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Dmitrieva ME, Malygina EV, Belyshenko AY, Shelkovnikova VN, Imidoeva NA, Morgunova MM, Telnova TY, Vlasova AA, Axenov-Gribanov DV. The Effects of a High Concentration of Dissolved Oxygen on Actinobacteria from Lake Baikal. Metabolites 2023; 13:830. [PMID: 37512537 PMCID: PMC10386110 DOI: 10.3390/metabo13070830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Among the diversity of microorganisms, the rarest and least explored are microorganisms that live in conditions of high oxygen in the environment and can experience the effects of natural oxidative stress. Here we suggest that the actinobacteria of Lake Baikal, sampled in the littoral zone, may produce natural products with antioxidant activity. The current study aimed to assess the effects of experimentally increased amounts of oxygen and ozone on the morphology of actinobacteria, DNA mutations, and antioxidant potential. In this experiment, we cultivated actinobacteria in liquid culture under conditions of natural aeration and increased concentrations of dissolved oxygen and ozone. Over a period of three months, bacterial samples were collected every week for further analysis. Morphological changes were assessed using the Gram method. A search for DNA mutations was conducted for the highly conserved 16S rRNA gene. The evaluation of antioxidant activity was performed using the DPPH test. The biotechnological potential was evaluated using high-resolution liquid chromatography-mass spectrometry approaches supplemented with the dereplication of natural products. We demonstrated the synthesis of at least five natural products by the Streptomyces sp. strain only under conditions of increased oxygen and ozone levels. Additionally, we showed morphological changes in Streptomyces sp. and nucleotide mutations in Rhodococcus sp. exposed to increased concentrations of dissolved oxygen and oxidative stress. Consequently, we demonstrated that an increased concentration of oxygen can influence Lake Baikal actinobacteria.
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Affiliation(s)
- Maria E Dmitrieva
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Ekaterina V Malygina
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Alexander Y Belyshenko
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Victoria N Shelkovnikova
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Natalia A Imidoeva
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Maria M Morgunova
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Tamara Y Telnova
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Anfisa A Vlasova
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
| | - Denis V Axenov-Gribanov
- Laboratory of Experimental Neurophysiology, Department for Research and Development, Irkutsk State University, 1 Karl Marx Str., 664003 Irkutsk, Russia
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Huang Y, Feng JC, Kong J, Sun L, Zhang M, Huang Y, Tang L, Zhang S, Yang Z. Community assemblages and species coexistence of prokaryotes controlled by local environmental heterogeneity in a cold seep water column. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161725. [PMID: 36669671 DOI: 10.1016/j.scitotenv.2023.161725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The distribution and heterogeneity characteristics of microbial communities in cold seep water columns are significant factors governing the efficiency of methane filtering and carbon turnover. However, this process is poorly understood. The diversity of vertically stratified microbial communities and the factors controlling the community assemblage process in the water column above the Haima cold seep were investigated in this study. The prokaryotic community diversities varied distinctly with vertical changes in hydrochemistry. Cyanobacteria dominated the light-transmitting layers and Proteobacteria dominated the deeper layers. With respect to microbial community assemblages and co-occurrence networks, stochastic processes were particularly important in shaping prokaryotic communities. In the shallow (≥85 m) and mesopelagic water columns (600-800 m), microbial community characteristics were affected by deterministic processes, reduced network connectivity, and modularity. Microbial community diversities and assemblage processes along a vertical profile were influenced by the vertical variations in pH, temperature, DIC, and nutrients. Stochastic processes may have facilitated the formation of complex co-occurrence networks. Briefly, the distribution of local environmental heterogeneity along the vertical dimension could drive unique microbial community assemblage and species coexistence patterns. This study provides new perspectives on how microorganisms adapt to the environment and build communities, and how species coexist in shared habitats.
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Affiliation(s)
- Yongji Huang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jing-Chun Feng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China.
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Liwei Sun
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Mingrui Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Yanyan Huang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Li Tang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Si Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
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3
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Iniesto M, Moreira D, Benzerara K, Reboul G, Bertolino P, Tavera R, López‐García P. Planktonic microbial communities from microbialite-bearing lakes sampled along a salinity-alkalinity gradient. LIMNOLOGY AND OCEANOGRAPHY 2022; 67:2718-2733. [PMID: 37064594 PMCID: PMC10087431 DOI: 10.1002/lno.12233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 07/12/2022] [Accepted: 09/04/2022] [Indexed: 06/19/2023]
Abstract
Continental freshwater systems are particularly vulnerable to environmental variation. Climate change-induced desertification and the anthropogenic exploitation of hydric resources result in the progressive evaporation and salinization of inland water bodies in many areas of the globe. However, how this process impacts microbial communities and their activities in biogeochemical cycles is poorly known. Here, we take a space-for-time substitution approach and characterize the prokaryotic and eukaryotic microbial communities of two planktonic cell-size fractions (0.2-5 μm and 5-30 μm) from lakes of diverse trophic levels sampled along a salinity-alkalinity gradient located in the Trans-Mexican Volcanic Belt (TMVB). We applied a 16S/18S rRNA gene metabarcoding strategy to determine the microbial community composition of 54 samples from 12 different lakes, from the low-salinity lake Zirahuén to the hypersaline residual ponds of Rincón de Parangueo. Except for systems at both extremes of the salinity gradient, most lakes along the evaporation trend bear actively forming microbialites, which harbor microbial communities clearly distinct from those of plankton. Several lakes were sampled in winter and late spring and the crater lakes Alchichica and Atexcac were sampled across the water column. Physicochemical parameters related to salinity-alkalinity were the most influential drivers of microbial community structure whereas trophic status, depth, or season were less important. Our results suggest that climate change and anthropogenic-induced hydric deficit could significantly affect microbial communities, potentially altering ecosystem functioning.
