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Acosta E, Nitsche F, Dorador C, Arndt H. Protist communities of microbial mats from the extreme environments of five saline Andean lagoons at high altitudes in the Atacama Desert. Front Microbiol 2024; 15:1356977. [PMID: 38572231 PMCID: PMC10987879 DOI: 10.3389/fmicb.2024.1356977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/08/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Heterotrophic protists colonizing microbial mats have received little attention over the last few years, despite their importance in microbial food webs. A significant challenge originates from the fact that many protists remain uncultivable and their functions remain poorly understood. Methods Metabarcoding studies of protists in microbial mats across high-altitude lagoons of different salinities (4.3-34 practical salinity units) were carried out to provide insights into their vertical stratification at the millimeter scale. DNA and cDNA were analyzed for selected stations. Results Sequence variants classified as the amoeboid rhizarian Rhogostoma and the ciliate Euplotes were found to be common members of the heterotrophic protist communities. They were accompanied by diatoms and kinetoplastids. Correlation analyses point to the salinity of the water column as a main driver influencing the structure of the protist communities at the five studied microbial mats. The active part of the protist communities was detected to be higher at lower salinities (<20 practical salinity units). Discussion We found a restricted overlap of the protist community between the different microbial mats indicating the uniqueness of these different aquatic habitats. On the other hand, the dominating genotypes present in metabarcoding were similar and could be isolated and sequenced in comparative studies (Rhogostoma, Euplotes, Neobodo). Our results provide a snapshot of the unculturable protist diversity thriving the benthic zone of five athalossohaline lagoons across the Andean plateau.
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Affiliation(s)
- Eduardo Acosta
- Department of General Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Frank Nitsche
- Department of General Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Hartmut Arndt
- Department of General Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
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Samylina OS, Kosyakova AI, Krylov AA, Sorokin DY, Pimenov NV. Salinity-induced succession of phototrophic communities in a southwestern Siberian soda lake during the solar activity cycle. Heliyon 2024; 10:e26120. [PMID: 38404883 PMCID: PMC10884861 DOI: 10.1016/j.heliyon.2024.e26120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/09/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
A variety of lakes located in the dry steppe area of southwestern Siberia are exposed to rapid climatic changes, including intra-century cycles with alternating dry and wet phases driven by solar activity. As a result, the salt lakes of that region experience significant fluctuations in water level and salinity, which have an essential impact on the indigenous microbial communities. But there are few microbiological studies that have analyzed this impact, despite its importance for understanding the functioning of regional water ecosystems. This work is a retrospective study aimed at analyzing how solar activity-related changes in hydrological regime affect phototrophic microbial communities using the example of the shallow soda lake Tanatar VI, located in the Kulunda steppe (Altai Region, Russia, southwestern Siberia). The main approach used in this study was the comparison of hydrochemical and microscopic data obtained during annual field work with satellite and solar activity data for the 12-year observation period (2011-2022). The occurrence of 33 morphotypes of cyanobacteria, two key morphotypes of chlorophytes, and four morphotypes of anoxygenic phototrophic bacteria was analyzed due to their easily recognizable morphology. During the study period, the lake surface changed threefold and the salinity changed by more than an order of magnitude, which strongly correlated with the phases of the solar activity cycles. The periods of high (2011-2014; 100-250 g/L), medium (2015-2016; 60 g/L), extremely low (2017-2020; 13-16 g/L), and low (2021-2022; 23-34 g/L) salinity with unique biodiversity of phototrophic communities were distinguished. This study shows that solar activity cycles determine the dynamics of the total salinity of a southwestern Siberian soda lake, which in turn determines the communities and microorganisms that will occur in the lake, ultimately leading to cyclical changes in alternative states of the ecosystem (dynamic stability).
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Affiliation(s)
- Olga S. Samylina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
| | - Anastasia I. Kosyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
- Faculty of Soil Science, Moscow State University, GSP-1, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Artem A. Krylov
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovskiy Prospekt, 36, 117997 Moscow, Russia
| | - Dimitry Yu. Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7-2, Moscow, 117312, Russia
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Ji C, Huang J, Zhang X, Yang G, Xing S, Fu W, Hao Z, Chen B, Zhang X. Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163244. [PMID: 37004770 DOI: 10.1016/j.scitotenv.2023.163244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.
