treatment, the abundance of cbbLR gene with CT, RT, and NT treatments were increased by 6.54, 4.73, and 2.78 times, respectively. Meanwhile, the abundance of nifH gene with CT, RT, and NT treatments were 5.32, 3.71, and 2.45 times higher than that of RTO treatment. The results also indicated that soil autotrophic Azotobacter and nitrogenase activity with CT and RT treatments were significantly higher (p < .05) than that of RTO treatment. There was an obvious difference in characteristic of soil N-fixing bacteria community between the application of crop residue and without crop residue input treatments. In summary, the results indicated that the abundance of N-fixing bacteria community in the double-cropping rice paddy field increased with conventional tillage and rotary tillage practice.
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Affiliation(s)
- Haiming Tang
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Chao Li
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Kaikai Cheng
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Lihong Shi
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Li Wen
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Weiyan Li
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Xiaoping Xiao
- Hunan Soil and Fertilizer Institute, Changsha, China
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23
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Zhong R, Zhang L, Chen L, Yang X, Zhang H. Modulation of cecal microbiota in laying hens via intake of genetically modified corn with the maroACC or mCry1Ac genes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:5450-5457. [PMID: 32562272 DOI: 10.1002/jsfa.10596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/24/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The present study investigated the chronic effect on the composition and proportions of the cecal microbiota of laying hens for 12 weeks after consuming two genetically modified (GM) corns containing the maroACC gene from the Agrobacterium tumefaciens strain (CC) and the mCry1Ac gene from the Bacillus thuringiensis strain (BT) in comparison with the isogenic corn (CT). RESULTS In total, 72 hens were randomly assigned to the CT corn-based diet, CC corn-based diet and BT corn-based diet. The absolute weights of abdominal fat, breast, thigh meat and organ weight were not affected by the dietary treatment. High-throughput 16S rRNA gene sequencing revealed a few differences in the composition of cecal microbiota among the treatments. The only difference with respect to bacterial family was that the cecal abundance of Porphyromonadaceae (3.46 versus 2.11%; P = 0.073) tended to be higher for birds consuming the CC diet than those birds consuming the CT diet. Birds fed the BT diet tended to have a higher abundance of Barnesiella (0.62 versus 0.13%; P = 0.057) and a lower abundance of unclassified Ruminococcaceae (0.64 versus 1.19%; P = 0.097) than those fed the CT diet. Considering beneficial intestinal Barnesiella, this decreases and ultimately clears the colonization of vancomycin-resistant Enterococcus. The unclassified Ruminococcaceae was a low-frequency and low-abundance bacterial taxa and was not associated with intestinal pathology. CONCLUSION These results indicate a similar modulation of cecal microbiota in laying hens by long-term feeding among transgenic CC corn, BT corn and non-transgenic corn and provide data for biosafety evaluation of the transgenic corn. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lilan Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoguang Yang
- National Institute of Nutrition and Food Safety, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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24
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Rapid Changes in Microbial Community Structures along a Meandering River. Microorganisms 2020; 8:microorganisms8111631. [PMID: 33105630 PMCID: PMC7690413 DOI: 10.3390/microorganisms8111631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/02/2022] Open
Abstract
Streams and rivers convey freshwater from lands to the oceans, transporting various organic particles, minerals, and living organisms. Microbial communities are key components of freshwater food webs and take up, utilize, and transform this material. However, there are still important gaps in our understanding of the dynamic of these organisms along the river channels. Using high-throughput 16S and 18S rRNA gene sequencing and quantitative PCR on a 11-km long transect of the Saint-Charles River (Quebec, CA), starting from its main source, the Saint-Charles Lake, we show that bacterial and protist community structures in the river drifted quickly but progressively downstream of its source. The dominant Operational Taxonomic Units (OTUs) of the lake, notably related to Cyanobacteria, decreased in proportions, whereas relative proportions of other OTUs, such as a Pseudarcicella OTU, increased along the river course, becoming quickly predominant in the river system. Both prokaryotic and protist communities changed along the river transect, suggesting a strong impact of the shift from a stratified lake ecosystem to a continuously mixed river environment. This might reflect the cumulative effects of the increasing water turbulence, fluctuations of physicochemical conditions, differential predation pressure in the river, especially in the lake outlet by benthic filter feeders, or the relocation of microorganisms, through flocculation, sedimentation, resuspension, or inoculation from the watershed. Our study reveals that the transit of water in a river system can greatly impact both bacterial and micro-eukaryotic community composition, even over a short distance, and, potentially, the transformation of materials in the water column.
