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Shao Q, Lin Z, Zhou C, Yan X. Bacterioplankton assembly and interspecies interactions follow trajectories of Gymnodinium-diatom bloom. MARINE ENVIRONMENTAL RESEARCH 2020; 160:105010. [PMID: 32907730 DOI: 10.1016/j.marenvres.2020.105010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
The underlying mechanisms of bacterioplankton community assembly and interspecies interactions during harmful algal blooms remain largely unclear. Using 16S rRNA gene amplicon sequencing, we analyzed the bacterioplankton communities over the continuous course of saxitoxin-producing Gymnodinium catenatum blooms and two diatom (i.e., Skeletonema costatum and Chaetoceros curvisetus) blooms in an anthropogenically controlled and eutrophic bay, East China Sea. The succession of bacterioplankton communities correlated with changes in the dynamics of algal species. Deterministic versus stochastic bacterioplankton community assemblage processes were quantified, demonstrating that stochastic processes increased when algal blooms happened. The occurrence of algal blooms caused weaker bacterioplankton interspecies interactions and higher degrees of cooperative activities, changed keystone taxa and diminished the stability of bacterial communities. These findings consequently have important implications for our understanding of bacterioplankton community ecology during algal blooms.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Zhongzhou Lin
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Chengxu Zhou
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
| | - Xiaojun Yan
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
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Adyasari D, Hassenrück C, Montiel D, Dimova N. Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD). PLoS One 2020; 15:e0235235. [PMID: 32598345 PMCID: PMC7323985 DOI: 10.1371/journal.pone.0235235] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/10/2020] [Indexed: 11/18/2022] Open
Abstract
Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.
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Affiliation(s)
- Dini Adyasari
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Christiane Hassenrück
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Daniel Montiel
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
- Geosyntec Consultants, Clearwater, FL, United States of America
| | - Natasha Dimova
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
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Linking Shifts in Bacterial Community Composition and Function with Changes in the Dissolved Organic Matter Pool in Ice-Covered Baiyangdian Lake, Northern China. Microorganisms 2020; 8:microorganisms8060883. [PMID: 32545218 PMCID: PMC7357102 DOI: 10.3390/microorganisms8060883] [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: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023] Open
Abstract
The relationship between CDOM (Chromophoric dissolved organic matter) and the bacterial community was investigated in ice-covered Baiyangdian Lake. The results showed that environmental parameters significantly differed in Baiyangdian Lake, whereas a-diversity was not significantly different. Moreover, the microbial and functional communities exhibited significant differences, and T (Temperature), pH, ORP (Oxidation-reduction potential), DO (Dissolved oxygen), NO3−-N, NH4+-N, and Mn (Manganese) were the main environmental factors of these differences, based on redundancy analysis and the Mantel test. Biomarkers of the microbial and functional communities were investigated through linear discriminant analysis effect size and STAMP analysis. The number of biomarkers in the natural area was highest among the typical zones, and most top functions were related to carbohydrate metabolism. Two protein-like components (C1 and C2) and one humic-like component (C3) were identified by parallel factor analysis, and C1 was positively related to C2 (R = 0.99, p < 0.001), indicating the same sources. Moreover, CDOM significantly differed among the typical zones (p < 0.001). The high biological index, fluorescence index, β:α, and low humification index indicated a strong autochthonous component and aquatic bacterial origin, which was consistent with the results of UV-vis absorption spectroscopy. Network analysis revealed non-random co-occurrence patterns. The bacterial and functional communities interacted closely with CDOM. The dominant genera were CL500-29_marine_group, Flavobacterium, Limnohabitans, and Candidatus_Aquirestis. Random forest analysis showed that C1, C2, and C3 are important predictors of α- and β-diversity in the water bacterial community and its functional composition. This study provides insight into the interaction between bacterial communities and DOM (Dissolved organic matter) in ice-covered Baiyangdian Lake.
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Jankowiak JG, Gobler CJ. The Composition and Function of Microbiomes Within Microcystis Colonies Are Significantly Different Than Native Bacterial Assemblages in Two North American Lakes. Front Microbiol 2020; 11:1016. [PMID: 32547511 PMCID: PMC7270213 DOI: 10.3389/fmicb.2020.01016] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
The toxic cyanobacterium Microcystis is one of the most pervasive harmful algal bloom (HAB) genera and naturally occurs in large colonies known to harbor diverse heterotrophic bacterial assemblages. While colony-associated microbiomes may influence Microcystis blooms, there remains a limited understanding of the structure and functional potential of these communities and how they may be shaped by changing environmental conditions. To address this gap, we compared the dynamics of Microcystis-attached (MCA), free-living (FL), and whole water (W) microbiomes during Microcystis blooms using next-generation amplicon sequencing (16S rRNA), a predictive metagenome software, and other bioinformatic approaches. Microbiomes were monitored through high resolution spatial-temporal surveys across two North American lakes, Lake Erie (LE) and Lake Agawam (LA; Long Island, NY, United States) in 2017, providing the largest dataset of these fractions to date. Sequencing of 126 samples generated 7,922,628 sequences that clustered into 7,447 amplicon sequence variants (ASVs) with 100% sequence identity. Across lakes, the MCA microbiomes were significantly different than the FL and W fractions being significantly enriched in Gemmatimonadetes, Burkholderiaceae, Rhizobiales, and Cytophagales and depleted of Actinobacteria. Further, although MCA communities harbored > 900 unique ASVs, they were significantly less diverse than the other fractions with diversity inversely related to bloom intensity, suggesting increased selection pressure on microbial communities as blooms intensified. Despite taxonomic differences between lakes, predicted metagenomes revealed conserved functional potential among MCA microbiomes. MCA communities were significantly enriched in pathways involved in N and P cycling and microcystin-degradation. Taxa potentially capable of N2-fixation were significantly enriched (p < 0.05) and up to four-fold more abundant within the MCA faction relative to other fractions, potentially aiding in the proliferation of Microcystis blooms during low N conditions. The MCA predicted metagenomes were conserved over 8 months of seasonal changes in temperature and N availability despite strong temporal succession in microbiome composition. Collectively, these findings indicate that Microcystis colonies harbor a statistically distinct microbiome with a conserved functional potential that may help facilitate bloom persistence under environmentally unfavorable conditions.
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Affiliation(s)
- Jennifer G. Jankowiak
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
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Marmen S, Blank L, Al-Ashhab A, Malik A, Ganzert L, Lalzar M, Grossart HP, Sher D. The Role of Land Use Types and Water Chemical Properties in Structuring the Microbiomes of a Connected Lake System. Front Microbiol 2020; 11:89. [PMID: 32117119 PMCID: PMC7029742 DOI: 10.3389/fmicb.2020.00089] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/15/2020] [Indexed: 02/04/2023] Open
Abstract
Lakes and other freshwater bodies are intimately connected to the surrounding land, yet to what extent land-use affects the quality of freshwater and the microbial communities living in various freshwater environments is largely unknown. We address this question through an analysis of the land use surrounding 46 inter-connected lakes located within seven different drainage basins in northern Germany, and the microbiomes of these lakes during early summer. Lake microbiome structure was not correlated with the specific drainage basin or by basin size, and bacterial distribution did not seem to be limited by distance. Instead, land use within the drainage basin could predict, to some extent, NO2 + NO3 concentrations in the water, which (together with temperature, chlorophyll a and total phosphorus) correlated to some extent with the water microbiome structure. Land use directly surrounding the water bodies, however, had little observable effects on water quality or the microbiome. Several microbial lineages, including Cyanobacteria and Verrucomicrobia, were differentially partitioned between the lakes. Significantly more data, including time-series measurements of land use and water chemical properties, are needed to fully understand the interaction between the environment and the organization of microbial communities.