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Affiliation(s)
- Miguel Iniesto
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - David Moreira
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - Karim Benzerara
- Institut de Minéralogie de Physique des Matériaux et de Cosmochimie, CNRSSorbonne Université, Muséum National d'Histoire NaturelleParisFrance
| | - Guillaume Reboul
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos NaturalesUniversidad Nacional Autónoma de MéxicoMexico CityMexico
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4
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Mikhailov IS, Galachyants YP, Bukin YS, Petrova DP, Bashenkhaeva MV, Sakirko MV, Blinov VV, Titova LA, Zakharova YR, Likhoshway YV. Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal. MICROBIAL ECOLOGY 2022; 84:404-422. [PMID: 34510242 DOI: 10.1007/s00248-021-01860-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.
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Affiliation(s)
- Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Sakirko
- 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
| | - Lubov A Titova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Sanseverino I, Pretto P, António DC, Lahm A, Facca C, Loos R, Skejo H, Beghi A, Pandolfi F, Genoni P, Lettieri T. Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese. MICROBIAL ECOLOGY 2022; 83:850-868. [PMID: 34766210 PMCID: PMC9016052 DOI: 10.1007/s00248-021-01914-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/26/2021] [Indexed: 05/09/2023]
Abstract
Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.
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Affiliation(s)
- Isabella Sanseverino
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Patrizia Pretto
- Biosearch Ambiente Srl, Via Tetti Gai 59, 10091, Alpignano, TO, Italy
| | - Diana Conduto António
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Armin Lahm
- Bioinformatics Project Support, P.za S.M. Liberatrice 18, 00153, Roma, Italy
| | - Chiara Facca
- Department of Environmental Science, Informatics and Statistics, University Ca' Foscari Venezia, Via Torino 155, 301702, Mestre, VE, Italy
| | - Robert Loos
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Helle Skejo
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Andrea Beghi
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Franca Pandolfi
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Pietro Genoni
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Teresa Lettieri
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy.
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Bukin YS, Kravtsova LS, Peretolchina TE, Fedotov AP, Tupikin AE, Kabilov MR, Sherbakov DY, Mincheva EV. DNA metabarcoding of benthic algae and associated eukaryotes from Lake Baikal in the face of rapid environmental changes. Vavilovskii Zhurnal Genet Selektsii 2022; 26:86-95. [PMID: 35342852 PMCID: PMC8894627 DOI: 10.18699/vjgb-22-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/05/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Here we report new data describing the biodiversity of phytobenthic communities based on DNA-metabarcoding using the 18S rDNA marker and the Illumina MiSeq system. The study was initiated due to the blooming of f ilamentous algae (mainly of the genus Spirogyra) and cyanobacteria in the coastal zone of Lake Baikal under climate change and anthropogenic impact. The composition and taxonomic diversity of algae and other organisms associated with them on different sites of Lake Baikal (near Bolshoi Ushkaniy Island, in Listvennichny Bay) and in the Kaya (within the city of Irkutsk, located in the same drainage basin as Lake Baikal) were determined using
DNAmetabarcoding.
About 15 thousand reads of the 18S rRNA marker were obtained by applying NGS (next-generation
sequencing). The species of algae dominating in the number of reads, as well as the diff icult-to-identify taxa
(Stramenopiles, Alveolata, Euglenozoa, Chromista, Rhizaria, Amoebozoa, etc.), which play an important role in the
functioning and formation of the structure of algal communities, were revealed. The Shannon index of the communities
studied ranges from 1.56 to 2.72. The advantages and weaknesses of using DNA-metabarcoding based on the
18S rRNA gene fragment for studying the structure of algal communities are shown. The advantage of this method is
the possibility to more fully determine the diversity of eukaryotes taxa, which are diff icult to identify by morphology,
without involving a large number of specialists, while the disadvantage of the method is the distortion that may occur
during the PCR. Here, ways of solving this problem are proposed. The results of the study show that the analysis
of the minor component of the eukaryotic community in samples (organisms with low biomass) consisting of a
mixture of multicellular and unicellular organisms requires a read-depths of at least 100,000 sequences per sample.
In general, the DNA-metabarcoding method is recommended for studying the structure of algal communities and
eukaryotes associated with them.
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Affiliation(s)
- Yu. S. Bukin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences; Irkutsk State University
| | - L. S. Kravtsova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
| | - T. E. Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
| | - A. P. Fedotov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
| | - A. E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - D. Yu. Sherbakov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
| | - E. V. Mincheva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
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Ghosh S, Sarangi AN, Mukherjee M, Singh D, Madhavi M, Tripathy S. Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India. Bioinform Biol Insights 2021; 15:11779322211025332. [PMID: 34220198 PMCID: PMC8221699 DOI: 10.1177/11779322211025332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.