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25
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Renteria AE, Maniakas A, Mfuna LE, Asmar MH, Gonzalez E, Desrosiers M. Low-dose and long-term azithromycin significantly decreases Staphylococcus aureus in the microbiome of refractory CRS patients. Int Forum Allergy Rhinol 2020; 11:93-105. [PMID: 32713109 DOI: 10.1002/alr.22653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 06/01/2020] [Accepted: 06/25/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND The sinonasal microbiome is believed to play an important role in the pathophysiology of refractory chronic rhinosinusitis (CRS). We evaluated changes in the microbiome following a 4-month course of low-dose azithromycin. Assessing microbiome alterations following such a treatment may help identify underlying mechanisms of this drug. METHODS A total of 48 adults with refractory CRS were enrolled in a double-blind, randomized, placebo-controlled trial. Patients were randomized to 250 mg of azithromycin or placebo 3 times weekly for 4 months. During this time, daily budesonide saline irrigations were continued. Sinonasal swabs were collected by endoscopically-assisted method prior to treatment initiation and at the end of it, and sent for 16S ribosomal RNA gene sequencing. High-resolution ANCHOR pipeline was used to infer and annotate putative species. The 2 patient groups were compared using DESeq2 differential abundance analysis. RESULTS From initiation to the end of azithromycin treatment, patients showed a significant difference in beta diversity analysis (p = 0.0004) along with a significant decrease in 71 different operational taxonomic units (OTUs) of Staphylococcus aureus (false discovery rate [FDR] < 0.05) obtained from the differential abundance analysis. This was not observed in placebo-treated patients. By the end of treatments, azithromycin-treated patients had a significant decrease in 29 different OTUs of S. aureus (FDR < 0.05) when compared to placebo. CONCLUSION A 4-month course of 250 mg of azithromycin 3 times weekly in patients with refractory CRS significantly decreases S. aureus abundance in the sinonasal microbiome. Considering the pathogenic role of S. aureus in the refractory CRS population, azithromycin may constitute an additional therapeutic option to help control this disease.
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Affiliation(s)
- Axel E Renteria
- Centre de Recherche du Centre Hospitalier, de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Département d'oto-rhino-laryngologie et chirurgie cervico-faciale du centre hospitalier, de l'Université de Montréal (CHUM), Montréal, QC, Canada
| | - Anastasios Maniakas
- Centre de Recherche du Centre Hospitalier, de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Département d'oto-rhino-laryngologie et chirurgie cervico-faciale du centre hospitalier, de l'Université de Montréal (CHUM), Montréal, QC, Canada.,Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Leandra Endam Mfuna
- Centre de Recherche du Centre Hospitalier, de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Marc-Henri Asmar
- Centre de Recherche du Centre Hospitalier, de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics (C3G), Department of Human Genetics, McGill University, Montréal, QC, Canada.,Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Martin Desrosiers
- Centre de Recherche du Centre Hospitalier, de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Département d'oto-rhino-laryngologie et chirurgie cervico-faciale du centre hospitalier, de l'Université de Montréal (CHUM), Montréal, QC, Canada
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The Efficacy of Hydrogen Peroxide in Mitigating Cyanobacterial Blooms and Altering Microbial Communities across Four Lakes in NY, USA. Toxins (Basel) 2020; 12:toxins12070428. [PMID: 32610617 PMCID: PMC7405413 DOI: 10.3390/toxins12070428] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 11/17/2022] Open
Abstract
Hydrogen peroxide (H2O2) has been proposed as an agent to mitigate toxic cyanobacterial blooms due to the heightened sensitivity of cyanobacteria to reactive oxygen species relative to eukaryotic organisms. Here, experiments were conducted using water from four diverse, eutrophic lake ecosystems to study the effects of H2O2 on cyanobacteria and non-target members of the microbial community. H2O2 was administered at 4 µg L-1 and a combination of fluorometry, microscopy, flow cytometry, and high throughput DNA sequencing were used to quantify the effects on eukaryotic and prokaryotic plankton communities. The addition of H2O2 resulted in a significant reduction in cyanobacteria levels in nearly all experiments (10 of 11), reducing their relative abundance from, on average, 85% to 29% of the total phytoplankton community with Planktothrix being highly sensitive, Microcystis being moderately sensitive, and Cylindrospermopsis being most resistant. Concurrently, eukaryotic algal levels increased in 75% of experiments. The bacterial phyla Actinobacteria, cyanobacteria, Planctomycetes, and Verrucomicrobia were most negatively impacted by H2O2, with Actinobacteria being the most sensitive. The ability of H2O2 to reduce, but not fully eliminate, cyanobacteria from the eutrophic water bodies studied here suggests it may not be an ideal mitigation approach in high biomass ecosystems.
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27
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Middleton JA, Sosa LL, Martin BC, Jones DL, Gleeson DB. Soil microbes of an urban remnant riparian zone have greater potential for N removal than a degraded riparian zone. Environ Microbiol 2020; 22:3302-3314. [DOI: 10.1111/1462-2920.15092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/05/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023]
Affiliation(s)
- Jen A. Middleton
- UWA School of Biological Sciences The University of Western Australia Perth WA 6009 Australia
- Ooid Scientific White Gum Valley WA 6163 Australia
| | - Laura L. Sosa
- School of Natural Sciences Bangor University Bangor LL57 2UW UK
| | - Belinda C. Martin
- UWA School of Biological Sciences The University of Western Australia Perth WA 6009 Australia
- Ooid Scientific White Gum Valley WA 6163 Australia
| | - Davey L. Jones
- School of Natural Sciences Bangor University Bangor LL57 2UW UK
- UWA School of Agriculture and Environment The University of Western Australia Perth WA 6009 Australia
| | - Deirdre B. Gleeson
- UWA School of Agriculture and Environment The University of Western Australia Perth WA 6009 Australia
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28
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Liu J, Ridgway HJ, Jones EE. Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential against Neonectria ditissima. J Appl Microbiol 2020; 128:1735-1753. [PMID: 31981438 DOI: 10.1111/jam.14587] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/29/2022]
Abstract
AIMS This research aimed to identify factors influencing endophyte community structure in apple shoots and the bioactivity of cultured representatives against the fungal pathogen Neonectria ditissima. METHODS AND RESULTS The endophyte community in leaves and stems of the apple cultivars 'Royal Gala' and 'Braeburn' were analysed by a cultivation-independent method (PCR-DGGE) which showed that tissue type, cultivar and site were determinant factors, with the endophyte taxa in 'Royal Gala' more variable than that in 'Braeburn', with leaf endophyte communities typically differing from stems in both cultivars. Seasonal (spring vs autumn) and regional (Nelson vs Hawke's Bay) variations were not obvious in woody stems. A collection of 783 bacterial and 87 fungal endophytes were recovered from leaves and stems of 'Royal Gala', 'Braeburn', 'Scilate' and/or 'Scifresh' from Nelson (nine sites) and Hawke's Bay (five sites) in spring and from Nelson (three sites) in autumn. A dual culture plating assay was used to test their ability to inhibit the mycelial growth of N. ditissima. Thirteen bacterial (mean of percent inhibition ≥20%) and 17 fungal isolates were antagonistic towards N. ditissima. These isolates belonged to the bacterial genera Bacillus and Pseudomonas, and fungal genera Chaetomium, Epicoccum, Biscogniauxia, Penicillium, Diaporthe, Phlyctema and two unidentified fungal isolates. CONCLUSIONS Endophyte communities in apple shoots were determined by tissue type, cultivar and site. Endophytic bacterial and fungal isolates inhibiting N. ditissima growth in vitro were found. SIGNIFICANCE AND IMPACT OF THE STUDY These results provided new evidence of factors influencing apple endophyte community in New Zealand. Endophytes with potential to reduce N. ditissima infection were identified, with the potential to be developed into a biocontrol strategy for European canker.