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Affiliation(s)
- Sophi Marmen
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Lior Blank
- Department of Plant Pathology and Weed Research, ARO, Volcani Center, Rishon Lezion, Israel
| | - Ashraf Al-Ashhab
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Microbial Metagenomics Division, Dead Sea and Arava Science Center, Masada, Israel
| | - Assaf Malik
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Lars Ganzert
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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Lukwambe B, Zhao L, Nicholaus R, Yang W, Zhu J, Zheng Z. Bacterioplankton community in response to biological filters (clam, biofilm, and macrophytes) in an integrated aquaculture wastewater bioremediation system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113035. [PMID: 31421576 DOI: 10.1016/j.envpol.2019.113035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/29/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Integrated systems with appropriate bio-filters can be used to treat aquaculture effluents. However, the information on bio-filters that alters the ecological functions of the bacterioplankton community (BC) in biodegradation of the aquaculture effluents remains controversial. In this study, we implemented a comprehensive restoration technology combined with bio-filters [biofilm, clam (Tegillarca granosa), and macrophytes (Spartina anglica)] to investigate their influence on the stability of the BC and nutrient removal. We found that the diversity of BC was linked with biogeochemical factors in processing and upcycling nitrogen-rich effluents into high-value biomass. The BC exhibited significant distinct patterns in the bio-filter areas. Potential biomarkers for constrained harmfully algae-bacteria (Nitriliruptoraceae, Bacillales, and Rhodobacteraceae) and nutrient removal were significantly higher in the bio-filters areas. The bio-filters significantly promoted the restoration effects of N and P balance by reducing 82.34% of total nitrogen (TN) and 81.64% of total phosphorus (TP) loads at the water interface. The main mechanisms for TN and TP removal and nutrient transformation were achieved by assimilation and absorption by the emergent macrophytes (Spartina anglica). The bio-filters significantly influenced the biodegradability and resolvability of particulate organic matter through ammonification, nitrification, and denitrification of microbes, which meliorated the nutrient removal. Beside bio-filter effects, the BC was significantly controlled by abiotic factors [nitrate (NO3--N), dissolved oxygen (DO), total nitrogen (TN), and water temperature (WT)], and biotic factors (chlorophyll ɑ and green algae). Our study revealed that the co-existence system with bio-filters may greatly improve our understanding on the ecological functions of the BC in aquaculture systems. Overall, combined bio-filters provide an opportunity for the development of efficient and optimized aquaculture wastewater treatment technology.
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Affiliation(s)
- Betina Lukwambe
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China; Department of Food Science and Technology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Li Zhao
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Regan Nicholaus
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China; Department of Natural Sciences, Mbeya University of Science and Technology, Mbeya, Tanzania
| | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315832, China
| | - Jinyong Zhu
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315832, China
| | - Zhongming Zheng
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315832, China.
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57
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Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. MICROBIOME 2019; 7:135. [PMID: 31630686 DOI: 10.1101/670067v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/22/2023]
Abstract
The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
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Affiliation(s)
- Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
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Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. MICROBIOME 2019; 7:135. [PMID: 31630686 PMCID: PMC6802176 DOI: 10.1186/s40168-019-0752-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/20/2023]
Abstract
The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
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Affiliation(s)
- Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
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59
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Ji B, Liang J, Ma Y, Zhu L, Liu Y. Bacterial community and eutrophic index analysis of the East Lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:682-688. [PMID: 31185357 DOI: 10.1016/j.envpol.2019.05.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/18/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
This study investigated bacterial diversities in surface water and sediment of the East Lake located in Wuhan, China. Bacterial community of lake water was mainly composed of Proteobacteria (31.1%), Actinobacteria (25.0%), Bacteroidetes (18.6%), Cyanobacteria (18.9%), Planctomycetes (2.4%) and Verrucomicrobia (1.4%), while more abundant and richer bacterial community was found in the sediments, e.g. 46.1% for Proteobacteria, 10.1% for Bacteroidetes, 8.7% for Chloroflexi, 8.4% for Acidobacteria, 5.0% for Cyanobacteria, 3.6% for Firmicutes, 3.1% for Planctomycetes, 2.8% for Actinobacteria and 2.3% for Nitrospirae. The decreased bacterial community richness and abundance was found in poor-quality water. Moreover, Bacterial Eutrophic Index (BEI) was firstly put forward to quantitatively describe the water quality of a freshwater ecosystem, which was defined as the ratio of abundance of Cyanobacteria and Actinobacteria in water. It was demonstrated BEI was well correlated to Carlson's Trophic State Index (TSI) (Spearman's ρ = 0.848, p < 0.01). The average TSI and BEI were determined to be 64 and 0.81, suggesting that East Lake could be classified as a medium eutrophic level.
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Affiliation(s)
- Bin Ji
- Department of Water and Wastewater Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore.
| | - Jiechao Liang
- Department of Water and Wastewater Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yingqun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore
| | - Lin Zhu
- Department of Water and Wastewater Engineering, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yu Liu
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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60
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Cabello-Yeves PJ, Rodriguez-Valera F. Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome. MICROBIOME 2019; 7:117. [PMID: 31439042 PMCID: PMC6706942 DOI: 10.1186/s40168-019-0731-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND The adaptation of a marine prokaryote to live in freshwater environments or vice versa is generally believed to be an unusual and evolutionary demanding process. However, the reasons are not obvious given the similarity of both kinds of habitats. RESULTS We have found major differences at the level of the predicted metaproteomes of marine and freshwater habitats with more acidic values of the isoelectric points (pI) in marine microbes. Furthermore, by comparing genomes of marine-freshwater phylogenetic relatives, we have found higher pI values (basic shift) in the freshwater ones. This difference was sharper in secreted > cytoplasmic > membrane proteins. The changes are concentrated on the surface of soluble proteins. It is also detectable at the level of total amino acid composition and involves similarly core and flexible genome- encoded proteins. CONCLUSIONS The marked changes at the level of protein amino acid composition and pI provide a tool to predict the preferred habitat of a culture or a metagenome-assembled genome (MAG). The exact physiological explanation for such variations in the pIs and electrostatic surface potentials is not known yet. However, these changes might reflect differences in membrane bioenergetics derived from the absence of significant Na+ concentrations in most freshwater habitats. In any case, the changes in amino acid composition in most proteins imply that a long evolutionary time is required to adapt from one type of habitat to the other.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, 03550, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, 03550, Alicante, Spain.
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
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61
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Reynoso G, Smith MR, Holmes CP, Keelan CR, McGrath SE, Alvarez GH, Coceano MA, Eldridge KA, Fried HI, Gilbert NE, Harris MT, Kohler LR, Modolo CM, Murray EA, Polisetti SM, Sales DJ, Walsh ES, Steffen MM. Bacterial community structure and response to nitrogen amendments in Lake Shenandoah (VA, USA). WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 80:675-684. [PMID: 31661447 DOI: 10.2166/wst.2019.311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microbial processes are critical to the function of freshwater ecosystems, yet we still do not fully understand the factors that shape freshwater microbial communities. Furthermore, freshwater ecosystems are particularly susceptible to effects of environmental change, including influx of exogenous nutrients such as nitrogen and phosphorus. To evaluate the impact of nitrogen loading on the microbial community structure of shallow freshwater lakes, water samples collected from Lake Shenandoah (Virginia, USA) were incubated with two concentrations of either ammonium, nitrate, or urea as a nitrogen source. The potential impact of these nitrogen compounds on the bacterial community structure was assessed via 16S rRNA amplicon sequencing. At the phylum level, the dominant taxa in Lake Shenandoah were comprised of Actinobacteria and Proteobacteria, which were not affected by exposure to the various nitrogen treatments. Overall, there was not a significant shift in the diversity of the bacterial community of Lake Shenandoah with the addition of nitrogen sources, indicating this shallow system may be constrained by other environmental factors.
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Affiliation(s)
- G Reynoso
- James Madison University, Harrisonburg, VA 22807, USA E-mail: ; Current address: Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - M R Smith
- James Madison University, Harrisonburg, VA 22807, USA E-mail: ; Current address: Texas A&M University, College Station, TX 77843, USA
| | - C P Holmes
- James Madison University, Harrisonburg, VA 22807, USA E-mail: ; Current address: Texas A&M University, College Station, TX 77843, USA
| | - C R Keelan
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - S E McGrath
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - G H Alvarez
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - M A Coceano
- James Madison University, Harrisonburg, VA 22807, USA E-mail: ; Current address: University of Wyoming, Laramie, WY 82071, USA
| | - K A Eldridge
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - H I Fried
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - N E Gilbert
- James Madison University, Harrisonburg, VA 22807, USA E-mail: ; Current address: University of Tennessee, Knoxville, TN 37996, USA
| | - M T Harris
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - L R Kohler
- James Madison University, Harrisonburg, VA 22807, USA E-mail: ; Current address: University of Kentucky, Lexington, KY 40508, USA
| | - C M Modolo
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - E A Murray
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - S M Polisetti
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - D J Sales
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - E S Walsh
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
| | - M M Steffen
- James Madison University, Harrisonburg, VA 22807, USA E-mail:
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Maresca JA, Keffer JL, Hempel PP, Polson SW, Shevchenko O, Bhavsar J, Powell D, Miller KJ, Singh A, Hahn MW. Light Modulates the Physiology of Nonphototrophic Actinobacteria. J Bacteriol 2019; 201:e00740-18. [PMID: 30692175 PMCID: PMC6482932 DOI: 10.1128/jb.00740-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 11/20/2022] Open
Abstract
Light is a source of energy and an environmental cue that is available in excess in most surface environments. In prokaryotic systems, conversion of light to energy by photoautotrophs and photoheterotrophs is well understood, but the conversion of light to information and the cellular response to that information have been characterized in only a few species. Our goal was to explore the response of freshwater Actinobacteria, which are ubiquitous in illuminated aquatic environments, to light. We found that Actinobacteria without functional photosystems grow faster in the light, likely because sugar transport and metabolism are upregulated in the light. Based on the action spectrum of the growth effect and comparisons of the genomes of three Actinobacteria with this growth rate phenotype, we propose that the photosensor in these strains is a putative CryB-type cryptochrome. The ability to sense light and upregulate carbohydrate transport during the day could allow these cells to coordinate their time of maximum organic carbon uptake with the time of maximum organic carbon release by primary producers.IMPORTANCE Sunlight provides information about both place and time. In sunlit aquatic environments, primary producers release organic carbon and nitrogen along with other growth factors during the day. The ability of Actinobacteria to coordinate organic carbon uptake and utilization with production of photosynthate enables them to grow more efficiently in the daytime, and it potentially gives them a competitive advantage over heterotrophs that constitutively produce carbohydrate transporters, which is energetically costly, or produce transporters only after detection of the substrate(s), which delays their response. Understanding how light cues the transport of organic carbon and its conversion to biomass is key to understanding biochemical mechanisms within the carbon cycle, the fluxes through it, and the variety of mechanisms by which light enhances growth.