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Affiliation(s)
- Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Mayuri Mukherjee
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madduluri Madhavi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Shao K, Yao X, Wu Z, Jiang X, Hu Y, Tang X, Xu Q, Gao G. The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China. BMC Microbiol 2021; 21:179. [PMID: 34126927 PMCID: PMC8201733 DOI: 10.1186/s12866-021-02252-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/17/2021] [Indexed: 11/19/2022] Open
Abstract
Background Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations. Results We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6–97.30 %), Actinobacteria (0.1–17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12–80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33–49.28 %). Other dominant bacterial genera including Massilia (0.06–25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01–22.86 %), Brevundimonas (0.01–12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08–23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4+ )were the dominant environmental drivers affecting the bacterial community variance. Conclusions The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02252-9.
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Affiliation(s)
- Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Xin Yao
- School of Environment and Planning, Liaocheng University, 252000, Liaocheng, China
| | - Zhaoshi Wu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Xingyu Jiang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Qiujin Xu
- Chinese Research Academy of Environmental Sciences, 100012, Beijing, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China.
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Rojas-Jimenez K, Araya-Lobo A, Quesada-Perez F, Akerman-Sanchez J, Delgado-Duran B, Ganzert L, Zavialov PO, Alymkulov S, Kirillin G, Grossart HP. Variation of bacterial communities along the vertical gradient in Lake Issyk Kul, Kyrgyzstan. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:337-347. [PMID: 33538408 DOI: 10.1111/1758-2229.12935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/19/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
We explored the diversity and community composition of bacteria along a vertical gradient in Lake Issyk Kul, Kyrgyzstan, one of the world's largest and deepest brackish lakes. We identified 4904 bacterial amplicon sequence variants based on the 16S rRNA gene analysis and determined significant changes in the composition, responding mainly to depth and salinity. A higher abundance of Proteobacteria and Bacteroidetes was observed in the surface waters and lake tributaries. Cyanobacteria were more abundant in the deep chlorophyll maximum from 28.5 to 128 m, while Planctomycetes and Chloroflexi were dominant in the deepest layers, from 128 to 600 m. According to our machine learning analyses, depth and temperature were the most critical environmental factors, with strong effects on Proteobacteria, Planctomycetes and Chloroflexi, while oxygen was associated with the variations in Cyanobacteria. We also observed that with increasing depth, the alpha diversity values increased. The dominance of Planctomycetes and Chloroflexi in the deepest layers can only be seen in a few lakes of the world. However, the lake is facing increasing anthropogenic and climatic pressure. There is an urgent need to understand better the ecological role and function of these unique deep-water microbial communities.
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Affiliation(s)
| | - Alex Araya-Lobo
- Escuela de Biología, Universidad de Costa Rica, San José, 11501, Costa Rica
| | | | | | | | - Lars Ganzert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, Stechlin, D-16775, Germany
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.7 Geomicrobiology, Telegrafenberg C-422, Potsdam, 14473, Germany
- University of Goettingen, Experimental Phycology and Culture Collection of Algae (EPSAG), Nikolausberger Weg 18, Goettingen, 37073, Germany
| | | | - Salmor Alymkulov
- Institute of Physics, National Academy of Sciences of Kyrgyz Republic, Chui Avenue, 265-a, Bishkek, 720071, Kyrgyzstan
| | - Georgiy Kirillin
- Department of Ecohydrology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, Berlin, D-12587, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, Stechlin, D-16775, Germany
- Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2, Potsdam, 14469, Germany
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10
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Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake. ISME JOURNAL 2021; 15:3412-3417. [PMID: 34012102 DOI: 10.1038/s41396-021-01011-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/08/2022]
Abstract
Lake Baikal is the deepest (~1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a ~600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.
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11
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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12
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Galachyants AD, Krasnopeev AY, Podlesnaya GV, Potapov SA, Sukhanova EV, Tikhonova IV, Zimens EA, Kabilov MR, Zhuchenko NA, Gorshkova AS, Suslova MY, Belykh OI. Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal. Microorganisms 2021; 9:842. [PMID: 33920057 PMCID: PMC8071047 DOI: 10.3390/microorganisms9040842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes. The diversity of rhodopsin-containing bacteria in neuston and plankton of Lake Baikal was comparable to other studied water bodies. Bacteroidetes along with Proteobacteria were the prevailing phyla, and Verrucomicrobia and Planctomycetes were also detected. The number of rhodopsin sequences unclassified to the phylum level was rather high: 29% in the water microbiomes and 22% in the epilithon. Diversity of rhodopsin-containing bacteria in epilithic biofilms was comparable with that in neuston and plankton at the phyla level. Unweighted pair group method with arithmetic mean (UPGMA) and non-metric multidimensional scaling (NMDS) analysis indicated a distinct discrepancy between epilithon and microbial communities of water (including neuston and plankton) in the 16S rRNA, pufM and rhodopsin genes.
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Affiliation(s)
- Agnia Dmitrievna Galachyants
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Andrey Yurjevich Krasnopeev
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Galina Vladimirovna Podlesnaya
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Sergey Anatoljevich Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Elena Viktorovna Sukhanova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Irina Vasiljevna Tikhonova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Ekaterina Andreevna Zimens
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Marsel Rasimovich Kabilov
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia Albertovna Zhuchenko
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Anna Sergeevna Gorshkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
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13
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Butina TV, Bukin YS, Petrushin IS, Tupikin AE, Kabilov MR, Belikov SI. Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics. Microorganisms 2021; 9:760. [PMID: 33916464 PMCID: PMC8066274 DOI: 10.3390/microorganisms9040760] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake's viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.