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Affiliation(s)
- J Liu
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
| | - H J Ridgway
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand.,The New Zealand Institute for Plant and Food Research Ltd, Christchurch, New Zealand
| | - E E Jones
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
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29
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Nuy JK, Hoetzinger M, Hahn MW, Beisser D, Boenigk J. Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients. Front Microbiol 2020; 11:154. [PMID: 32117171 PMCID: PMC7031163 DOI: 10.3389/fmicb.2020.00154] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/22/2020] [Indexed: 12/05/2022] Open
Abstract
Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e., physico-chemistry, presence of microeukaryotes and geographic position for the diversity and prevalence has not been investigated for both taxa before. Here, we present the first pan-European study on this topic, comprising 255 freshwater lakes. We investigated Limnohabitans and Polynucleobacter using an amplicon sequencing approach of partial 16S rRNA genes along environmental gradients. We show that physico-chemical factors had the greatest impact on both genera. Analyses on environmental gradients revealed an exceptionally broad ecological spectrum of operational taxonomic units (OTUs). Despite the coarse resolution of the genetic marker, we found OTUs with contrasting environmental preferences within Polynucleobacter and Limnohabitans subclusters. Such an ecological differentiation has been characterized for PnecC and LimC before but was so far unknown for less well studied subclusters such as PnecA and PnecB. Richness and abundance of OTUs are geographically clustered, suggesting that geographic diversity patterns are attributable to region-specific physico-chemical characteristics (e.g., pH and temperature) rather than latitudinal gradients or lake sizes.
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Affiliation(s)
- Julia K Nuy
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
| | - Matthias Hoetzinger
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg Essen, Essen, Germany
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30
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Chen J, Wang P, Wang C, Wang X, Miao L, Liu S, Yuan Q, Sun S. Distinct Assembly Mechanisms Underlie Similar Biogeographic Patterns of Rare and Abundant Bacterioplankton in Cascade Reservoirs of a Large River. Front Microbiol 2020; 11:158. [PMID: 32117173 PMCID: PMC7020914 DOI: 10.3389/fmicb.2020.00158] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/22/2020] [Indexed: 12/21/2022] Open
Abstract
Bacterioplankton communities commonly consist of few highly abundant species and a large number of rare species that play key roles in biogeochemical cycles of aquatic ecosystems. However, little is known about the biogeographic assemblies of these communities, especially in large rivers suffering from cascade dam regulation. Here, we used a 16S rRNA gene amplicon sequencing approach to investigate the biogeographic patterns and underlying assembly mechanisms of abundant and rare bacterioplankton taxa in cascade reservoirs of the Jinsha River in China. The results revealed species loss of bacterioplankton due to dam construction, which was more significant for rare taxa than for abundant ones. The distributions of abundant and rare taxa exhibited similar spatial and temporal patterns, which were significantly distinct between winter and summer and between upstream and downstream reservoirs. Both spatial (dispersal-related process) and environmental (selection process) factors seemed to together govern the assembly and biogeography of abundant and rare taxa, although both factors explained only a small fraction of variation in the rare taxa. More importantly, environmental factors explained more community variation in abundant sub-community than that in rare sub-community. Co-occurrence network analysis revealed that abundant species with closer interactions were more often located in a central position of the network compared with rare species. Nevertheless, half of the keystone species were rare species and may play important roles in maintaining the network stability. Overall, these findings indicate that distinct assembly mechanisms underlie the similar biogeography of rare and abundant bacteria in cascade reservoirs of a large river.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Shenghao Sun
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
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31
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Hylling O, Nikbakht Fini M, Ellegaard-Jensen L, Muff J, Madsen HT, Aamand J, Hansen LH. A novel hybrid concept for implementation in drinking water treatment targets micropollutant removal by combining membrane filtration with biodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133710. [PMID: 31756842 DOI: 10.1016/j.scitotenv.2019.133710] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
Groundwater extracted for drinking water production is commonly treated by aeration and sand filtration. However, this simple treatment is typically unable to remove pesticide residues. As a solution, bioaugmentation of sand filter units (i.e., the addition of specific degrader strains) has been proposed as an alternative "green" technology for targeted pesticide removal. However, the introduced degraders are challenged by (i) micropollutant levels of target residue, (ii) the oligotrophic environment and (iii) competition and predation by the native microorganisms, leading to loss of population and degradation potential. To overcome these challenges, we propose the introduction of a novel hybrid treatment step to the overall treatment process in which reverse osmosis filtration and biodegradation are combined to remove a target micropollutant. Here, the reverse osmosis produces a concentrated retentate that will act as a feed to a dedicated biofilter unit, intended to promote biodegradation potential and stability of an introduced degrader. Subsequently, the purified retentate will be re-mixed with the permeate from reverse osmosis, for re-mineralization and downstream consumption. In our study, we investigated the effect of reverse osmosis retentates on the degradation potential of an introduced degrader. This paper provides the first promising results of this hybrid concept using the 2,6-dichlorobenzamide (BAM)-degrading bacteria Aminobacter sp. MSH1 in batch experiments, spiked with radiolabeled BAM. The results showed an increased degradation potential of MSH1 in retentate waters versus untreated water. Colony-forming units and qPCR showed a stable MSH1 population, despite higher concentrations of salts and metals, and increased growth of native bacteria.