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Affiliation(s)
- Julia A Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Jessica L Keffer
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Priscilla P Hempel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Olga Shevchenko
- Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Jaysheel Bhavsar
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Deborah Powell
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Kelsey J Miller
- Department of Biology, University of Delaware, Newark, Delaware, USA
| | - Archana Singh
- Department of Biology, University of Delaware, Newark, Delaware, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
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63
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Ung P, Peng C, Yuk S, Tan R, Ann V, Miyanaga K, Tanji Y. Dynamics of bacterial community in Tonle Sap Lake, a large tropical flood-pulse system in Southeast Asia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:414-423. [PMID: 30754009 DOI: 10.1016/j.scitotenv.2019.01.351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/15/2019] [Accepted: 01/26/2019] [Indexed: 06/09/2023]
Abstract
Tonle Sap Lake, the largest freshwater body in Southeast Asia, plays an important role in lives and environment. The lake is reportedly under anthropogenic pressure and suffers from eutrophication. The floating villagers suffer from waterborne diseases. However, the shift in bacterial community due to human activities in this great lake has not yet been reported. We aimed to determine the dynamics of the bacterial community and their concentration in the lake using 67 surface waters, 53 sub-layer waters and 59 sediment samples by Next Generation Sequencing (NGS). The bacterial communities in the surface water and sub-layer water were similar but they differed from the sediment; however, their abundance showed spatiotemporal variations. The bacterial diversity reached the highest value in the dry season but lowest value in the rainy season in the surface water and sediment. Their diversity in the sub-layer water was highest in the transition from dry to rainy season. The total 16S rRNA gene copy number in the sediment were >100 times higher than that measured in the water. The Cyanobacteria, Actinobacteria, and Proteobacteria concentrations in the lake water increased in the dry season and reached a peak in the transition from dry to rainy season. The concentrations of Proteobacteria and Firmicutes elevated in the lake water and sediment, respectively, in the floating villages which were >10 times higher than the places with non-point sources. The bacterial concentration and its diversity in the Tonle Sap Lake changed based on the lake water volume between rainy and dry season. The bacterial concentration in the Tonle Sap Lake diluted with the water inflow from Mekong River and its tributaries in the rainy season. As influenced by the fecal waste, the bacterial community in the floating villages differed from the places with non-point source.
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Affiliation(s)
- Porsry Ung
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-15 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; Faculty of Chemical and Food Engineering, Institute of Technology of Cambodia, Russian Federation Blvd., P.O. Box 86, 12156 Phnom Penh, Cambodia
| | - Chanthol Peng
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-15 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; Faculty of Chemical and Food Engineering, Institute of Technology of Cambodia, Russian Federation Blvd., P.O. Box 86, 12156 Phnom Penh, Cambodia
| | - Sokunsreiroat Yuk
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-15 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; Faculty of Chemical and Food Engineering, Institute of Technology of Cambodia, Russian Federation Blvd., P.O. Box 86, 12156 Phnom Penh, Cambodia
| | - Reasmey Tan
- Food Technology and Nutrition Research Unit, Research and Innovation Center, Institute of Technology of Cambodia, Russian Federation Blvd., P.O. Box 86, 12156 Phnom Penh, Cambodia
| | - Vannak Ann
- Faculty of Hydrology and Water Resources Engineering, Institute of Technology of Cambodia, Russian Federation Blvd., P.O. Box 86, 12156 Phnom Penh, Cambodia
| | - Kazuhiko Miyanaga
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-15 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yasunori Tanji
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-15 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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64
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Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical 'helper' catalase. ISME JOURNAL 2019; 13:2252-2263. [PMID: 31073214 DOI: 10.1038/s41396-019-0432-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 03/18/2019] [Accepted: 04/24/2019] [Indexed: 01/21/2023]
Abstract
The actinobacterial acI lineage is among the most successful and ubiquitous freshwater bacterioplankton found on all continents, often representing more than half of all microbial cells in the lacustrine environment and constituting multiple ecotypes. However, stably growing pure cultures of the acI lineage have not been established despite various cultivation efforts based on ecological and genomic studies on the lineage, which is in contrast to the ocean from which abundant microorganisms such as Prochlorococcus, Pelagibacter, and Nitrosopumilus have been isolated. Here, we report the first two pure cultures of the acI lineage successfully maintained by supplementing the growth media with catalase. Catalase was critical for stabilizing the growth of acI strains irrespective of the genomic presence of the catalase-peroxidase (katG) gene. The two strains, representing two novel species, displayed differential phenotypes and distinct preferences for reduced sulfurs and carbohydrates, some of which were difficult to predict based on genomic information. Our results suggest that culture of previously uncultured freshwater bacteria can be facilitated by a simple catalase-supplement method and indicate that genome-based metabolic prediction can be complemented by physiological analyses.
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65
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Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment. WATER 2019. [DOI: 10.3390/w11030467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial community structure and metabolism are critical factors for ecosystem functioning since they affect remineralization of nutrients and carbon flow. We used Illumina sequencing of 16SrRNA V3-V4 regions to investigate whether bacterial assemblage composition differs between four samples from two lakes in the geographic region of Epirus (Greece) characterized by distinct oligotrophic to eutrophic/hypereutrophic conditions as revealed by chlorophyll-a values. We found high similarity (>60%) for bacterial assemblages recovered from the two lakes when eutrophic/hypereutrophic conditions prevailed. Distinct bacterial communities appeared in oligotrophic and mesotrophic waters. Low temperature was occasionally an important factor in shaping the bacterial community. In parallel, microcosm experiments were performed to estimate respiration rates of bacterioplankton at in situ temperature and under a 2 °C temperature increase scenario. Differently assembled communities were found to display similar rates except under hypereutrophic conditions when respiration increased significantly, leading to hypoxic conditions. Temperature increase did not affect respiration rates. Overall this study indicated a clear differentiation of bacterial communities between sites of different trophic state. However, different communities responded similarly under a specific range of chlorophyll-a values and resisted small scale temperature perturbations. Different results were found for hypereutrophic conditions and this has implications for ecosystems functioning, given the increasing occurrence of eutrophication events.
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66
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Reddy B, Dubey SK. River Ganges water as reservoir of microbes with antibiotic and metal ion resistance genes: High throughput metagenomic approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:443-451. [PMID: 30579213 DOI: 10.1016/j.envpol.2018.12.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 06/09/2023]
Abstract
The large scale usage of antibiotics and trace elements leads to their progressive release in the environment, and ultimately the spread of antibiotic resistance genes (ARGs) and metal ion resistance genes (MRGs) in bacteria. A high-throughput metagenomic sequencing of the microbial community in water and sediments in the river Ganges harboring resistance genes was performed. The results revealed that the river harbors a broad spectrum of resistance genes with high abundance in sediments. The highly dominant ARGs type was beta-lactam, multidrug/efflux and elfamycin. The ARGs such as (tuf, parY, ileS, mfd) were highly abundant in water and sediments. The MRGs subtype acn was the most abundant metal resistance gene in water and sediments. Majority of ARGs types showed significant (p ≤ 0.05) positive correlation with the MRGs types in the river environment suggesting their distribution and transfer to be possibly linked. Taxonomic classification revealed that Proteobacteria and Actinobacteria were the two most abundant phyla in water and sediments. Arcobacter, Terrimicrobium, Acidibacter and Pseudomonas were the most abundant genera. This study suggests that antibiotics and metals are the driving force for the emergence of resistance genes, and their subsequent propagation and accumulation in the environmental bacteria. The present metagenomic investigation highlights significance of such study, and attracts attention for the mitigation of pollutants associated with the propagation of ARGs and MRGs in the river environment.