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Affiliation(s)
- Tatyana V. Butina
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Yurij S. Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Ivan S. Petrushin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Sergey I. Belikov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
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14
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David GM, Moreira D, Reboul G, Annenkova NV, Galindo LJ, Bertolino P, López-Archilla AI, Jardillier L, López-García P. Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake. Environ Microbiol 2020; 23:1436-1451. [PMID: 33270368 DOI: 10.1111/1462-2920.15346] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023]
Abstract
Identifying which abiotic and biotic factors determine microbial community assembly is crucial to understand ecological processes and predict how communities will respond to environmental change. While global surveys aim at addressing this question in the world's oceans, equivalent studies in large freshwater systems are virtually lacking. Being the oldest, deepest and most voluminous freshwater lake on Earth, Lake Baikal offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Here, we characterized the structure of planktonic microbial eukaryotic communities (0.2-30 μm cell size) along a North-South latitudinal gradient (~600 km) from samples collected in coastal and pelagic waters and from surface to the deepest zones (5-1400 m) using an 18S rRNA gene metabarcoding approach. Our results show complex and diverse protist communities dominated by alveolates (ciliates and dinoflagellates), ochrophytes and holomycotan lineages, with cryptophytes, haptophytes, katablepharids and telonemids in moderate abundance and many low-frequency lineages, including several typical marine members, such as diplonemids, syndinians and radiolarians. Depth had a strong significant effect on protist community stratification. By contrast, the effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic communities were significantly more interconnected than communities from the dark water column and suggest specific biotic interactions between autotrophic, heterotrophic and parasitic lineages that influence protist community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, our comprehensive protist survey constitutes a useful reference to monitor ongoing community shifts.
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Affiliation(s)
- Gwendoline M David
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guillaume Reboul
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Nataliia V Annenkova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Luis J Galindo
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Ludwig Jardillier
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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15
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Zhang L, Cheng Y, Qian C, Lu W. Bacterial community evolution along full-scale municipal wastewater treatment processes. JOURNAL OF WATER AND HEALTH 2020; 18:665-680. [PMID: 33095191 DOI: 10.2166/wh.2020.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sewage pollution is a major threat to public health because sewage is always accompanied by pathogens. Generally, wastewater treatment plants (WWTP) receive and treat sewage to control pathogenic risks and improve environmental health. This study investigated the changes in the bacterial community over the course of treatment by a WWTP. Illumina MiSeq high-throughput sequencing was performed to characterize the bacterial communities in the WWTP. This study found that potential pathogens in the WWTP, especially the genera Arcobacter and Acinetobacter, were greatly reduced. In addition, high chemical oxygen demand levels provided excessive growth substrates for the genera Hyphomicrobium and Rhodoplanes, the abundance of which could exceed autotrophic bacteria, increasing the ammonium removal. According to the network analysis, the bacterial assemblage was not randomly arranged in the WWTP, and various defined processes led to higher intra-phylum (such as Proteobacteria) coexistence than expected. Moreover, the metabolic functions of bacterial communities significantly improved in the WWTP compared with the influent. Together, the data in this study emphasize the need to understand the bacterial community of WWTPs better. When analyzing the risks of WWTP drainage systems to the environment and human health, these data should be considered.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China E-mail:
| | - Yanan Cheng
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China E-mail:
| | - Chang Qian
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China E-mail:
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China
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16
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Abstract
The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i. The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.e., not impacted with organohalogens of anthropogenic origin). The broad environmental distribution of Dehalococcoidia, as well as other organohalide-respiring bacteria, supports the concept of active halogen cycling and the natural formation of organohalogens in various ecosystems. Dechlorination reduces recalcitrance and renders organics susceptible to metabolic oxidation by diverse microbial taxa. During reductive dechlorination, hydrogenotrophic organohalide-respiring bacteria, in particular Dehalococcoidia, can consume hydrogen to low consumption threshold concentrations (<0.3 nM) and enable syntrophic oxidation processes. These functional attributes and the broad distribution imply that Dehalococcoidia play relevant roles in carbon cycling in anoxic ecosystems.
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17
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Zemskaya TI, Cabello-Yeves PJ, Pavlova ON, Rodriguez-Valera F. Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth. Appl Microbiol Biotechnol 2020; 104:6079-6090. [PMID: 32424436 DOI: 10.1007/s00253-020-10660-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/19/2022]
Abstract
Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments. KEY POINTS: • The chemical composition and limnic features of the deepest lake on Earth determine the vital activity of microorganisms. • The diversity, ecology, and role of individual taxa of microorganisms were studied using cultivation and molecular methods. • Data of large metagenomic datasets in the epipelagic and bathypelagic layers of the water column in southern Baikal were discussed.
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Affiliation(s)
- Tamara I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Olga N Pavlova
- 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.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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18
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Paver SF, Newton RJ, Coleman ML. Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry. Environ Microbiol 2019; 22:433-446. [PMID: 31736217 PMCID: PMC6973239 DOI: 10.1111/1462-2920.14862] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 10/29/2019] [Accepted: 11/14/2019] [Indexed: 11/29/2022]
Abstract
The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.