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Affiliation(s)
- Ole Hylling
- Aarhus University, Dept. Environmental Science, Section for Environmental Microbiology & Biotechnology, Roskilde, Denmark
| | - Mahdi Nikbakht Fini
- Aalborg University, Dept. of Chemistry and Bioscience/Section of Chemical Engineering, Esbjerg, Denmark
| | - Lea Ellegaard-Jensen
- Aarhus University, Dept. Environmental Science, Section for Environmental Microbiology & Biotechnology, Roskilde, Denmark
| | - Jens Muff
- Aalborg University, Dept. of Chemistry and Bioscience/Section of Chemical Engineering, Esbjerg, Denmark
| | - Henrik Tækker Madsen
- Aalborg University, Dept. of Chemistry and Bioscience/Section of Chemical Engineering, Esbjerg, Denmark; Saltkraft Aps, Sønderborg, Denmark
| | - Jens Aamand
- Geological Survey of Denmark & Greenland (GEUS), Dept. of Geochemistry, Copenhagen, Denmark
| | - Lars Hestbjerg Hansen
- Aarhus University, Dept. Environmental Science, Section for Environmental Microbiology & Biotechnology, Roskilde, Denmark; University of Copenhagen, Dept. of Plant- and Environmental Science, Section for Microbial Ecology and Biotechnology, Copenhagen, Denmark.
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Dedysh SN, Henke P, Ivanova AA, Kulichevskaya IS, Philippov DA, Meier‐Kolthoff JP, Göker M, Huang S, Overmann J. 100‐year‐old enigma solved: identification, genomic characterization and biogeography of the yet uncultured
Planctomyces bekefii. Environ Microbiol 2019; 22:198-211. [DOI: 10.1111/1462-2920.14838] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Svetlana N. Dedysh
- Winogradsky Institute of MicrobiologyResearch Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Petra Henke
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ‐GermanCollection of Microorganisms and Cell Cultures Braunschweig Germany
| | - Anastasia A. Ivanova
- Winogradsky Institute of MicrobiologyResearch Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Irina S. Kulichevskaya
- Winogradsky Institute of MicrobiologyResearch Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland WatersRussian Academy of Sciences Borok 152742 Russia
| | - Jan P. Meier‐Kolthoff
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ‐GermanCollection of Microorganisms and Cell Cultures Braunschweig Germany
| | - Markus Göker
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ‐GermanCollection of Microorganisms and Cell Cultures Braunschweig Germany
| | - Sixing Huang
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ‐GermanCollection of Microorganisms and Cell Cultures Braunschweig Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ‐GermanCollection of Microorganisms and Cell Cultures Braunschweig Germany
- Braunschweig University of Technology Braunschweig Germany
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Seasonal dynamics of aerobic anoxygenic phototrophs in freshwater lake Vlkov. Folia Microbiol (Praha) 2019; 64:705-710. [DOI: 10.1007/s12223-019-00735-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/15/2019] [Indexed: 11/25/2022]
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Li X, Garbeva P, Liu X, Klein Gunnewiek PJA, Clocchiatti A, Hundscheid MPJ, Wang X, de Boer W. Volatile-mediated antagonism of soil bacterial communities against fungi. Environ Microbiol 2019; 22:1025-1035. [PMID: 31580006 PMCID: PMC7064993 DOI: 10.1111/1462-2920.14808] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 11/30/2022]
Abstract
Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil‐borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non‐sterile soil inoculums during exposure to volatiles emitted by soil‐derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile‐mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.