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Affiliation(s)
- Chuning Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Jiu Huang
- School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Xuemeng Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; RDFZ Chaoyang School, Beijing 100028, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Ramos-Tapia I, Salinas P, Núñez R, Cortez D, Soto J, Paneque M. Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems. Microbiol Spectr 2023; 11:e0520022. [PMID: 37102964 PMCID: PMC10269505 DOI: 10.1128/spectrum.05200-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
The lacustrine systems of La Brava and La Punta, located in the Tilopozo sector in the extreme south of Salar de Atacama, are pristine high-altitude Andean lakes found along the central Andes of South America. This shallow ecosystem suffers from permanent evaporation, leading to falling water levels, causing it to recede or disappear during the dry season. This dynamic causes physicochemical changes in lakes, such as low nutrient availability, pH change, and dissolved metals, which can influence the composition of the microbial community. In this study, we used a metataxonomic approach (16S rRNA hypervariable regions V3 to V4) to characterize the sedimentary microbiota of these lakes. To understand how the water column affects and is structured in the microbiota of these lakes, we combined the analysis of the persistence of the water column through satellite images and physicochemical characterization. Our results show a significant difference in abiotic factors and microbiota composition between La Punta and La Brava lakes. In addition, microbiota analysis revealed compositional changes in the ecological disaggregation (main and isolated bodies) and antagonistic changes in the abundance of certain taxa between lakes. These findings are an invaluable resource for understanding the microbiological diversity of high Andean lakes using a multidisciplinary approach that evaluates the microbiota behavior in response to abiotic factors. IMPORTANCE In this study, we analyzed the persistence of the water column through satellite images and physicochemical characterization to investigate the composition and diversity in High Andean Lake Systems in a hyperarid environment. In addition to the persistence of the water column, this approach can be used to analyze changes in the morphology of saline accumulations and persistence of snow or ice; for example, for establishing variable plant cover over time and evaluating the microbiota associated with soils with seasonal changes in plants. This makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. In our case, it was used to study microorganisms capable of resisting desiccation and water restriction for a considerable period and adapting to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration.
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Affiliation(s)
- Ignacio Ramos-Tapia
- Departamento de Metagenómica, Fundación Bionostra Chile Research, San Miguel, Santiago, Chile
| | - Pamela Salinas
- Departamento de Metagenómica, Fundación Bionostra Chile Research, San Miguel, Santiago, Chile
| | - Reynaldo Núñez
- Departamento de Metagenómica, Fundación Bionostra Chile Research, San Miguel, Santiago, Chile
| | - Donna Cortez
- Departamento de Metagenómica, Fundación Bionostra Chile Research, San Miguel, Santiago, Chile
| | - Jorge Soto
- Departamento de Metagenómica, Fundación Bionostra Chile Research, San Miguel, Santiago, Chile
| | - Manuel Paneque
- Laboratory of Bioenergy and Environmental Biotechnology, Department of Environmental Sciences and Natural Resources, Faculty of Agricultural Sciences, University of Chile, La Pintana, Santiago, Chile
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Bryanskaya AV, Shipova AA, Rozanov AS, Kolpakova OA, Lazareva EV, Uvarova YE, Efimov VM, Zhmodik SM, Taran OP, Goryachkovskaya TN, Peltek SE. Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient. BIOLOGY 2022; 11:biology11040605. [PMID: 35453804 PMCID: PMC9031644 DOI: 10.3390/biology11040605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.
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Affiliation(s)
- Alla V. Bryanskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Correspondence: or ; Tel.: +7-383-363-4963 (ext. 4120)
| | - Aleksandra A. Shipova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Alexei S. Rozanov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Oxana A. Kolpakova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena V. Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Yulia E. Uvarova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Vadim M. Efimov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey M. Zhmodik
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Oxana P. Taran
- FRC Krasnoyarsk Science Center SB RAS, Institute of Chemistry and Chemical Technology SB RAS, 660036 Krasnoyarsk, Russia;
| | - Tatyana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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Naik R, Sharma L. Spatio-temporal modelling for the evaluation of an altered Indian saline Ramsar site and its drivers for ecosystem management and restoration. PLoS One 2021; 16:e0248543. [PMID: 34292947 PMCID: PMC8297798 DOI: 10.1371/journal.pone.0248543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022] Open
Abstract
Saline lakes occupy 44% and 23% of the volume and area of all lakes that are tending to suffer from extended dryness, reduced hydro period, or complete desiccation by 2025. The current study is conducted on Sambhar Salt Lake, the largest inland saline Ramsar, site of India, contributing to 9.86% of total salt production. The lake is under threat due to illegal salt pan encroachment, losing brine worth 300 million USD. The objective was to identify the key drivers that affect the lake at a landscape level. Geospatial modelling was conducted for 96 years (1963–2059) at a decadal scale, integrating ground data (birds-soil-water). Land Use Land Cover (LULC) classification was conducted using CORONA aerial imagery of 1963, along with Landsat imageries, using supervised classification for 1972, 1981, 1992, 2009, and 2019, and future prediction for 2029, 2039, 2049, and 2059. Further, images were classified into 8 classes that include the Aravali hills, barren land, saline soil, salt crust, salt pans, wetland, settlement, and vegetation. Past trends show a reduction of wetland from 30.7 to 3.4% at a constant rate (4.23%) to saline soil, which subsequently seemed to increase by 9.3%, increasing thereby the barren land by 4.2%; salt pans by 6.6%, and settlement by 1.2% till 2019. Future predictions show loss of 40% wetland and 120% of saline soil and net increase in 30% vegetation, 40% settlement, 10% salt pan, 5% barren land, and a net loss of 20%, each by Aravali hills and salt crust. Additionally, the ground result shows its alteration and reduction of migratory birds from 3 million to 3000. In the light of UN Decade on Ecosystem Restoration (2021–2030), restoration strategies are suggested; if delayed, more restoration capital may be required than its revenue generation.