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Affiliation(s)
- Sara F Paver
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
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19
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Zhang L, Cheng Y, Gao G, Jiang J. Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16203966. [PMID: 31627458 PMCID: PMC6844080 DOI: 10.3390/ijerph16203966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022]
Abstract
Sediment bacterial communities are critical for the circulation of nutrients in lake ecosystems. However, the bacterial community function and co-occurrence models of lakes have not been studied in depth. In this study, we observed significant seasonal changes and non-significant spatial changes in the beta diversity and community structure of sediment bacteria in Lake Chaohu. Through linear discriminant analysis effect size (LEfSe), we observed that certain taxa (from phylum to genus) have consistent enrichment between seasons. The sudden appearance of a Firmicutes population in spring samples from the Zhaohe River, an estuary of Lake Chaohu, and the dominance of Firmicutes populations in other regions suggested that exogenous pollution and environmental induction strongly impacted the assembly of bacterial communities in the sediments. Several taxa that serve as intermediate centers in Co-occurrence network analysis (i.e., Pedosphaeraceae, Phycisphaeraceae, Anaerolineaceae, and Geobacteraceae) may play an important role in sediments. Furthermore, compared with previous studies of plants and animals, the results of our study suggest that various organisms, including microorganisms, are resistant to environmental changes and/or exogenous invasions, allowing them to maintain their community structure.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China.
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Yu Cheng
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China.
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Jiahu Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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20
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Salmaso N. Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes. Front Microbiol 2019; 10:2257. [PMID: 31636614 PMCID: PMC6788347 DOI: 10.3389/fmicb.2019.02257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/17/2019] [Indexed: 12/04/2022] Open
Abstract
In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O2 conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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21
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Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community. Int J Mol Sci 2019; 20:ijms20184415. [PMID: 31500341 PMCID: PMC6770359 DOI: 10.3390/ijms20184415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/23/2022] Open
Abstract
Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO2/H2). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH4 L−1 d−1) was highest in the culture grown with tryptone, yeast extract, and CO2/H2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.
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22
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Zakharenko AS, Galachyants YP, Morozov IV, Shubenkova OV, Morozov AA, Ivanov VG, Pimenov NV, Krasnopeev AY, Zemskaya TI. Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal. MICROBIAL ECOLOGY 2019; 78:269-285. [PMID: 30483839 DOI: 10.1007/s00248-018-1299-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.
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Affiliation(s)
- Aleksandra S Zakharenko
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia.
| | - Yuriy P Galachyants
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Igor V Morozov
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga V Shubenkova
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Alexey A Morozov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Vyacheslav G Ivanov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Nikolay V Pimenov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Andrey Y Krasnopeev
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Tamara I Zemskaya
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
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23
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Aguilar P, Dorador C, Vila I, Sommaruga R. Bacterioplankton composition in tropical high-elevation lakes of the Andean plateau. FEMS Microbiol Ecol 2019; 94:4810748. [PMID: 29346530 PMCID: PMC6018938 DOI: 10.1093/femsec/fiy004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/15/2018] [Indexed: 01/12/2023] Open
Abstract
High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbor a unique genomic repertoire, but their composition and diversity are largely unknown. Here, we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (≥4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. Operational taxonomic units (OTUs) composition was significantly different among lakes and between seasons. Members of the class Opitutae, Spartobacteria, Burkholderiales and Actinobacteria were dominant, but only the hgcI clade (Actinobacteria) and the Comamonadaceae family (Burkholderiales) were shared between seasons among the three lakes. In general, a large percentage (up to 42%) of the rare OTUs was unclassified even at the family level. In one lake, a pycnocline and an anoxic water layer with high abundance of Thiocapsa sp. was found in the wet season indicating that the known polymictic thermal condition is not always given. Our study highlights the particular BCC of tropical high-elevation lakes and also how little is known about the variability in physico-chemical conditions of these ecosystems.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Technikerstr 25, Innsbruck 6020, Austria
| | - Cristina Dorador
- Laboratory of Microbial Complexity and Functional Ecology, Instituto Antofagasta & Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Chile.,Centre for Biotechnology and Bioengineering (CeBiB), Beaucheff 851 Antofagasta, Chile
| | - Irma Vila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Av. Libertador Bernardo O'Higgins 1058 Santiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Technikerstr 25, Innsbruck 6020, Austria
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24
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The effect of 16S rRNA region choice on bacterial community metabarcoding results. Sci Data 2019; 6:190007. [PMID: 30720800 PMCID: PMC6362892 DOI: 10.1038/sdata.2019.7] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/13/2018] [Indexed: 12/01/2022] Open
Abstract
In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.