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Affiliation(s)
- Xiaogang Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.,Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Xiaojiao Liu
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Paulien J A Klein Gunnewiek
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Anna Clocchiatti
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Maria P J Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Xingxiang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
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35
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Lawrence JR, Waiser MJ, Swerhone GD, Roy JL, Paule A, Korber DR. N,N-Diethyl-m-Toluamide Exposure at an Environmentally Relevant Concentration Influences River Microbial Community Development. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:2414-2425. [PMID: 31365141 PMCID: PMC6856691 DOI: 10.1002/etc.4550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/29/2019] [Accepted: 07/26/2019] [Indexed: 06/10/2023]
Abstract
Studies of the South Saskatchewan River confirmed that N,N-diethyl-m-toluamide (DEET) is ubiquitous at 10 to 20 ng/L, whereas in effluent-dominated Wascana Creek, levels of 100 to 450 ng/L were observed. Effects of DEET exposure were assessed in microbial communities using a wide variety of measures. Communities developed in rotating annular reactors with either 100 or 500 ng/L DEET, verified using gas chromatography-mass spectrometry analyses. Microscale analyses indicated that both DEET concentrations resulted in significant (p < 0.05) declines in photosynthetic biomass, whereas bacterial biomass was unaffected. There was no detectable effect of DEET on the levels of chlorophyll a. However, pigment analyses indicated substantial shifts in algal-cyanobacterial community structure, with reductions of green algae and some cyanobacterial groups at 500 ng/L DEET. Protozoan/micrometazoan grazers increased in communities exposed to 500 ng/L, but not 100 ng/L, DEET. Based on thymidine incorporation or utilization of carbon sources, DEET had no significant effects on metabolic activities. Fluorescent lectin-binding analyses showed significant (p < 0.05) changes in glycoconjugate composition at both DEET concentrations, consistent with altered community structure. Principal component cluster analyses of denaturing gradient gel electrophoresis indicated that DEET exposure at either concentration significantly changed the bacterial community (p < 0.05). Analyses based on 16S ribosomal RNA of community composition confirmed changes with DEET exposure, increasing detectable beta-proteobacteria, whereas actinobacteria and acidimicrobia became undetectable. Further, cyanobacteria in the subclass Oscillatoriophycideae were similarly not detected. Thus, DEET can alter microbial community structure and function, supporting the need for further evaluation of its effects in aquatic habitats. Environ Toxicol Chem 2019;38:2414-2425. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
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Affiliation(s)
- John R. Lawrence
- Environment and Climate Change CanadaSaskatoonSaskatchewanCanada
| | - Marley J. Waiser
- Environment and Climate Change CanadaSaskatoonSaskatchewanCanada
| | | | - Julie L. Roy
- Environment and Climate Change CanadaSaskatoonSaskatchewanCanada
| | - Armelle Paule
- Global Institute for Water SecurityUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Darren R. Korber
- Department of Food and Bioproducts SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
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36
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Vieira S, Sikorski J, Gebala A, Boeddinghaus RS, Marhan S, Rennert T, Kandeler E, Overmann J. Bacterial colonization of minerals in grassland soils is selective and highly dynamic. Environ Microbiol 2019; 22:917-933. [DOI: 10.1111/1462-2920.14751] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/14/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Selma Vieira
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B, 38124 Braunschweig Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B, 38124 Braunschweig Germany
| | - Aurelia Gebala
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Runa S. Boeddinghaus
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Sven Marhan
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Thilo Rennert
- Department of Soil Chemistry and PedologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Ellen Kandeler
- Department of Soil BiologyUniversity of Hohenheim, Institute of Soil Science and Land Evaluation Emil‐Wolff‐Straße 27, 70599 Stuttgart Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B, 38124 Braunschweig Germany
- Braunschweig University of Technology Braunschweig Germany
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37
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Goetghebuer L, Bonal M, Faust K, Servais P, George IF. The Dynamic of a River Model Bacterial Community in Two Different Media Reveals a Divergent Succession and an Enhanced Growth of Most Strains Compared to Monocultures. MICROBIAL ECOLOGY 2019; 78:313-323. [PMID: 30680433 DOI: 10.1007/s00248-019-01322-w] [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: 10/13/2018] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
The dynamic of a community of 20 bacterial strains isolated from river water was followed in R2 broth and in autoclaved river water medium for 27 days in batch experiments. At an early stage of incubation, a fast-growing specialist strain, Acinetobater sp., dominated the community in both media. Later on, the community composition in both media diverged but was highly reproducible across replicates. In R2, several strains previously reported to degrade multiple simple carbon sources prevailed. In autoclaved river water, the community was more even and became dominated by several strains growing faster or exclusively in that medium. Those strains have been reported in the literature to degrade complex compounds. Their growth rate in the community was 1.5- to 7-fold greater than that observed in monoculture. Furthermore, those strains developed simultaneously in the community. Together, our results suggest the existence of cooperative interactions within the community incubated in autoclaved river water.
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Affiliation(s)
- Lise Goetghebuer
- Ecology of Aquatic Systems, Université libre de Bruxelles, Campus Plaine, CP 221, 1050, Brussels, Belgium
| | - Mathias Bonal
- Ecology of Aquatic Systems, Université libre de Bruxelles, Campus Plaine, CP 221, 1050, Brussels, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), Katholieke Universiteit Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Pierre Servais
- Ecology of Aquatic Systems, Université libre de Bruxelles, Campus Plaine, CP 221, 1050, Brussels, Belgium
| | - Isabelle F George
- Ecology of Aquatic Systems, Université libre de Bruxelles, Campus Plaine, CP 221, 1050, Brussels, Belgium.
