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Wu G, Zhang H, Huang T, Song Y, Liu X, Liu X, Wang X, Pei T, Xu G, Wang Z. Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model. WATER RESEARCH 2025; 282:123626. [PMID: 40262432 DOI: 10.1016/j.watres.2025.123626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 04/03/2025] [Accepted: 04/09/2025] [Indexed: 04/24/2025]
Abstract
Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.
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Affiliation(s)
- Guilin Wu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Haihan Zhang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China.
| | - Tinglin Huang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Yutong Song
- School of Future Technology, Xi'an University of Architecture and Technology, Xi'an, China
| | - Xiang Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Xiaoyan Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Xiaolong Wang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Tingting Pei
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Guojia Xu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Zhihan Wang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountain, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
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Gao L, Rao MPN, Liu YH, Wang PD, Lian ZH, Abdugheni R, Jiang HC, Jiao JY, Shurigin V, Fang BZ, Li WJ. SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas. MICROBIAL ECOLOGY 2024; 87:135. [PMID: 39482450 PMCID: PMC11527964 DOI: 10.1007/s00248-024-02442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 10/02/2024] [Indexed: 11/03/2024]
Abstract
Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.
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Affiliation(s)
- Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Manik Prabhu Narsing Rao
- Facultad de Ingeniería, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, 3460000, Sede Talca, Talca, Chile
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, People's Republic of China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, People's Republic of China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Hong-Chen Jiang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, People's Republic of China
| | - Vyacheslav Shurigin
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
- Department of Microbiology and Biotechnology, Faculty of Biology, National University of Uzbekistan, 100174, Tashkent, Uzbekistan.
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, People's Republic of China.
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Fu Q, Ma K, Zhao J, Li J, Wang X, Zhao M, Fu X, Huang D, Chen H. Metagenomics unravel distinct taxonomic and functional diversities between terrestrial and aquatic biomes. iScience 2024; 27:111047. [PMID: 39435150 PMCID: PMC11492093 DOI: 10.1016/j.isci.2024.111047] [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: 05/30/2024] [Revised: 08/28/2024] [Accepted: 09/23/2024] [Indexed: 10/23/2024] Open
Abstract
Microbes in terrestrial and aquatic ecosystems play crucial roles in driving ecosystem functions, but currently, there is a lack of comparison regarding their taxonomic and functional diversities. Here, we conducted a global analysis to investigate the disparities in microbial taxonomy and microbial-mediated biogeochemical cycles between terrestrial and aquatic ecosystems. Results showed a higher relative abundance of bacteria, especially Actinobacteria and Acidobacteria, in soil than water metagenomes, leading to a greater proportion of genes related to membrane transport, regulatory, and cellular signaling. Moreover, there was a higher abundance of genes associated with carbohydrate, sulfur, and potassium metabolisms in the soil, while those involved in nitrogen and iron metabolisms were more prevalent in the water. Thus, both soil and water microbiomes exhibited unique taxonomic and functional properties associated with biogeochemical processes, providing valuable insights into predicting and understanding the adaptation of microbes in different ecosystems in the face of climate change.
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Affiliation(s)
- Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Kayan Ma
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xueying Wang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Meiqi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Dandan Huang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
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4
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Mazur-Marzec H, Andersson AF, Błaszczyk A, Dąbek P, Górecka E, Grabski M, Jankowska K, Jurczak-Kurek A, Kaczorowska AK, Kaczorowski T, Karlson B, Kataržytė M, Kobos J, Kotlarska E, Krawczyk B, Łuczkiewicz A, Piwosz K, Rybak B, Rychert K, Sjöqvist C, Surosz W, Szymczycha B, Toruńska-Sitarz A, Węgrzyn G, Witkowski A, Węgrzyn A. Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes. FEMS Microbiol Rev 2024; 48:fuae024. [PMID: 39366767 PMCID: PMC11500664 DOI: 10.1093/femsre/fuae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 09/21/2024] [Accepted: 10/03/2024] [Indexed: 10/06/2024] Open
Abstract
Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.