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Affiliation(s)
- Bhaskar Reddy
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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67
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Ren L, Song X, He D, Wang J, Tan M, Xia X, Li G, Tan Y, Wu QL. Bacterioplankton Metacommunity Processes across Thermal Gradients: Weaker Species Sorting but Stronger Niche Segregation in Summer than in Winter in a Subtropical Bay. Appl Environ Microbiol 2019; 85:e02088-18. [PMID: 30367007 PMCID: PMC6328778 DOI: 10.1128/aem.02088-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/23/2018] [Indexed: 11/20/2022] Open
Abstract
Thermal effluents from nuclear power plants greatly change the environmental and ecological conditions of the receiving marine water body, but knowledge about their impact on microbial ecology is limited. Here we used high-throughput sequencing of the 16S rRNA gene to examine marine bacterioplankton metacommunity assembly across thermal gradients in two representative seasons (i.e., winter and summer) in a subtropical bay located on the northern coast of the South China Sea. We found high heterogeneity in bacterioplankton community compositions (BCCs) across thermal gradients and between seasons. The spatially structured temperature gradient created by thermal effluents was the key determinant of BCCs, but its influence differed by season. Using a metacommunity approach, we found that in the thermal discharge area, i.e., where water is frequently exchanged with surrounding seawater and thermal effluent water, the BCC spatial patterns were shaped by species sorting rather than by mass effects from surrounding seawater or by dilution of thermal effluent water by surrounding seawater. However, this effect of species sorting was weaker in summer than in winter seawater. In both seasons, the bacterioplankton community structure was predominately determined by niche sharing; however, the relative importance of niche segregation was enhanced in summer seawater. Our findings suggest that for the seasonal differences in metacommunity processes, the BCCs of subtropical summer seawater were more sensitive to temperature and were more difficult to predict than those of winter seawater in the face of different intensities of thermal impacts.IMPORTANCE Understanding the mechanisms of bacterial community assembly across environmental gradients is one of the major goals of marine microbial ecology. Thermal effluents from two nuclear power plants have been present in the subtropical Daya Bay for more than 20 years and have generated a comparatively stable and long thermal gradient (a temperature increase from 0 to 10°C). The environmental patches across thermal gradients are heterogeneous and very strongly interconnected on a microbial scale; thus, this is a useful model for the study of the metacommunity processes (i.e., patch dynamics, species sorting, mass effects, and neutral processes) that underlie marine bacterioplankton assembly. The significance of our research is to reveal how environmental conditions and dispersal-related processes interact to influence bacterioplankton metacommunity processes and their seasonal differences across thermal gradients. Our results may advance the understanding of marine microbial ecology under future conditions of global warming.
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Affiliation(s)
- Lijuan Ren
- Key Laboratory of Tropical Marine Bioresources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xingyu Song
- Key Laboratory of Tropical Marine Bioresources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Dan He
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Meiting Tan
- Key Laboratory of Tropical Marine Bioresources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bioresources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bioresources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bioresources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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Cabello-Yeves PJ, Picazo A, Camacho A, Callieri C, Rosselli R, Roda-Garcia JJ, Coutinho FH, Rodriguez-Valera F. Ecological and genomic features of two widespread freshwater picocyanobacteria. Environ Microbiol 2018; 20:3757-3771. [PMID: 30117250 DOI: 10.1111/1462-2920.14377] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/08/2018] [Indexed: 12/15/2022]
Abstract
We present two genomes of widespread freshwater picocyanobacteria isolated by extinction dilution from a Spanish oligotrophic reservoir. Based on microscopy and genomic properties, both picocyanobacteria were tentatively designated Synechococcus lacustris Tous, formerly described as a metagenome assembled genome (MAG) from the same habitat, and Cyanobium usitatum Tous, described here for the first time. Both strains were purified in unicyanobacterial cultures, and their genomes were sequenced. They are broadly distributed in freshwater systems; the first seems to be a specialist on temperate reservoirs (Tous, Amadorio, Dexter, Lake Lanier, Sparkling), and the second appears to also be abundant in cold environments including ice-covered lakes such as Lake Baikal, Lake Erie or the brackish Baltic Sea. Having complete genomes provided access to the flexible genome that does not assemble in MAGs. We found several genomic islands in both genomes, within which there were genes for nitrogen acquisition, transporters for a wide set of compounds and biosynthesis of phycobilisomes in both strains. Some of these regions of low coverage in metagenomes also included antimicrobial compounds, transposases and phage defence systems, including a novel type III CRISPR-Cas phage defence system that was only detected in Synechococcus lacustris Tous.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | | | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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69
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Mehrshad M, Salcher MM, Okazaki Y, Nakano SI, Šimek K, Andrei AS, Ghai R. Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi. MICROBIOME 2018; 6:176. [PMID: 30285851 PMCID: PMC6169038 DOI: 10.1186/s40168-018-0563-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 09/21/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11. RESULTS Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway. CONCLUSIONS Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.
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Affiliation(s)
- Maliheh Mehrshad
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
| | - Michaela M Salcher
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, CH-8802, Kilchberg, Switzerland
| | - Yusuke Okazaki
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
| | - Shin-Ichi Nakano
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
| | - Karel Šimek
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Stefan Andrei
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
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Cho BC, Hardies SC, Jang GI, Hwang CY. Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6 T adapted to coastal planktonic lifestyle. BMC Genomics 2018; 19:625. [PMID: 30134835 PMCID: PMC6106888 DOI: 10.1186/s12864-018-5019-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/14/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Pontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environment in which members of Microbactericeae have not been previously characterized. RESULTS The genome of P. salivibrio CL-TW6T was a single chromosome of 1,760,810 bp. Genomes of this small size are typically found in bacteria growing slowly in oligotrophic zones and said to be streamlined. Phylogenetic analysis showed it to represent a lineage originating in the Microbacteriaceae radiation occurring before the snowball Earth glaciations, and to have a closer relationship with some streamlined bacteria known through metagenomic data. Several genomic characteristics typical of streamlined bacteria are found: %G + C is lower than non-streamlined members of the phylum; there are a minimal number of rRNA and tRNA genes, fewer paralogs in most gene families, and only two sigma factors; there is a noticeable absence of some nonessential metabolic pathways, including polyketide synthesis and catabolism of some amino acids. There was no indication of any phage genes or plasmids, however, a system of active insertion elements was present. P. salivibrio appears to be unusual in having polyrhamnose-based cell wall oligosaccharides instead of mycolic acid or teichoic acid-based oligosaccharides. Oddly, it conducts sulfate assimilation apparently for sulfating cell wall components, but not for synthesizing amino acids. One gene family it has more of, rather than fewer of, are toxin/antitoxin systems, which are thought to down-regulate growth during nutrient deprivation or other stressful conditions. CONCLUSIONS Because of the relatively small number of paralogs and its relationship to the heavily characterized Mycobacterium tuberculosis, we were able to heavily annotate the genome of P. salivibrio CL-TW6T. Its streamlined status and relationship to streamlined metagenomic constructs makes it an important reference genome for study of the streamlining concept. The final evolutionary trajectory of CL-TW6 T was to adapt to growth in a non-oligotrophic coastal zone. To understand that adaptive process, we give a thorough accounting of gene content, contrasting with both oligotrophic streamlined bacteria and large genome bacteria, and distinguishing between genes derived by vertical and horizontal descent.
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Affiliation(s)
- Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Stephen C. Hardies
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Chung Yeon Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
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71
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Zhong L, Li D, Wang M, Chen X, Bian W, Zhu G. Dynamics of the bacterial community in a channel catfish nursery pond with a cage-pond integration system. Can J Microbiol 2018; 64:954-967. [PMID: 30118606 DOI: 10.1139/cjm-2018-0268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The changes in the bacterial community composition in a channel catfish nursery pond with a cage-pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage-pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.