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Affiliation(s)
- Rajashree Naik
- Department of Environmental Science, School of Earth Sciences, Central University of Rajasthan, Bandarsindri, Ajmer, Rajasthan, India
| | - Laxmikant Sharma
- Department of Environmental Science, School of Earth Sciences, Central University of Rajasthan, Bandarsindri, Ajmer, Rajasthan, India
- * E-mail:
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Diversity of actinobacteria in sediments of Qaidam Lake and Qinghai Lake, China. Arch Microbiol 2021; 203:2875-2885. [PMID: 33751173 DOI: 10.1007/s00203-021-02277-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/27/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
Using 16S rRNA gene analysis and high-throughput, the diversity and community structure of actinobacteria in the sediments of Qaidam Lake and Qinghai Lake with different salinity and alkalinity in Qinghai-Xizang Plateau were studied, and the differences of actinobacteria community structure and their relationship with environmental factors were discussed. A total of 77 genera belonging to actinobacteria were found in the samples, of which 31 genera were found in the sediment samples of Qaidam Lake with 19 genera being dominant genera, such as Actinomycetes, Corynebacterium, Morella, Bifidobacterium, and 69 genera were found in the sediment samples of Qinghai Lake with 17 genera becoming dominant, such as Ilumattalaer, Actinotalea, Aquihaans and so on. The correlation analysis of environmental factors and community showed that the community structure of the two salt lakes was mainly affected by total salinity, total organic carbon) (TOC) and CO32-, among which TOC was the most influential factor. The functional differences of metabolic pathway enrichment analysis (KEGG) showed that there was a high abundance of metabolic-related functions in the two salt lakes. There were significant differences in the biosynthesis of energy metabolism and other secondary metabolites between the two salt lakes, which may be the main reason for the difference of actinomycete community. The results show that the actinobacteria diversity was rich in the plateau salt lakes, and affected by a variety of physicochemical factors. In addition, there were a large number of unculturable actinobacteria in the sediment, which provides a theoretical basis for the excavation and utilization of actinobacteria resources in salt lakes.
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Bryanskaya AV, Shipova AA, Rozanov AS, Volkova OA, Lazareva EV, Uvarova YE, Goryachkovskaya TN, Peltek SE. Metagenomics dataset used to characterize microbiome in water and sediments of the lake Solenoe (Novosibirsk region, Russia). Data Brief 2020; 34:106709. [PMID: 33490329 PMCID: PMC7807203 DOI: 10.1016/j.dib.2020.106709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/14/2020] [Accepted: 12/28/2020] [Indexed: 11/24/2022] Open
Abstract
This is data on the microbial diversity in the floating cyanobacterial community and sediment samples from the lake Solenoe (Novosibirsk region, Russia) obtained by metagenomic methods. Such a detailed data of the microbial diversity of the Novosibirsk oblast lake ecosystem was carried out for the first time. The purpose of our work was to reveal microbial taxonomic diversity and abundance, metabolic pathways and new enzyme findings the studied lake ecosystem using the next-generation sequencing (NGS) technology and metagenomic analysis. The data was obtained using metagenomics DNA whole genome sequencing (WGS) on Illumina NextSeq and NovaSeq. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with the BioProjects and SRA accession numbers: PRJNA493912 (SRR7943696), PRJNA493952 (SRR7943839) and PRJNA661775 (SRR12601635, SRR12601634, SRR12601633) corresponding to floating cyanobacterial community and sediment layers samples, respectively.