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38
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Kiersztyn B, Chróst R, Kaliński T, Siuda W, Bukowska A, Kowalczyk G, Grabowska K. Structural and functional microbial diversity along a eutrophication gradient of interconnected lakes undergoing anthropopressure. Sci Rep 2019; 9:11144. [PMID: 31366993 PMCID: PMC6668414 DOI: 10.1038/s41598-019-47577-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
We present the results of an analysis of the 16S rRNA-based taxonomical structure of bacteria together with an analysis of carbon source utilization ability using EcoPlate (Biolog, USA) metabolic fingerprinting assessment against the backdrop of physicochemical parameters in fifteen interconnected lakes. The lakes exhibit a wide spectrum of trophic gradients and undergo different intensities of anthropopressure. Sequences of V3–V4 16S rRNA genes binned by taxonomic assignment to family indicated that bacterial communities in the highly eutrophicated lakes were distinctly different from the bacterial communities in the meso-eutrophic lakes (ANOSIM r = 0.99, p = 0.0002) and were characterized by higher richness and more diverse taxonomical structure. Representatives of the Actinobacteria, Proteobacteria, Cyanobacteria, Planctomycetes, Verrucomicrobia, Bacteroides phyla predominated. In most cases their relative abundance was significantly correlated with lake trophic state. We found no similar clear relationship of community-level physiological profiling with lake trophic state. However, we found some significant links between the taxonomic and metabolic structure of the microbes in the studied lakes (Mantel’s correlation r = 0.22, p = 0.006). The carbon source utilization ability of the studied microorganisms was affected not only by the taxonomic groups present in the lakes but also by various characteristics like a high PO43− concentration inhibiting the utilization of phosphorylated carbon.
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Affiliation(s)
- Bartosz Kiersztyn
- Microbial Ecology and Environmental Biotechnology Department, Institute of Botany, Faculty of Biology, University of Warsaw; Biological and Chemical Research Centre, Warszawa, Poland.
| | - Ryszard Chróst
- Microbial Ecology and Environmental Biotechnology Department, Institute of Botany, Faculty of Biology, University of Warsaw; Biological and Chemical Research Centre, Warszawa, Poland
| | - Tomasz Kaliński
- Microbial Ecology and Environmental Biotechnology Department, Institute of Botany, Faculty of Biology, University of Warsaw; Biological and Chemical Research Centre, Warszawa, Poland
| | - Waldemar Siuda
- Microbial Ecology and Environmental Biotechnology Department, Institute of Botany, Faculty of Biology, University of Warsaw; Biological and Chemical Research Centre, Warszawa, Poland
| | - Aleksandra Bukowska
- Microbial Ecology and Environmental Biotechnology Department, Institute of Botany, Faculty of Biology, University of Warsaw; Biological and Chemical Research Centre, Warszawa, Poland
| | - Grzegorz Kowalczyk
- Microbial Ecology and Environmental Biotechnology Department, Institute of Botany, Faculty of Biology, University of Warsaw; Biological and Chemical Research Centre, Warszawa, Poland
| | - Karolina Grabowska
- Microbial Ecology and Environmental Biotechnology Department, Institute of Botany, Faculty of Biology, University of Warsaw; Biological and Chemical Research Centre, Warszawa, Poland
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39
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Avilez C, Alfaro MA, Salazar F, Encina C, Verdugo C, Martínez O, Collins MT, Salgado M. Fate of Mycobacterium avium subsp. paratuberculosis and changes in bacterial diversity populations in dairy slurry after chemical treatments. J Appl Microbiol 2019; 127:370-378. [PMID: 31009147 DOI: 10.1111/jam.14288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 11/27/2022]
Abstract
AIMS A major drawback of using dairy slurry as fertilizer is that it may contains pathogens such as Mycobacterium avium subsp. paratuberculosis (MAP), and it could represent a risk to animal and public health. Thus, the aim of this study was to evaluate the fate of MAP and bacterial communities in dairy slurry after chemical treatments. METHODS AND RESULTS Cattle slurry, naturally contaminated with MAP, was collected from a dairy herd and divided into 32 glass bottles which were assigned to eight different treatments (control, 3·0% CaO, 0·5% NaOH; 0·087%, 0·11% and 0·14% H2 SO4 ; and 1·0 and 2·5% KMnO4 ). Treated dairy slurry samples were evaluated at 0, 1, 3, 7, 15, 30 and 60-days following treatment application for viable MAP and dairy slurry pH, and in addition temperature in this material was monitored continuously. Bacterial counts were estimated at each sampling time. A Bayesian zero-inflated Poisson mixed model was fitted to assess the effect of each treatment on the count of MAP cells. Model results indicated that only the 3·0% CaO treatment had a statistically important negative effect on MAP counts during the study period. For most treatments, MAP was undetectable immediately after chemical treatment but re-appeared over time, in some replicates at low concentrations. However, in those cases MAP counts were not statistically different than the control treatment. Regarding the fate of the other bacterial populations, the Firmicutes phylum was the dominant population in the un-treated slurry while Clostridia class members were among the most prevalent bacteria after the application of most chemical treatments. CONCLUSION Only 3% CaO treatment had a statistically important negative effect on MAP viability in cattle slurry. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides evidence of MAP partial control in dairy slurry. This information should be considered as a best management practice to reduce MAP and other pathogens for slurry management on dairy farms.
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Affiliation(s)
- C Avilez
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile.,Facultad de Ciencias Veterinarias, Escuela de Graduados, Universidad Austral de Chile, Valdivia, Chile
| | - M A Alfaro
- Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Remehue, Osorno, Chile
| | - F Salazar
- Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Remehue, Osorno, Chile
| | - C Encina
- OMICS, Universidad Austral de Chile, Valdivia, Chile
| | - C Verdugo
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile
| | - O Martínez
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | - M T Collins
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - M Salgado
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile
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40
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Shen L, Ouyang L, Zhu Y, Trimmer M. Spatial separation of anaerobic ammonium oxidation and nitrite‐dependent anaerobic methane oxidation in permeable riverbeds. Environ Microbiol 2019; 21:1185-1195. [DOI: 10.1111/1462-2920.14554] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural MeteorologyDepartment of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology Nanjing 210044 China
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Liao Ouyang
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Yizhu Zhu
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Mark Trimmer
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
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41
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Piwosz K, Shabarova T, Tomasch J, Šimek K, Kopejtka K, Kahl S, Pieper DH, Koblížek M. Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS). THE ISME JOURNAL 2018; 12:2640-2654. [PMID: 29980795 PMCID: PMC6194029 DOI: 10.1038/s41396-018-0213-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/01/2018] [Accepted: 06/09/2018] [Indexed: 01/07/2023]
Abstract
The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria.