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Affiliation(s)
- Liqiang Zhong
- a Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China.,c University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daming Li
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Minghua Wang
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Xiaohui Chen
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Wenji Bian
- b Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Guangwei Zhu
- a Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,c University of Chinese Academy of Sciences, Beijing 100049, China
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72
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Keshri J, Pradeep Ram AS, Nana PA, Sime-Ngando T. Taxonomical Resolution and Distribution of Bacterioplankton Along the Vertical Gradient Reveals Pronounced Spatiotemporal Patterns in Contrasted Temperate Freshwater Lakes. MICROBIAL ECOLOGY 2018; 76:372-386. [PMID: 29340714 DOI: 10.1007/s00248-018-1143-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
We examined the relationship between viruses and co-occurring bacterial communities across spatiotemporal scale in two contrasting freshwater lakes, namely meromictic Lake Pavin and dimictic Lake Aydat (Central France). Next-generation sequencing of 16S rRNA genes suggested distinct patterns in bacterioplankton community composition (BCC) between the lakes over depths and seasons. BCC were generally dominated by members of Actinobacteria, Proteobacteria, and Bacteroidetes covering about 95% of all sequences. Oxygen depletion at the bottom waters in Aydat and existence of permanent anoxia in the monimolimnion of Pavin resulted in the occurrence and dominance of lesser known members of lake communities such as Methylotenera, Methylobacter, Gallionella, Sulfurimonas, and Syntrophus in Pavin and Methylotenera and Sulfuritalea in Aydat. Differences in BCC appeared strongly related to dissolved oxygen concentration, temperature, viral infection, and virus-to-bacteria ratio. UniFrac analysis indicated a clear distinction in BCC when the percentage of viral infected bacterial cells and virus-to-bacteria ratio exceeded a threshold level of 10% and 5, respectively, suggesting a link between viruses and their potential bacterial host communities. Our study revealed that in both the lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.
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Affiliation(s)
- J Keshri
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, Volcani Centre, 50250, Bet Dagan, Israel
| | - A S Pradeep Ram
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France.
| | - P A Nana
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France
| | - T Sime-Ngando
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France
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73
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Berner C, Bertos-Fortis M, Pinhassi J, Legrand C. Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea. Front Microbiol 2018; 9:1562. [PMID: 30090087 PMCID: PMC6068395 DOI: 10.3389/fmicb.2018.01562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
Frequencies and biomass of Baltic Sea cyanobacterial blooms are expected to be higher in future climate conditions, but also of longer duration as a result of increased sea surface temperature. Concurrently, climate predictions indicate a reduced salinity in the Baltic Sea. These climate-driven changes are expected to alter not solely the phytoplankton community but also the role of microbial communities for nutrient remineralization. Here, we present the response of summer plankton communities (filamentous cyanobacteria, picocyanobacteria, and heterotrophic bacteria) to the interplay of increasing temperature (from 16 to 18°C and 20°C) and reduced salinity (from salinity 6.9 to 5.9) in the Baltic Proper (NW Gotland Sea) using a microcosm approach. Warmer temperatures led to an earlier peak of cyanobacterial biomass, while yields were reduced. These conditions caused a decrease of nitrogen-fixers (Dolichospermum sp.) biomass, while non nitrogen-fixers (Pseudanabaena sp.) increased. Salinity reduction did not affect cyanobacterial growth nor community composition. Among heterotrophic bacteria, Actinobacteria showed preference for high temperature, while Gammaproteobacteria thrived at in situ temperature. Heterotrophic bacteria community changed drastically at lower salinity and resembled communities at high temperature. Picocyanobacteria and heterotrophic bacterial biomass had a pronounced increase associated with the decay of filamentous cyanobacteria. This suggests that shifts in community composition of heterotrophic bacteria are influenced both directly by abiotic factors (temperature and salinity) and potentially indirectly by cyanobacteria. Our findings suggest that at warmer temperature, lower yield of photosynthetic cyanobacteria combined with lower proportion of nitrogen-fixers in the community could result in lower carbon export to the marine food web with consequences for the decomposer community of heterotrophic bacteria.
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Affiliation(s)
- Christoffer Berner
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mireia Bertos-Fortis
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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74
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Abstract
Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.
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75
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Hu D, Cha G, Gao B. A Phylogenomic and Molecular Markers Based Analysis of the Class Acidimicrobiia. Front Microbiol 2018; 9:987. [PMID: 29867887 PMCID: PMC5962788 DOI: 10.3389/fmicb.2018.00987] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/27/2018] [Indexed: 01/22/2023] Open
Abstract
Recent metagenomic surveys of microbial community suggested that species associated with the class Acidimicrobiia are abundant in diverse aquatic environments such as acidic mine water, waste water sludge, freshwater, or marine habitats, but very few species have been cultivated and characterized. The current taxonomic framework of Acidimicrobiia is solely based on 16S rRNA sequence analysis of few cultivable representatives, and no molecular, biochemical, or physiological characteristics are known that can distinguish species of this class from the other bacteria. This study reports the phylogenomic analysis for 20 sequenced members of this class and reveals another three major lineages in addition to the two recognized families. Comparative analysis of the sequenced Acidimicrobiia species identified 15 conserved signature indels (CSIs) in widely distributed proteins and 26 conserved signature proteins (CSPs) that are either specific to this class as a whole or to its major lineages. This study represents the most comprehensive phylogenetic analysis of the class Acidimicrobiia and the identified CSIs and CSPs provide useful molecular markers for the identification and delineation of species belonging to this class or its subgroups.
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Affiliation(s)
- Danyu Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guihong Cha
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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76
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Di Cesare A, Cabello-Yeves PJ, Chrismas NAM, Sánchez-Baracaldo P, Salcher MM, Callieri C. Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization. BMC Genomics 2018; 19:259. [PMID: 29661139 PMCID: PMC5902973 DOI: 10.1186/s12864-018-4648-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/05/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. So far, it has not been shown whether these unicellular picocyanobacteria have the potential for nitrogen fixation. Here, we present the draft-genome of the new pink-pigmented Synechococcus-like strain Vulcanococcus limneticus. sp. nov., isolated from the volcanic Lake Albano (Central Italy). RESULTS The novel species Vulcanococcus limneticus sp. nov. falls inside the sub-cluster 5.2, close to the estuarine/marine strains in a maximum-likelihood phylogenetic tree generated with 259 marker genes with representatives from marine, brackish, euryhaline and freshwater habitats. V.limneticus sp. nov. possesses a complete nitrogenase and nif operon. In an experimental setup under nitrogen limiting and non-limiting conditions, growth was observed in both cases. However, the nitrogenase genes (nifHDK) were not transcribed, i.e., V.limneticus sp. nov. did not fix nitrogen, but instead degraded the phycobilisomes to produce sufficient amounts of ammonia. Moreover, the strain encoded many other pathways to incorporate ammonia, nitrate and sulphate, which are energetically less expensive for the cell than fixing nitrogen. The association of the nif operon to a genomic island, the relatively high amount of mobile genetic elements (52 transposases) and the lower observed GC content of V.limneticus sp. nov. nif operon (60.54%) compared to the average of the strain (68.35%) support the theory that this planktonic strain may have obtained, at some point of its evolution, the nif operon by horizontal gene transfer (HGT) from a filamentous or heterocystous cyanobacterium. CONCLUSIONS In this study, we describe the novel species Vulcanococcus limneticus sp. nov., which possesses a complete nif operon for nitrogen fixation. The finding that in our experimental conditions V.limneticus sp. nov. did not express the nifHDK genes led us to reconsider the actual ecological meaning of these accessory genes located in genomic island that have possibly been acquired via HGT.
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Affiliation(s)
- Andrea Di Cesare
- National Research Council CNR-ISE, Largo Tonolli 50, 28922, Verbania, Italy.,Department of Earth, Environmental, and Life Sciences, University of Genoa, 16132, Genoa, Italy
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Nathan A M Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK.,Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
| | | | - Michaela M Salcher
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cristiana Callieri
- National Research Council CNR-ISE, Largo Tonolli 50, 28922, Verbania, Italy.
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77
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Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F. Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Appl Environ Microbiol 2018; 84:e02132-17. [PMID: 29079621 PMCID: PMC5734018 DOI: 10.1128/aem.02132-17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022] Open
Abstract
We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacterubique strains, as well as a phage infecting the widespread freshwater bacterium PolynucleobacterIMPORTANCE Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Tamara I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Alexandra S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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78
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Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. ISME JOURNAL 2017; 12:742-755. [PMID: 29222442 PMCID: PMC5962901 DOI: 10.1038/s41396-017-0001-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 08/16/2017] [Accepted: 10/09/2017] [Indexed: 01/25/2023]
Abstract
To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed “tribes”) that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.
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79
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Cabello-Yeves PJ, Ghai R, Mehrshad M, Picazo A, Camacho A, Rodriguez-Valera F. Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs. Front Microbiol 2017; 8:2131. [PMID: 29163419 PMCID: PMC5673642 DOI: 10.3389/fmicb.2017.02131] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022] Open
Abstract
The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbes.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
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80
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Neuenschwander SM, Ghai R, Pernthaler J, Salcher MM. Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. ISME JOURNAL 2017; 12:185-198. [PMID: 29027997 DOI: 10.1038/ismej.2017.156] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2-1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the 'Black Queen' hypothesis). Genome analyses, moreover, revealed a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria ('Candidatus Nanopelagicales') with two new genera ('Candidatus Nanopelagicus' and 'Candidatus Planktophila') and nine new species.