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Affiliation(s)
- Alla V Bryanskaya
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Aleksandra A Shipova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Alexei S Rozanov
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Oxana A Volkova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Elena V Lazareva
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 3 Koptyuga Aven., Novosibirsk 630090, Russia
| | - Yulia E Uvarova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Tatyana N Goryachkovskaya
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Sergey E Peltek
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
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9
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Orlov YL, Ignatov AN, Galieva ER, Dobrovolskaya OB. Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school. BMC Microbiol 2020; 20:348. [PMID: 33228539 PMCID: PMC7686665 DOI: 10.1186/s12866-020-02038-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119146, Moscow, Russia. .,Novosibirsk State University, 630090, Novosibirsk, Russia. .,Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia. .,Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.
| | - Alexander N Ignatov
- Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia.,PhytoEngineering R&D Centre, 141880, Moscow Region, Moscow, Russia
| | | | - Oxana B Dobrovolskaya
- Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia.,Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia
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10
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Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta. Microorganisms 2020; 8:microorganisms8081181. [PMID: 32756460 PMCID: PMC7464526 DOI: 10.3390/microorganisms8081181] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 11/23/2022] Open
Abstract
Due to the low incidence of precipitation attributed to climate change, many high-altitude Andean lakes (HAALs) and lagoons distributed along the central Andes in South America may soon disappear. This includes La Brava–La Punta, a brackish lake system located south of the Salar de Atacama within a hyper-arid and halophytic biome in the Atacama Desert. Variations in the physicochemical parameters of the water column can induce changes in microbial community composition, which we aimed to determine. Sixteen sampling points across La Brava–La Punta were studied to assess the influence of water physicochemical properties on the aquatic microbial community, determined via 16S rRNA gene analysis. Parameters such as pH and the concentrations of silica, magnesium, calcium, salinity, and dissolved oxygen showed a more homogenous pattern in La Punta samples, whereas those from La Brava had greater variability; pH and total silica were significantly different between La Brava and La Punta. The predominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The genera Psychroflexus (36.85%), Thiomicrospira (12.48%), and Pseudomonas (7.81%) were more abundant in La Brava, while Pseudospirillum (20.73%) and Roseovarius (17.20%) were more abundant in La Punta. Among the parameters, pH was the only statistically significant factor influencing the diversity within La Brava lake. These results complement the known microbial diversity and composition in the HAALs of the Atacama Desert.
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11
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Seasonal Shift in Physicochemical Factors Revealed the Ecological Variables that Modulate the Density of Acinetobacter Species in Freshwater Resources. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17103606. [PMID: 32455589 PMCID: PMC7277360 DOI: 10.3390/ijerph17103606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 11/16/2022]
Abstract
Certain environmental variables are responsible for the survival of microorganisms in aquatic environments. The influence of these environmental factors in each season (winter, autumn, spring and summer) of the year can be used to track changes in a microbial population in freshwater resources. In this study, we assessed the effect of seasonal shifts in environmental variables including temperature, pH, total dissolved solids (TDS), total suspended solids (TSS), biochemical oxygen demand (BOD) and turbidity (TBS) among others on the density of Acinetobacter species in the Great Fish, Keiskamma and Tyhume rivers in the Eastern Cape Province, South Africa. Water samples and values of the environmental factors were taken from the rivers for 12 months. The density of presumptive Acinetobacter species was estimated from the culture of water samples on a CHROMagar selective medium, while the Acinetobacter-specific recA gene was targeted for the identification of Acinetobacter species using PCR assay. The multivariate relationship between seasons and changes in variables was created using PCA, while the effect of seasonal shifts in the environmental variables on the density of Acinetobacter species was evaluated using correlation test and topological graphs. Positive association patterns were observed between the seasons, environmental factors and the bacterial density in the rivers. In addition, temperature, TBS, TSS and BOD tended to influence the bacterial density more than other physicochemical factors in the rivers across the seasons. Of the total 1107 presumptive Acinetobacter species, 844 were confirmed as Acinetobacter species. Therefore, these findings suggested that the rivers contain Acinetobacter species that could be useful for basic and applied study in ecology or biotechnology, while their clinical relevance in causing diseases cannot be underestimated.
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12
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Metagenome-Assembled Genome of Halomonas sp. Isolate SL48-SHIP-3 from the Microbial Mat of Salt Lake Number 48 (Novosibirsk Region, Russia). Microbiol Resour Announc 2019; 8:8/49/e01293-19. [PMID: 31806750 PMCID: PMC6895310 DOI: 10.1128/mra.01293-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Halomonas sp. isolate SL48-SHIP-3 genome was obtained from metagenomics sequencing of the microbial mat of Salt Lake Number 48 (54.201806N, 78.179194E; Novosibirsk region, Russia). The sequenced and annotated genome is 2,575,909 bp and encodes 2,368 genes. The Halomonas sp. isolate SL48-SHIP-3 genome was obtained from metagenomics sequencing of the microbial mat of Salt Lake Number 48 (54.201806N, 78.179194E; Novosibirsk region, Russia). The sequenced and annotated genome is 2,575,909 bp and encodes 2,368 genes.