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25
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Microorganisms Collected from the Surface of Freshwater Lakes Using a Drone Water Sampling System (DOWSE). WATER 2019. [DOI: 10.3390/w11010157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
New tools and technology are needed to study microorganisms in freshwater environments. Little is known about spatial distribution and ice nucleation activity (INA) of microorganisms in freshwater lakes. We developed a system to collect water samples from the surface of lakes using a 3D-printed sampling device tethered to a drone (DOWSE, DrOne Water Sampling SystEm). The DOWSE was used to collect surface water samples at different distances from the shore (1, 25, and 50 m) at eight different freshwater lakes in Austria in June 2018. Water samples were filtered, and microorganisms were cultured on two different media types, TSA (a general growth medium) and KBC (a medium semi-selective for bacteria in the genus Pseudomonas). Mean concentrations (colony forming units per mL, or CFU/mL) of bacteria cultured on TSA ranged from 19,800 (Wörthersee) to 210,500 (Gosaulacke) CFU/mL, and mean concentrations of bacteria cultured on KBC ranged from 2590 (Ossiachersee) to 11,000 (Vorderer Gosausee) CFU/mL. There was no significant difference in sampling distance from the shore for concentrations of microbes cultured on TSA (p = 0.28). A wireless bathymetry sensor was tethered to the drone to map temperature and depth across the sampling domain of each of the lakes. At the 50 m distance from the shore, temperature ranged from 17 (Hinterer Gosausee, and Gosaulacke) to 26 °C (Wörthersee), and depth ranged from 2.8 (Gosaulacke) to 11.1 m (Grundlsee). Contour maps of concentrations of culturable bacteria across the drone sampling domain revealed areas of high concentrations (hot spots) in some of the lakes. The percentage of ice-nucleation active (ice+) bacteria cultured on KBC ranged from 0% (0/64) (Wörthersee) to 58% (42/72) (Vorderer Gosausee), with a mean of 28% (153/544) for the entire sample set. Future work aims to elucidate the structure and function of entire microbial assemblages within and among the Austrian lakes.
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26
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Mikhailov IS, Zakharova YR, Bukin YS, Galachyants YP, Petrova DP, Sakirko MV, Likhoshway YV. Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom. MICROBIAL ECOLOGY 2019; 77:96-109. [PMID: 29882155 DOI: 10.1007/s00248-018-1212-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 05/28/2018] [Indexed: 05/25/2023]
Abstract
The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.
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Affiliation(s)
- Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033.
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Maria V Sakirko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk, Russia, 664033
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27
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Galachyants AD, Tomberg IV, Sukhanova EV, Shtykova YR, Suslova MY, Zimens EA, Blinov VV, Sakirko MV, Domysheva VM, Belykh OI. Bacterioneuston in Lake Baikal: Abundance, Spatial and Temporal Distribution. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E2587. [PMID: 30463268 PMCID: PMC6266163 DOI: 10.3390/ijerph15112587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/12/2018] [Accepted: 11/18/2018] [Indexed: 11/21/2022]
Abstract
An aquatic surface microlayer covers more than 70% of the world's surface. Our knowledge about the biology of the surface microlayer of Lake Baikal, the most ancient lake on Earth with a surface area of 31,500 km², is still scarce. The total bacterial abundance, the number of cultured heterotrophic temporal bacteria, and the spatial distribution of bacteria in the surface microlayer and underlying waters of Lake Baikal were studied. For the first time, the chemical composition of the surface microlayer of Lake Baikal was determined. There were significant differences and a direct relationship between the total bacterial abundance in the surface microlayer and underlying waters of Lake Baikal, as well as between the number of cultured heterotrophic bacteria in studied water layers in the period of summer stratification. In the surface microlayer, the share of cultured heterotrophic bacteria was higher than in the underlying waters. The surface microlayer was characterized by enrichment with PO₄3-, total organic carbon and suspended particulate matter compared to underlying waters. A direct relationship was found between the number of bacteria in the surface microlayer and environmental factors, including temperature, total organic carbon and suspended particulate matter concentration.
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Affiliation(s)
- Agnia D Galachyants
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Irina V Tomberg
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Elena V Sukhanova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Yulia R Shtykova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Maria Yu Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Ekaterina A Zimens
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Vadim V Blinov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Maria V Sakirko
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Valentina M Domysheva
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
| | - Olga I Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya, Irkutsk 664033, Russia.
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28
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Kong Z, Kou W, Ma Y, Yu H, Ge G, Wu L. Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake. Can J Microbiol 2018; 64:786-797. [DOI: 10.1139/cjm-2018-0126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring–winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.
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Affiliation(s)
- Zhaoyu Kong
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
- Key Laboratory of Aquatic Resources and Utilization of Jiangxi, Nanchang University, Nanchang 330022, China
| | - Wenbo Kou
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Yantian Ma
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Haotian Yu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Gang Ge
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
- Key Laboratory of Aquatic Resources and Utilization of Jiangxi, Nanchang University, Nanchang 330022, China
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29
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Ji B, Qin H, Guo S, Chen W, Zhang X, Liang J. Bacterial communities of four adjacent fresh lakes at different trophic status. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:388-394. [PMID: 29649784 DOI: 10.1016/j.ecoenv.2018.03.086] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 05/20/2023]
Abstract
Knowing the microbial compositions in fresh lakes is significant to explore the mechanisms of eutrophication and algal blooms. This study reported on the bacterial communities of the four adjacent fresh lakes at different trophic status by Illumina MiSeq Platform, which were Tangxun Lake (J1), Qingling Lake (J2), Huangjia Lake (J3) and Niushan Lake (J4) in Wuhan, China. J1 had the highest salinity and phosphorus. J2 was abundant in TC (Total Carbon)/TOC (Total Organic Carbon.), calcium and magnesium. J3 had the highest content of nitrogen, iron and pollution of heavy metals. High-throughput sequencing analysis of the 16S rRNA gene revealed that the eutrophic lakes (J1, J2 and J3) were dominated by Cyanobacteria (46.1% for J1, 40.8% for J2, 33.4% for J3) and the oligotrophic lake (J4) was dominated by Actinobacteria (34.2%). An increase of Cyanobacteria could inhibit the growth of Proteobacteria, Actinobacteria and Bacteroidetes. Functional inferences from 16S rRNA sequences suggested that J4 had more abundant bacteria with regard to substrate metabolism than J1, J2, and J3. Burkholderia and Fluviicola might be a suggestion of good water quality. The results demonstrated that the bacterial community could well reflect the water quality of the four lakes.