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Affiliation(s)
- Stefan M Neuenschwander
- Limnological Station, Institute of Microbial and Plant Biology, University of Zurich, Zurich, Switzerland
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Jakob Pernthaler
- Limnological Station, Institute of Microbial and Plant Biology, University of Zurich, Zurich, Switzerland
| | - Michaela M Salcher
- Limnological Station, Institute of Microbial and Plant Biology, University of Zurich, Zurich, Switzerland.,Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czech Republic
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81
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Paliaga P, Korlević M, Ivančić I, Najdek M. Limited influence of primary treated sewage waters on bacterial abundance, production and community composition in coastal seawaters. MARINE ENVIRONMENTAL RESEARCH 2017; 131:215-226. [PMID: 29032852 DOI: 10.1016/j.marenvres.2017.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
The response of bacteria in terms of abundance, production and community structure to changes induced by the discharge of primary treated sewage waters was investigated combining microbiological, chemical and molecular tools. The primary treatment did not affect substantially the bacterial community structure in wastewaters and did not reduce the concentrations of fecal indicators. The spatial distribution of the sewage plume was governed by vertical stratification and currents. Bacterial abundance and production in the sea receiving waste waters depended predominantly on environmental conditions. In the waters with the highest concentration of fecal pollution indicators the bacterial community was characterized by allochthonous bacteria belonging to Epsilonproteobacteria, Firmicutes, Gammaproteobacteria and Bacteroidetes. The latter two taxa were also present in unpolluted waters but had a different structure, typical for oligotrophic environments. Although the impact of primary treated sewage waters was limited, a sanitary risk persisted due to the relevant presence of potentially pathogenic bacteria.
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Affiliation(s)
- Paolo Paliaga
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Ingrid Ivančić
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
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82
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Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. mSystems 2017; 2:mSystems00091-17. [PMID: 28861526 PMCID: PMC5574706 DOI: 10.1128/msystems.00091-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/08/2017] [Indexed: 11/20/2022] Open
Abstract
The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organism’s metabolic pathways or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more-intensive metabolic reconstruction efforts and can also provide new hypotheses about the specific contributions that microbes make to ecosystem-scale metabolic processes. An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework,” which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482–14487, 2008, https://doi.org/10.1073/pnas.0806162105), enables computational analysis of metabolic reconstructions while providing new insights into a microbe’s metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs. IMPORTANCE The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organism’s metabolic pathways or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more-intensive metabolic reconstruction efforts and can also provide new hypotheses about the specific contributions that microbes make to ecosystem-scale metabolic processes.
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83
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Cabello-Yeves PJ, Haro-Moreno JM, Martin-Cuadrado AB, Ghai R, Picazo A, Camacho A, Rodriguez-Valera F. Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs. Front Microbiol 2017; 8:1151. [PMID: 28680419 PMCID: PMC5478717 DOI: 10.3389/fmicb.2017.01151] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/07/2017] [Indexed: 11/28/2022] Open
Abstract
Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high abundance levels in these two lakes located at similar altitudes and temperate latitudes. These new genomes have the smallest estimated size (2.2 Mb) and average intergenic spacer length (20 bp) of any previously sequenced freshwater Synechococcus, which may contribute to their success in oligotrophic freshwater systems. Fluorescent in situ hybridization confirmed that Synechococcus sp. Tous comprises small cells (0.987 ± 0.139 μm length, 0.723 ± 0.119 μm width) that amount to 90% of the picocyanobacteria in Tous. They appear together in a phylogenomic tree with Synechococcus sp. RCC307 strain, the main representative of sub-cluster 5.3 that has itself one of the smallest marine Synechococcus genomes. We detected a type II phycobilisome (PBS) gene cluster in both genomes, which suggests that they belong to a phycoerythrin-rich pink low-light ecotype. The decrease of acidic proteins and the higher content of basic transporters and membrane proteins in the novel Synechococcus genomes, compared to marine representatives, support their freshwater specialization. A sulfate Cys transporter which is absent in marine but has been identified in many freshwater cyanobacteria was also detected in Synechococcus sp. Tous. The RuBisCo subunits from this microbe are phylogenetically close to the freshwater amoeba Paulinella chromatophora symbiont, hinting to a freshwater origin of the carboxysome operon of this protist. The novel genomes enlarge the known diversity of freshwater Synechococcus and improve the overall knowledge of the relationships among members of this genus at large.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
| | - Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
| | - Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Center of the Academy of Sciences of the Czech RepublicČeské Budějovice, Czechia
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of ValenciaValencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of ValenciaValencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
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84
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Iliev I, Yahubyan G, Marhova M, Apostolova E, Gozmanova M, Gecheva G, Kostadinova S, Ivanova A, Baev V. Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs. J Basic Microbiol 2017; 57:669-679. [PMID: 28543439 DOI: 10.1002/jobm.201700137] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/21/2017] [Accepted: 05/06/2017] [Indexed: 12/21/2022]
Abstract
Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA). Analysis of the metagenomic amplicon datasets, including quality filtering, clustering of Operational Taxonomic Units and taxonomy assignment revealed that 78.45% of the microbial communities between the two reservoirs were overlapping. The diversity (H) and Pielou's evenness (J) indices declined along the longitudinal axis of both reservoirs. The estimated values for the Shannon diversity index are typically observed in oligotrophic lakes. The microbial communities of both reservoirs were dominated by Proteobacteria, followed by Actinobacteria and Bacteroidetes all comprised over 95% of the relative abundance, regardless of the reservoir's large hydrogeological differences. The bacterioplankton was characterized by high phylogenetic heterogeneity in the taxonomic structure, being distributed among 211 genera. The genera Limnohabitans and Rhodoferax held the absolute predominance, implying their significance in the aquatic food webs. The obtained data can contribute to the better systematic understanding of the microbial diversity of freshwater environments.
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Affiliation(s)
- Ivan Iliev
- Faculty of Biology, Department of Biotechnology and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Mariana Marhova
- Faculty of Biology, Department of Biotechnology and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Elena Apostolova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Mariyana Gozmanova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Gana Gecheva
- Faculty of Biology, Department of Ecology and Environmental Conservation, University of Plovdiv, Plovdiv, Bulgaria
| | - Sonya Kostadinova
- Faculty of Biology, Department of Biotechnology and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | | | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
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85
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Mohiuddin MM, Salama Y, Schellhorn HE, Golding GB. Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens. WATER RESEARCH 2017; 115:360-369. [PMID: 28340372 DOI: 10.1016/j.watres.2017.02.057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 05/06/2023]
Abstract
Recreational waters and adjacent beach sands harbor complex microbial communities which may contain human pathogens that cannot be detected by conventional methods. Here, we investigate the diversity of bacterial populations inhabiting four freshwater beaches of the Great Lakes region using shotgun metagenomic sequencing approach. Our analysis suggests that average taxonomic richness and alpha diversity are significantly higher (P < 0.001) in beach sands compared to the corresponding water environments. Compared to the water environments, beach sands harbored taxa from a more diverse range of phyla, including a higher proportion of sequences from unclassified phyla. Unique phyla were also identified in sand which included species from Aquificae, Candidatus Microgenomates, Latescibacteria, and Candidatus Aminicenantes. Sequences originating from pathogens were detected in both sand and water, with some pathogens enriched in both environments. Both lakes exhibited similar community composition suggesting that geographic location did not appear to have any major impact on bacterial diversity. These findings reveal the diversity of bacterial communities of freshwater beaches and highlight the importance of monitoring pathogens in recreational beaches, especially in the sand environment of these beaches.
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Affiliation(s)
- Mahi M Mohiuddin
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yasser Salama
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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86
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The effect of reconstruction works on planktonic bacterial diversity of a unique thermal lake revealed by cultivation, molecular cloning and next generation sequencing. Arch Microbiol 2017; 199:1077-1089. [PMID: 28417144 DOI: 10.1007/s00203-017-1379-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/01/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022]
Abstract
The aim of this study was to gain detailed information about the diversity of planktonic bacterial communities of a worldwide special peat bedded natural thermal spa lake, and to reveal the effect of a lake wall reconstruction work. To compare the efficiency of different methods used for analyzing bacterial diversity, cultivation, molecular cloning and pyrosequencing were applied simultaneously. Despite the almost unchanged physical-chemical parameters and cell count values of lake water, remarkable differences were observed in the planktonic bacterial community structures during and after the reconstruction by all applied microbiological approaches. Rhodobacter sp. was found to be one of the most abundant community members during the works probably due to the sediment stirring effect of the reconstruction. Following the reconstruction higher diversity was detected than during the works by all approaches. Bacterial strains related to species Chryseobacterium and Exiguobacterium, furthermore sequences related to Arcobacter, Gemmobacter and MWH-UniP1 aquatic group were identified in the highest proportion at that time. Although the differences revealed by cultivation based and independent community structures were significant, only minor disparities were found by molecular cloning and next generation sequencing techniques.