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Affiliation(s)
- Kasia Piwosz
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic
| | - Tanja Shabarova
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, 37005, Česke Budějovice, Czech Republic
| | - Jürgen Tomasch
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Karel Šimek
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, 37005, Česke Budějovice, Czech Republic
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, CZ-37005, České Budějovice, Czech Republic
| | - Silke Kahl
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Dietmar H Pieper
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, Novohradská 237, 37981, Třeboň, Czech Republic.
- Faculty of Science, University of South Bohemia in České Budějovice, CZ-37005, České Budějovice, Czech Republic.
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Paver SF, Muratore D, Newton RJ, Coleman ML. Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems. mSystems 2018; 3:e00232-18. [PMID: 30443603 PMCID: PMC6234284 DOI: 10.1128/msystems.00232-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022] Open
Abstract
Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change. IMPORTANCE The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.
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Affiliation(s)
- Sara F. Paver
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Daniel Muratore
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Maureen L. Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
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43
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Bock C, Salcher M, Jensen M, Pandey RV, Boenigk J. Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes. Front Microbiol 2018; 9:1290. [PMID: 29963032 PMCID: PMC6014231 DOI: 10.3389/fmicb.2018.01290] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/28/2018] [Indexed: 01/15/2023] Open
Abstract
Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray-Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.
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Affiliation(s)
- Christina Bock
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Michaela Salcher
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland.,Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Manfred Jensen
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Ram Vinay Pandey
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Vienna, Austria.,Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Jens Boenigk
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
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44
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Tandon K, Yang SH, Wan MT, Yang CC, Baatar B, Chiu CY, Tsai JW, Liu WC, Tang SL. Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan. Microbes Environ 2018; 33:120-126. [PMID: 29681561 PMCID: PMC6031399 DOI: 10.1264/jsme2.me17148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes—located 21 km apart and with disparate trophic characteristics—and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica.,Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University
| | | | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd
| | | | | | | | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University
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Cryptophyta as major bacterivores in freshwater summer plankton. ISME JOURNAL 2018; 12:1668-1681. [PMID: 29463895 PMCID: PMC6018765 DOI: 10.1038/s41396-018-0057-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023]
Abstract
Small bacterivorous eukaryotes play a cardinal role in aquatic food webs and their taxonomic classification is currently a hot topic in aquatic microbial ecology. Despite increasing interest in their diversity, core questions regarding predator–prey specificity remain largely unanswered, e.g., which heterotrophic nanoflagellates (HNFs) are the main bacterivores in freshwaters and which prokaryotes support the growth of small HNFs. To answer these questions, we fed natural communities of HNFs from Římov reservoir (Czech Republic) with five different bacterial strains of the ubiquitous betaproteobacterial genera Polynucleobacter and Limnohabitans. We combined amplicon sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting eukaryotic 18 S rRNA genes to track specific responses of the natural HNF community to prey amendments. While amplicon sequencing provided valuable qualitative data and a basis for designing specific probes, the number of reads was insufficient to accurately quantify certain eukaryotic groups. We also applied a double-hybridization technique that allows simultaneous phylogenetic identification of both predator and prey. Our results show that community composition of HNFs is strongly dependent upon prey type. Surprisingly, Cryptophyta were the most abundant bacterivores, although this phylum has been so far assumed to be mainly autotrophic. Moreover, the growth of a small lineage of Cryptophyta (CRY1 clade) was strongly stimulated by one Limnohabitans strain in our experiment. Thus, our study is the first report that colorless Cryptophyta are major bacterivores in summer plankton samples and can play a key role in the carbon transfer from prokaryotes to higher trophic levels.
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Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans. Appl Environ Microbiol 2017; 84:AEM.02116-17. [PMID: 29030444 DOI: 10.1128/aem.02116-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/07/2017] [Indexed: 11/20/2022] Open
Abstract
The genus Limnohabitans (Comamonadaceae, Betaproteobacteria) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genes pufLM and bchY in 28 of 46 strains from three Limnohabitans lineages. The pufM sequences obtained are very closely related to environmental pufM sequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophic Limnohabitans in nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic Limnohabitans strains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus Limnohabitans and also among all potentially photosynthetic Betaproteobacteria strains. The expression of photosynthetic complexes was detected in a culture of Limnohabitans planktonicus II-D5T using spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescent in situ hybridization.IMPORTANCE The data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genus Limnohabitans, indicating that they may have a novel role in freshwater habitats.