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Affiliation(s)
- Bin Ji
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China; Hubei Key Laboratory of Regional Development and Environmental Response (Hubei University), Wuhan 430062, China.
| | - Hui Qin
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Shaodong Guo
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Wei Chen
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xuechun Zhang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Jiechao Liang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
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30
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Salmaso N, Albanese D, Capelli C, Boscaini A, Pindo M, Donati C. Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake. MICROBIAL ECOLOGY 2018; 76:125-143. [PMID: 29192335 DOI: 10.1007/s00248-017-1120-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing (HTS) was used to analyze the seasonal variations in the bacterioplankton community composition (BCC) in the euphotic layer of a large and deep lake south of the Alps (Lake Garda). The BCC was analyzed throughout two annual cycles by monthly samplings using the amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by the MiSeq Illumina platform. The dominant and most diverse bacterioplankton phyla were among the more frequently reported in freshwater ecosystems, including the Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctomycetes. As a distinctive feature, the development of the BCC showed a cyclical temporal pattern in the two analyzed years and throughout the euphotic layer. The recurring temporal development was controlled by the strong seasonality in water temperature and thermal stratification, and by cyclical temporal changes in nutrients and, possibly, by the remarkable annual cyclical development of cyanobacteria and eukaryotic phytoplankton hosting bacterioplankton that characterizes Lake Garda. Further downstream analyses of operational taxonomic units associated to cyanobacteria allowed confirming the presence of the most abundant taxa previously identified by microscopy and/or phylogenetic analyses, as well as the presence of other small Synechococcales/Chroococcales and rare Nostocales never identified so far in the deep lakes south of the Alps. The implications of the high diversity and strong seasonality are relevant, opening perspectives for the definition of common and discriminating patterns characterizing the temporal and spatial distribution in the BCC, and for the application of the new sequencing technologies in the monitoring of water quality in large and deep lakes.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy.
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Camilla Capelli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
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31
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Potapov S, Belykh O, Krasnopeev A, Gladkikh A, Kabilov M, Tupikin A, Butina T. Assessing the diversity of the g23 gene of T4-like bacteriophages from Lake Baikal with high-throughput sequencing. FEMS Microbiol Lett 2018; 365:4693836. [PMID: 29228190 DOI: 10.1093/femsle/fnx264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/04/2017] [Indexed: 01/09/2023] Open
Abstract
Based on second generation sequencing (MiSeq platform, Illumina), we determined the genetic diversity of T4-like bacteriophages of the family Myoviridae by analysing fragments of the major capsid protein gene g23 in the plankton of Lake Baikal. The sampling depth in our study was significantly higher than in those obtained by the Sanger method before. We obtained 33 701 sequences of the g23 gene fragments, 141 operational taxonomic units (OTUs) of which were identified. 86 OTUs (60.9%) had the closest relatives from lakes Bourget and Annecy, and 28 OTUs (19.8%) had the highest identity with the Baikal g23 clones, which had been previously identified in the northern and southern basins of the lake by the Sanger method. The remaining OTUs were similar to the clones from other ecosystems. We showed a high genetic diversity of T4-type bacteriophages and a genetic difference with the phage communities from other ecosystems.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
| | - Olga Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
| | - Andrey Krasnopeev
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
| | - Anna Gladkikh
- Laboratory of Cholera, Irkutsk Antiplague Research Institute of Siberia and Far East, Irkutsk 664047, Russia
| | - Marsel Kabilov
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Aleksey Tupikin
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Tatyana Butina
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
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32
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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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Scherer PI, Millard AD, Miller A, Schoen R, Raeder U, Geist J, Zwirglmaier K. Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes. Front Microbiol 2017; 8:2387. [PMID: 29255452 PMCID: PMC5722842 DOI: 10.3389/fmicb.2017.02387] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/20/2017] [Indexed: 02/01/2023] Open
Abstract
Bacterioplankton plays an essential role in aquatic ecosystems, and cyanobacteria are an influential part of the microbiome in many water bodies. In freshwaters used for recreational activities or drinking water, toxic cyanobacteria cause concerns due to the risk of intoxication with cyanotoxins, such as microcystins. In this study, we aimed to unmask relationships between toxicity, cyanobacterial community composition, and environmental factors. At the same time, we assessed the correlation of a genetic marker with microcystin concentration and aimed to identify the main microcystin producer. We used Illumina MiSeq sequencing to study the bacterioplankton in two recreational lakes in South Germany. We quantified a microcystin biosynthesis gene (mcyB) using qPCR and linked this information with microcystin concentration to assess toxicity. Microcystin biosynthesis gene (mcyE)-clone libraries were used to determine the origin of microcystin biosynthesis genes. Bloom toxicity did not alter the bacterial community composition, which was highly dynamic at the lowest taxonomic level for some phyla such as Cyanobacteria. At the OTU level, we found distinctly different degrees of temporal variation between major bacteria phyla. Cyanobacteria and Bacteroidetes showed drastic temporal changes in their community compositions, while the composition of Actinobacteria remained rather stable in both lakes. The bacterial community composition of Alpha- and Beta-proteobacteria remained stable over time in Lake Klostersee, but it showed temporal variations in Lake Bergknappweiher. The presence of potential microcystin degraders and potential algicidal bacteria amongst prevalent Bacteroidetes and Alphaproteobacteria implied a role of those co-occurring heterotrophic bacteria in cyanobacterial bloom dynamics. Comparison of both lakes studied revealed a large shared microbiome, which was shaped toward the lake specific community composition by environmental factors. Microcystin variants detected were microcystin-LR, -RR, and -YR. The maximum microcystin concentrations measured was 6.7 μg/L, a value still acceptable for recreational waters but not drinking water. Microcystin concentration correlated positively with total phosphorus and mcyB copy number. We identified low abundant Microcystis sp. as the only microcystin producer in both lakes. Therefore, risk assessment efforts need to take into account the fact that non-dominant species may cause toxicity of the blooms observed.