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87
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Kang I, Kim S, Islam MR, Cho JC. The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures. Sci Rep 2017; 7:42252. [PMID: 28186143 PMCID: PMC5301498 DOI: 10.1038/srep42252] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/06/2017] [Indexed: 02/07/2023] Open
Abstract
The acI lineage of the phylum Actinobacteria is the most abundant bacterial group in most freshwater lakes. However, due to difficulties in laboratory cultivation, only two mixed cultures and some incomplete single-amplified or metagenome-derived genomes have been reported for the lineage. Here, we report the initial cultivation and complete genome sequences of four novel strains of the acI lineage from the tribes acI-A1, -A4, -A7, and -C1. The acI strains, initially isolated by dilution-to-extinction culturing, eventually failed to be maintained as axenic cultures. However, the first complete genomes of the acI lineage were successfully obtained from these initial cultures through whole genome amplification applied to more than hundreds of cultured acI cells. The genome sequences exhibited features of genome streamlining and showed that the strains are aerobic chemoheterotrophs sharing central metabolic pathways, with some differences among tribes that may underlie niche diversification within the acI lineage. Actinorhodopsin was found in all strains, but retinal biosynthesis was complete in only A1 and A4 tribes.
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Affiliation(s)
- Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Suhyun Kim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Md Rashedul Islam
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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88
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Ren L, He D, Chen Z, Jeppesen E, Lauridsen TL, Søndergaard M, Liu Z, Wu QL. Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms. ISME JOURNAL 2016; 11:613-625. [PMID: 27935593 DOI: 10.1038/ismej.2016.159] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 09/22/2016] [Accepted: 10/05/2016] [Indexed: 01/09/2023]
Abstract
The current climate warming and eutrophication are known to interactively threaten freshwater biodiversity; however, the interactive effects on lacustrine bacterioplankton diversity remain to be determined. Here, we analyzed the spring bacterioplankton community composition (BCC) in 24 outdoor, flow-through mesocosms (mimicking shallow lake environments) under 3 temperature scenarios and 2 nutrient regimes. Our results revealed that neither long-term warming (8.5 years) nor nutrient enrichment had significant effects on bacterioplankton alpha diversity, whereas long-term enhanced warming (elevated 50% above the IPCC A2 climate scenario) and nutrient enrichment in combination increased bacterioplankton beta diversity. We also found that BCC shifted significantly under enhanced warming and nutrient-enriched conditions towards decreased relative abundances of Actinobacteria, Bacteroidetes and Betaproteobacteria, whereas the percentages of Cyanobacteria, total rare phyla and unclassified phyla significantly increased. Null-model tests indicated that deterministic processes played a more important role than stochastic processes in determining BCC. However, the relative importance of stochasticity, primarily ecological drift, was enhanced and contributed to the increased beta diversity of BCC under enhanced warming and nutrient-enriched conditions. Overall, our study suggests that the synergetic effects of warming and nutrient enrichment may result in high variability in the composition of bacterioplankton communities in lacustrine water bodies.
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Affiliation(s)
- Lijuan Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Dan He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Zhen Chen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, Silkeborg, Denmark.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Torben L Lauridsen
- Department of Bioscience, Aarhus University, Silkeborg, Denmark.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Martin Søndergaard
- Department of Bioscience, Aarhus University, Silkeborg, Denmark.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Zhengwen Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China.,Department of Ecology, Jinan University, Guangzhou, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China.,Department of Ecology, Jinan University, Guangzhou, China
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89
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Lee CS, Kim M, Lee C, Yu Z, Lee J. The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health. Front Microbiol 2016; 7:1826. [PMID: 27909431 PMCID: PMC5112438 DOI: 10.3389/fmicb.2016.01826] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/31/2016] [Indexed: 12/03/2022] Open
Abstract
The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches. From the samples, 110,000 quality-checked bacterial 16S rRNA gene sequences were obtained and analyzed, resulting in an observation of 4500 bacterial operational taxonomic units (OTUs). The most abundant bacteria were Mycobacterium and Arthrobacter of the Actinobacteria (33.2%), Exiguobacterium and Paenisporosarcina of the Firmicutes (23.4%), Planktothrix and Synechococcus of the Cyanobacteria (20.8%), and Methylocystis and Polynucleobacter of the Proteobacteria (16.3%). Considerable spatial and temporal variations were observed in the bacterial community of Actinobacteria, Cyanobacteria, and Firmicutes, where the bacterial community structure was greatly influenced by hydrological and weather conditions. The most influential factors were (1) water inflow for Bacteroidia and Clostridia, (2) turbidity for Gammaproteobacteria, (3) precipitation for Bacilli, and (4) temperature and pH for Cyanobacteria. One noticeable microbial interaction in the bacterial community was a significant negative relationship between Cyanobacteria and Bacilli (P < 0.05). Concerning beach water quality, the level of the genetic markers for cyanobacterial toxin (mcyA) was linked to the abundance of Cyanobacteria. In addition, unique distributions of the genera Enterococcus, Staphylococcus, Streptococcus, Bacteroides, Clostridium, Finegoldia, Burkholderia, and Klebsiella, together with a high density of fecal indicator Escherichia coli, were markedly observed in the sample from Madison Lake on July 13, suggesting a distinctly different source of bacterial loading into the lake, possibly fecal contamination. In conclusion, deep sequencing-based microbial community analysis can provide detailed profiles of bacterial communities and information on potential public health risks at freshwater beaches.
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Affiliation(s)
- Chang Soo Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State UniversityColumbus, OH, USA
| | - Minseok Kim
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA
| | - Cheonghoon Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State UniversityColumbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State UniversityColumbus, OH, USA
- Department of Food Science and Technology, The Ohio State UniversityColumbus, OH, USA
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90
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Zhu L, Zancarini A, Louati I, De Cesare S, Duval C, Tambosco K, Bernard C, Debroas D, Song L, Leloup J, Humbert JF. Bacterial Communities Associated with Four Cyanobacterial Genera Display Structural and Functional Differences: Evidence from an Experimental Approach. Front Microbiol 2016; 7:1662. [PMID: 27822204 PMCID: PMC5076464 DOI: 10.3389/fmicb.2016.01662] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/05/2016] [Indexed: 01/03/2023] Open
Abstract
To overcome the limitations associated with studying the interactions between bacterial communities (BCs) and cyanobacteria in natural environments, we compared the structural and functional diversities of the BCs associated with 15 non-axenic cyanobacterial strains in culture and two natural BCs sampled during cyanobacterial blooms. No significant differences in richness and diversity were found between the natural and cultivated BCs, although some of the cyanobacterial strains had been isolated 11 years earlier. Moreover, these BCs shared some similar characteristics, such as a very low abundance of Actinobacteria, but they display significant differences at the operational taxonomic unit (OTU) level. Overall, our findings suggest that BCs associated with cyanobacteria in culture are good models to better understand the interactions between heterotrophic bacteria and cyanobacteria. Additionally, BCs associated with heterocystous cyanobacterial strains cultivated in Z8X culture medium without nitrate (Aphanizomenon–Dolichospermum) demonstrated significant differences compared to BCs associated with non-heterocystous strains cultivated in Z8 culture medium (Planktothrix–Microcystis) in terms of their composition and their ability to utilize different carbon sources, suggesting the potential influence of cyanobacterial metabolism and/or culture media on associated BCs. Finally, half of the dominant OTUs in these BCs were specifically associated with cyanobacteria or other phytoplankton, whereas the remaining OTUs were generally associated with ecosystems containing high organic matter content, such as sludge or intestines.