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13
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Metagenome-Assembled Genome Sequence of Phormidium sp. Strain SL48-SHIP, Isolated from the Microbial Mat of Salt Lake Number 48 (Novosibirsk Region, Russia). Microbiol Resour Announc 2019; 8:8/31/e00651-19. [PMID: 31371542 PMCID: PMC6675990 DOI: 10.1128/mra.00651-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Phormidium sp. strain SL48-SHIP genome was obtained from metagenomics sequencing of the microbial mat of Salt Lake No. 48 (54.201806 N, 78.179194 E; Novosibirsk Region, Russia). The sequenced and annotated genome is 4,384,607 bp and encodes 3,807 genes. The Phormidium sp. strain SL48-SHIP genome was obtained from metagenomics sequencing of the microbial mat of Salt Lake No. 48 (54.201806 N, 78.179194 E; Novosibirsk Region, Russia). The sequenced and annotated genome is 4,384,607 bp and encodes 3,807 genes.
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14
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The Role of Pseudomonas in Heterotrophic Nitrification: A Case Study on Shrimp Ponds ( Litopenaeus vannamei) in Soc Trang Province. Microorganisms 2019; 7:microorganisms7060155. [PMID: 31146455 PMCID: PMC6616971 DOI: 10.3390/microorganisms7060155] [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: 05/02/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 01/08/2023] Open
Abstract
Based on a total of 6,295,650 sequences from the V3 and V4 regions (16S ribosomal RNA), the composition of the microorganism communities in the water of three Litopenaeus vannamei (Decapoda, Whiteleg shrimp; Soc Trang, Vietnam) ponds were identified. Pseudomonas (10–20.29%), Methylophilus (13.26–24.28%), and Flavobacterium (2.6–19.29%) were the most abundant genera. The total ammonia (TAN) concentration (p = 0.025) and temperature (p = 0.015) were significantly correlated with the relative abundance of Pseudomonas in two bacterial communities (ST1, ST4), whereas the predictive functions of microorganism communities based on 16S rRNA gene data was estimated using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST), which showed that nitrogen metabolism was significantly negatively correlated (p = 0.049) with TAN concentration. The abundance of Pseudomonas and nitrogen metabolism increased with a decrease in TAN concentration. The correlation between TAN concentration and the abundance of Pseudomonas was followed by the isolation, and heterotrophic nitrifying performance analysis was used to confirm our findings. Six Pseudomonas strains capable of heterotrophic nitrification were isolated from the three water samples and showed a complete reduction of 100 mg/L NH4Cl during a 96-h cultivation. These results indicate the potential of applying Pseudomonas in shrimp ponds for water treatment.
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15
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Liu K, Ding X, Tang X, Wang J, Li W, Yan Q, Liu Z. Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils. Front Microbiol 2018. [PMID: 29535703 PMCID: PMC5835090 DOI: 10.3389/fmicb.2018.00352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.
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Affiliation(s)
- Kaihui Liu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Xiaowei Ding
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Xiaofei Tang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiome Research Center and School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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16
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Laskar F, Das Purkayastha S, Sen A, Bhattacharya MK, Misra BB. Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems. J Basic Microbiol 2017; 58:101-119. [PMID: 29083035 DOI: 10.1002/jobm.201700341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022]
Abstract
About half of the global methane (CH4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.
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Affiliation(s)
- Folguni Laskar
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Aniruddha Sen
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Biswapriya B Misra
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, Texas, USA
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17
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Spatial and Temporal Dynamics of Potentially Toxic Cyanobacteria in the Riverine Region of a Temperate Estuarine System Altered by Weirs. WATER 2017. [DOI: 10.3390/w9110819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Baranova AV, Orlov YL. The papers presented at 7th Young Scientists School "Systems Biology and Bioinformatics" (SBB'15): Introductory Note. Introduction. BMC Genet 2016; 17 Suppl 1:20. [PMID: 26822407 PMCID: PMC4895277 DOI: 10.1186/s12863-015-0326-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ancha V Baranova
- Research Center for Medical Genetics RAMS, Moscow, Russian Federation. .,Center for the Study of Chronic Metabolic Diseases, School of System Biology, George Mason University, Fairfax, VA, USA.
| | - Yuriy L Orlov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Lavrentieva ave., 10, Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090, Russian Federation
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