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Yasuda T, Waki M, Fukumoto Y, Hanajima D, Kuroda K, Suzuki K, Matsumoto T, Uenishi H. Community structure of denitrifying and total bacteria during nitrogen accumulation in an ammonia‐loaded biofilter. J Appl Microbiol 2017; 123:1498-1511. [DOI: 10.1111/jam.13603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 09/26/2017] [Accepted: 09/30/2017] [Indexed: 11/29/2022]
Affiliation(s)
- T. Yasuda
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - M. Waki
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - Y. Fukumoto
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - D. Hanajima
- Hokkaido Agricultural Research Center National Agriculture and Food Research Organization Sapporo Hokkaido Japan
| | - K. Kuroda
- Kyushu Okinawa Agricultural Research Center National Agriculture and Food Research Organization Koshi Kumamoto Japan
| | - K. Suzuki
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - T. Matsumoto
- Institute of Crop Science National Agricultural and Food Research Organization Tsukuba Ibaraki Japan
| | - H. Uenishi
- Institute of Agrobiological Sciences National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
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Antiqueira PAP, Petchey OL, Romero GQ. Warming and top predator loss drive ecosystem multifunctionality. Ecol Lett 2017; 21:72-82. [PMID: 29098798 DOI: 10.1111/ele.12873] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/17/2017] [Accepted: 10/04/2017] [Indexed: 11/29/2022]
Abstract
Global change affects ecosystem functioning both directly by modifications in physicochemical processes, and indirectly, via changes in biotic metabolism and interactions. Unclear, however, is how multiple anthropogenic drivers affect different components of community structure and the performance of multiple ecosystem functions (ecosystem multifunctionality). We manipulated small natural freshwater ecosystems to investigate how warming and top predator loss affect seven ecosystem functions representing two major dimensions of ecosystem functioning, productivity and metabolism. We investigated their direct and indirect effects on community diversity and standing stock of multitrophic macro and microorganisms. Warming directly increased multifunctional ecosystem productivity and metabolism. In contrast, top predator loss indirectly affected multifunctional ecosystem productivity via changes in the diversity of detritivorous macroinvertebrates, but did not affect ecosystem metabolism. In addition to demonstrating how multiple anthropogenic drivers have different impacts, via different pathways, on ecosystem multifunctionality components, our work should further spur advances in predicting responses of ecosystems to multiple simultaneous environmental changes.
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Affiliation(s)
- Pablo Augusto P Antiqueira
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Owen L Petchey
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Gustavo Quevedo Romero
- Departamento de Biologia Animal, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.,Brazilian Research Network on Climate Change (Rede Clima)
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The Limnohabitans Genus Harbors Generalistic and Opportunistic Subtypes: Evidence from Spatiotemporal Succession in a Canyon-Shaped Reservoir. Appl Environ Microbiol 2017; 83:AEM.01530-17. [PMID: 28842542 DOI: 10.1128/aem.01530-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/22/2017] [Indexed: 11/20/2022] Open
Abstract
We studied the diversity of Limnohabitans using reverse line blot hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov reservoir (Czech Republic). To examine the succession of distinct lineages, we performed (i) a study of an intensive spring sampling program at the lacustrine part of the Římov reservoir (from ice melt through a phytoplankton peak to the clear-water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the compositions of distinct Limnohabitans lineages allowed for the identification of "generalists" that were always present throughout the whole season as well as "specialists" that appeared in the reservoir only for limited periods of time or irregularly. Our results indicate that some phytoplankton groups, such as cryptophytes or cyanobacteria, and zooplankton composition were the major factors modulating the distribution and dynamics of distinct Limnohabitans lineages. The highest Limnohabitans diversity was observed during the spring algal bloom, whereas the lowest was during the summer cyanobacterial bloom. The microdiversity also markedly increased upstream in the reservoir, being highest at the inflow, and thus likely reflecting strong influences of the watershed.IMPORTANCE The genus Limnohabitans is a typical freshwater bacterioplankton and is believed to play a significant role in inland freshwater habitats. This work is unique in detecting and tracing different closely related lineages of this bacterial genus in its natural conditions using the semiquantitative reverse line blot hybridization method and in discovering the factors influencing the microdiversity, subtype alternations, and seasonality.
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50
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Cai W, Li Y, Niu L, Zhang W, Wang C, Wang P, Meng F. New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures. WATER RESEARCH 2017; 123:495-504. [PMID: 28689132 DOI: 10.1016/j.watres.2017.06.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/17/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
The composition and distribution characteristics of bacterial communities in biofilms attached to hydraulic concrete structure (HCS) surfaces were investigated for the first time in four reservoirs in the middle and lower reaches of the Yangtze River Basin using 16S rRNA Miseq sequencing. High microbial diversity was found in HCS biofilms, and notable differences were observed in different types of HCS. Proteobacteria, Cyanobacteria and Chloroflexi were the predominant phyla, with respective relative abundances of 35.3%, 25.4% and 13.0%. The three most abundant genera were Leptolyngbya, Anaerolineaceae and Polynucleobacter. The phyla Beta-proteobacteria and Firmicutes and genus Lyngbya were predominant in CGP, whereas the phyla Cyanobacteria and Chloroflexi and genera Leptolyngbya, Anaerolinea and Polynucleobacter survived better in land walls and bank slopes. Dissolved oxygen, ammonia nitrogen and temperature were characterized as the main factors driving the bacterial community composition. The most abundant groups of metabolic functions were also identified as ammonia oxidizers, sulphate reducers, and dehalogenators. Additionally, functional groups related to biocorrosion were found to account for the largest proportion (14.0% of total sequences) in gate piers, followed by those in land walls (11.5%) and bank slopes (10.2%). Concrete gate piers were at the greatest risk of biocorrosion with the most abundant negative bacterial groups, especially for sulphate reducers. Thus, it should be paid high attention to the biocorrosion prevention of concrete gate piers. Overall, this study contributed to the optimization of microbial control and the improvement of the safety management for water conservation structures.
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Affiliation(s)
- Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
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