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Affiliation(s)
- Lin Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesWuhan, China; UPMC-INRA, iEES-Paris UMR 7618Paris, France
| | | | - Imen Louati
- UPMC-INRA, iEES-Paris UMR 7618 Paris, France
| | | | - Charlotte Duval
- CNRS, MCAM, Muséum National d'Histoire Naturelle, UMR 7245, Sorbonne Universités Paris, France
| | | | - Cécile Bernard
- CNRS, MCAM, Muséum National d'Histoire Naturelle, UMR 7245, Sorbonne Universités Paris, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, Université de Clermont-Ferrand Clermont-Ferrand, France
| | - Lirong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan, China
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91
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Kurilkina MI, Zakharova YR, Galachyants YP, Petrova DP, Bukin YS, Domysheva VM, Blinov VV, Likhoshway YV. Bacterial community composition in the water column of the deepest freshwater Lake Baikal as determined by next-generation sequencing. FEMS Microbiol Ecol 2016; 92:fiw094. [PMID: 27162182 DOI: 10.1093/femsec/fiw094] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 01/01/2023] Open
Abstract
The composition of bacterial communities in Lake Baikal in different hydrological periods and at different depths (down to 1515 m) has been analyzed using pyrosequencing of the 16S rRNA gene V3 variable region. Most of the resulting 34 562 reads of the Bacteria domain have clustered into 1693 operational taxonomic units (OTUs) classified with the phyla Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, Acidobacteria and Cyanobacteria. It has been found that their composition at the family level and relative contributions to bacterial communities distributed over the water column vary depending on hydrological period. The number of OTUs and the parameters of taxonomic richness (ACE, Chao1 indices) and diversity (Shannon and inverse Simpson index) reach the highest values in water layers. The composition of bacterial communities in these layers remains relatively constant, whereas that in surface layers differs between hydrological seasons. The dynamics of physicochemical conditions over the water column and their relative constancy in deep layers are decisive factors in shaping the pattern of bacterial communities in Lake Baikal.
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Affiliation(s)
- Maria I Kurilkina
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P Petrova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Valentina M Domysheva
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
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92
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Sangwan N, Xia F, Gilbert JA. Recovering complete and draft population genomes from metagenome datasets. MICROBIOME 2016; 4:8. [PMID: 26951112 PMCID: PMC4782286 DOI: 10.1186/s40168-016-0154-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/05/2016] [Indexed: 05/03/2023]
Abstract
Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
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Affiliation(s)
- Naseer Sangwan
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
- Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA.
| | - Fangfang Xia
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA.
- Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA.
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.
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93
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Skvortsov T, de Leeuwe C, Quinn JP, McGrath JW, Allen CCR, McElarney Y, Watson C, Arkhipova K, Lavigne R, Kulakov LA. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland. PLoS One 2016; 11:e0150361. [PMID: 26927795 PMCID: PMC4771703 DOI: 10.1371/journal.pone.0150361] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.
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Affiliation(s)
- Timofey Skvortsov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Colin de Leeuwe
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John P. Quinn
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - John W. McGrath
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Christopher C. R. Allen
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Yvonne McElarney
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Catherine Watson
- Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - Ksenia Arkhipova
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Leonid A. Kulakov
- School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
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94
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Kaluzhnaya OV, Itskovich VB. Distinctive features of the microbial diversity and the polyketide synthase genes spectrum in the community of the endemic Baikal sponge Swartschewskia papyracea. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416010099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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95
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Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F. Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea. Appl Environ Microbiol 2016; 82:1599-1612. [PMID: 26729711 PMCID: PMC4771326 DOI: 10.1128/aem.03381-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/11/2015] [Indexed: 11/20/2022] Open
Abstract
We present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts of Actinobacteria and Alphaproteobacteria, while Gammaproteobacteria and Betaproteobacteria were present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes from Actinobacteria, Thaumarchaea, and Alphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of the Alphaproteobacteria) or freshwater (a member of the Actinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon " Candidatus Nitrosopelagicus" or the actinobacterium "Candidatus Actinomarina," were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.
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Affiliation(s)
- Maliheh Mehrshad
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Rohit Ghai
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Seyed Abolhassan Shahzadeh Fazeli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
- Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
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96
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TAKAHASHI T, TAKASE K, TAKESHITA K, KAWANO H, MAMIZUKA M, KIZU H. State Transition of Musty-odor-producing Cyanobacteria and 2-Methylisoborneol in the Serikawa Dam Reservoir. ACTA ACUST UNITED AC 2016. [DOI: 10.2965/jswe.39.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
| | | | | | | | | | - Hideaki KIZU
- Water Purification Division, Oita City Waterworks Bureau
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97
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Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing. World J Microbiol Biotechnol 2015; 32:10. [PMID: 26712625 DOI: 10.1007/s11274-015-1962-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
The changes of microbial community in aquaculture systems under the effects of stocking densities and seasonality were investigated in tilapia ponds. Total DNAs were extracted from the water samples, 16S rRNA gene was amplified and the bacterial community analyzed by Illumina high-throughput sequencing obtaining 3486 OTUs, from a total read of 715,842 sequences. Basing on the analysis of bacterial compositions, richness, diversity, bacterial 16S rRNA gene abundance, water sample comparisons and existence of specific bacterial taxa within three fish ponds in a 4 months period, the study conclusively observed that the dominant phylum in all water samples were similar, and they included; Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes and Chlorobi, distributed in different proportions in the different months and ponds. The seasonal changes had a more pronounced effect on the bacterioplankton community than the stocking densities; however some differences between the ponds were more likely caused by feed coefficient than by stocking densities. At the same time, most bacterial communities were affected by the nutrient input except phylum Cyanobacteria that was also affected by the feed control of tilapia.
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98
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Hugerth LW, Larsson J, Alneberg J, Lindh MV, Legrand C, Pinhassi J, Andersson AF. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol 2015; 16:279. [PMID: 26667648 PMCID: PMC4699468 DOI: 10.1186/s13059-015-0834-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/12/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. RESULTS We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts. CONCLUSIONS We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.
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Affiliation(s)
- Luisa W Hugerth
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
| | - John Larsson
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Johannes Alneberg
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
| | - Markus V Lindh
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Anders F Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
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99
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Yang J, Li X, Huang L, Jiang H. Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau. Front Microbiol 2015; 6:1345. [PMID: 26648925 PMCID: PMC4663260 DOI: 10.3389/fmicb.2015.01345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/16/2015] [Indexed: 11/13/2022] Open
Abstract
The actinobacterial diversity was investigated in the sediments of five cold springs in Wuli region on the Qinghai-Tibet Plateau using 16S rRNA gene phylogenetic analysis. The actinobacterial communities of the studied cold springs were diverse and the obtained actinobacterial operational taxonomic units were classified into 12 actinobacterial orders (e.g., Acidimicrobiales, Corynebacteriales, Gaiellales, Geodermatophilales, Jiangellales, Kineosporiales, Micromonosporales, Micrococcales, Nakamurellales, Propionibacteriales, Pseudonocardiales, Streptomycetales) and unclassified Actinobacteria. The actinobacterial composition varied among the investigated cold springs and were significantly correlated (r = 0.748, P = 0.021) to environmental variables. The actinobacterial communities in the cold springs were more diverse than other cold habitats on the Tibetan Plateau, and their compositions showed unique geographical distribution characteristics. Statistical analyses showed that biogeographical isolation and unique environmental conditions might be major factors influencing actinobacterial distribution among the investigated cold springs.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Xiaoyan Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
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100
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Louati I, Pascault N, Debroas D, Bernard C, Humbert JF, Leloup J. Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus. PLoS One 2015; 10:e0140614. [PMID: 26579722 PMCID: PMC4651346 DOI: 10.1371/journal.pone.0140614] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 09/27/2015] [Indexed: 12/21/2022] Open
Abstract
The factors and processes driving cyanobacterial blooms in eutrophic freshwater ecosystems have been extensively studied in the past decade. A growing number of these studies concern the direct or indirect interactions between cyanobacteria and heterotrophic bacteria. The presence of bacteria that are directly attached or immediately adjacent to cyanobacterial cells suggests that intense nutrient exchanges occur between these microorganisms. In order to determine if there is a specific association between cyanobacteria and bacteria, we compared the bacterial community composition during two cyanobacteria blooms of Anabaena (filamentous and N2-fixing) and Microcystis (colonial and non-N2 fixing) that occurred successively within the same lake. Using high-throughput sequencing, we revealed a clear distinction between associated and free-living communities and between cyanobacterial genera. The interactions between cyanobacteria and bacteria appeared to be based on dissolved organic matter degradation and on N recycling, both for N2-fixing and non N2-fixing cyanobacteria. Thus, the genus and potentially the species of cyanobacteria and its metabolic capacities appeared to select for the bacterial community in the phycosphere.
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Affiliation(s)
- Imen Louati
- iEES-PARIS, UMR 7618 (UPMC-CNRS-INRA-IRD-UPEC-Paris Diderot), UPMC, Paris, France
| | - Noémie Pascault
- iEES-PARIS, UMR 7618 (UPMC-CNRS-INRA-IRD-UPEC-Paris Diderot), UPMC, Paris, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Clermont Université Blaise Pascal, Aubière, France
| | - Cécile Bernard
- MCAM MNHN, UMR CNRS 7245, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
| | | | - Julie Leloup
- iEES-PARIS, UMR 7618 (UPMC-CNRS-INRA-IRD-UPEC-Paris Diderot), UPMC, Paris, France
- * E-mail:
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