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Affiliation(s)
- Pia I Scherer
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Andrew D Millard
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Andreas Miller
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Renate Schoen
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Uta Raeder
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Juergen Geist
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Katrin Zwirglmaier
- Limnological Research Station Iffeldorf, Aquatic Systems Biology Unit, Department of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
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34
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Okazaki Y, Fujinaga S, Tanaka A, Kohzu A, Oyagi H, Nakano SI. Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes. THE ISME JOURNAL 2017; 11:2279-2293. [PMID: 28585941 PMCID: PMC5607371 DOI: 10.1038/ismej.2017.89] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/16/2017] [Accepted: 05/05/2017] [Indexed: 02/01/2023]
Abstract
The oxygenated hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that the communities in the oxygenated hypolimnia were distinct from those in the epilimnia and identified several predominant lineages inhabiting multiple lakes. Catalyzed reporter deposition fluorescence in situ hybridization revealed that abundant hypolimnion-specific lineages, CL500-11 (Chloroflexi), CL500-3, CL500-37, CL500-15 (Planctomycetes) and Marine Group I (Thaumarchaeota), together accounted for 1.5-32.9% of all bacterioplankton in the hypolimnion of the lakes. Furthermore, an analysis of single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of different sub-populations between lakes and water layers among the lineages occurring in the entire water layer (for example, acI-B1 and acI-A7). Collectively, these results provide the first comprehensive overview of the bacterioplankton community in the oxygenated hypolimnion of deep freshwater lakes.
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Affiliation(s)
- Yusuke Okazaki
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Shohei Fujinaga
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Atsushi Tanaka
- National Institute for Environmental Studies, Tsukuba, Japan
| | - Ayato Kohzu
- National Institute for Environmental Studies, Tsukuba, Japan
| | - Hideo Oyagi
- College of Humanities and Sciences, Nihon University, Tokyo, Japan
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35
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Yang Y, Higgins SA, Yan J, Şimşir B, Chourey K, Iyer R, Hettich RL, Baldwin B, Ogles DM, Löffler FE. Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes. ISME JOURNAL 2017; 11:2767-2780. [PMID: 28809851 DOI: 10.1038/ismej.2017.127] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 06/12/2017] [Accepted: 06/16/2017] [Indexed: 12/15/2022]
Abstract
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene. 16S rRNA gene amplicon and qPCR analyses revealed a predominance of Dhgm sequences, but Dehalococcoides mccartyi (Dhc) biomarker genes were not detected. The enumeration of Dhgm 16S rRNA genes demonstrated VC-dependent growth, and 6.55±0.64 × 108 cells were measured per μmole of chloride released. Metagenome sequencing enabled the assembly of a Dhgm draft genome, and 52 putative reductive dehalogenase (RDase) genes were identified. Proteomic workflows identified a putative VC RDase with 49 and 56.1% amino acid similarity to the known VC RDases VcrA and BvcA, respectively. A survey of 1,173 groundwater samples collected from 111 chlorinated solvent-contaminated sites in the United States and Australia revealed that Dhgm 16S rRNA genes were frequently detected and outnumbered Dhc in 65% of the samples. Dhgm are likely greater contributors to reductive dechlorination of chlorinated solvents in contaminated aquifers than is currently recognized, and non-polluted environments represent sources of organohalide-respiring bacteria with novel RDase genes.
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Affiliation(s)
- Yi Yang
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Steven A Higgins
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jun Yan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Burcu Şimşir
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Robert L Hettich
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
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36
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Sessitsch A, Smalla K, Johnson L, Mitter B. Editorial: Special thematic issue on microbe-assisted crop production. FEMS Microbiol Ecol 2016; 92:fiw167. [PMID: 27495243 DOI: 10.1093/femsec/fiw167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, Braunschweig 38104, Germany
| | - Linda Johnson
- Agresearch Grasslands Research Centre, Forage Improvement, Tennent Drive, Palmerston North 4442, New Zealand
| | - Birgit Mitter
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
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