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Affiliation(s)
- Hanna Mazur-Marzec
- Department of Marine Biology and Biotechnology, University of Gdansk, Al. Piłsudskiego 46, PL-81-378 Gdynia, Poland
| | - Anders F Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23A, SE-171 65 Solna, Stockholm, Sweden
| | - Agata Błaszczyk
- Department of Marine Biology and Biotechnology, University of Gdansk, Al. Piłsudskiego 46, PL-81-378 Gdynia, Poland
| | - Przemysław Dąbek
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, PL-70-383 Szczecin, Poland
| | - Ewa Górecka
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, PL-70-383 Szczecin, Poland
| | - Michał Grabski
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822 Gdansk, Poland
| | - Katarzyna Jankowska
- Department of Environmental Engineering Technology, Gdansk University of Technology, Narutowicza 11/12, PL-80-233 Gdansk, Poland
| | - Agata Jurczak-Kurek
- Department of Evolutionary Genetics and Biosystematics, University of Gdansk, Wita Stwosza 59, PL-80-308 Gdansk, Poland
| | - Anna K Kaczorowska
- Collection of Plasmids and Microorganisms, University of Gdansk, Wita Stwosza 59, PL-80-308 Gdansk, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdansk, Wita Stwosza 59, PL-80-308 Gdansk, Poland
| | - Bengt Karlson
- Swedish Meteorological and Hydrological Institute
, Research and Development, Oceanography, Göteborgseskaderns plats 3, Västra Frölunda SE-426 71, Sweden
| | - Marija Kataržytė
- Marine Research Institute, Klaipėda University, Universiteto ave. 17, LT-92294 Klaipeda, Lithuania
| | - Justyna Kobos
- Department of Marine Biology and Biotechnology, University of Gdansk, Al. Piłsudskiego 46, PL-81-378 Gdynia, Poland
| | - Ewa Kotlarska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81-712 Sopot, Poland
| | - Beata Krawczyk
- Department of Biotechnology and Microbiology, Gdansk University of Technology, Narutowicza 11/12, PL-80-233 Gdansk, Poland
| | - Aneta Łuczkiewicz
- Department of Environmental Engineering Technology, Gdansk University of Technology, Narutowicza 11/12, PL-80-233 Gdansk, Poland
| | - Kasia Piwosz
- National Marine Fisheries Research Institute, Kołłątaja 1, PL-81-332 Gdynia, Poland
| | - Bartosz Rybak
- Department of Environmental Toxicology, Faculty of Health Sciences with Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Dębowa 23A, PL-80-204 Gdansk, Poland
| | - Krzysztof Rychert
- Pomeranian University in Słupsk, Arciszewskiego 22a, PL-76-200 Słupsk, Poland
| | - Conny Sjöqvist
- Environmental and Marine Biology, Åbo Akademi University, Henriksgatan 2, FI-20500 Åbo, Finland
| | - Waldemar Surosz
- Department of Marine Biology and Biotechnology, University of Gdansk, Al. Piłsudskiego 46, PL-81-378 Gdynia, Poland
| | - Beata Szymczycha
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81-712 Sopot, Poland
| | - Anna Toruńska-Sitarz
- Department of Marine Biology and Biotechnology, University of Gdansk, Al. Piłsudskiego 46, PL-81-378 Gdynia, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, PL-80-308 Gdansk, Poland
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, PL-70-383 Szczecin, Poland
| | - Alicja Węgrzyn
- University Center for Applied and Interdisciplinary Research, University of Gdansk, Kładki 24, 80-822 Gdansk, Poland
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Van Gray JB, Ayayee P. Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization. Environ Microbiol 2024; 26:e16628. [PMID: 38757470 DOI: 10.1111/1462-2920.16628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
The degradation of freshwater systems by salt pollution is a threat to global freshwater resources. Salinization is commonly identified by increased specific conductance (conductivity), a proxy for salt concentrations. However, conductivity fails to account for the diversity of salts entering freshwaters and the potential implications this has on microbial communities and functions. We tested 4 types of salt pollution-MgCl2, MgSO4, NaCl, and Na2SO4-on bacterial taxonomic and functional α-, β-diversity of communities originating from streams in two distinct localities (Nebraska [NE] and Ohio [OH], USA). Community responses depended on the site of origin, with NE and OH exhibiting more pronounced decreases in community diversity in response to Na2SO4 and MgCl2 than other salt amendments. A closer examination of taxonomic and functional diversity metrics suggests that core features of communities are more resistant to induced salt stress and that marginal features at both a population and functional level are more likely to exhibit significant structural shifts based on salt specificity. The lack of uniformity in community response highlights the need to consider the compositional complexities of salinization to accurately identify the ecological consequences of instances of salt pollution.
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Affiliation(s)
- Jonathon B Van Gray
- The Ohio State University CFAES Wooster, Agriculture Technical Institute, Wooster, Ohio, USA
| | - Paul Ayayee
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
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Martínez-Alvarez L, Ramond JB, Vikram S, León-Sobrino C, Maggs-Kölling G, Cowan DA. With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities. Appl Environ Microbiol 2023; 89:e0062923. [PMID: 37971255 PMCID: PMC10734447 DOI: 10.1128/aem.00629-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/24/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.
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Affiliation(s)
- Laura Martínez-Alvarez
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
- Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Carlos León-Sobrino
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
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Yangyao J, Chen H, Wang Y, Kan P, Yao J, Zhang D, Sun W, Yao Z. Metagenomic insights into the functional genes across transects in a typical estuarine marsh. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159593. [PMID: 36272486 DOI: 10.1016/j.scitotenv.2022.159593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Salt marshes are potentially one of the most efficient carbon (C) sinks worldwide and perform important ecosystem functions, but sea level rise alters marsh sediments properties and thus threatens microbial roles in ecosystem functioning. Yet, the mechanisms of interactions of biochemical processes with microorganisms and their functions are still not fully understood. Here, this study investigated metagenomic taxonomic and functional profiling from the water-land conjugation up to about 300 m, 1000 m, and 2500 m in three parallel transects, respectively, in Hangzhou Bay, China. The results showed that soil physicochemical factors drove metagenomic taxonomic and functional genes in the 2500-m transect significantly different from other sites. The 2500-m transect had a greater abundance of Chloroflexi and Acidobacteria but lower in Proteobacteria. The metagenomic functional genes related to Phosphorus Metabolism (PHO) and Potassium Metabolism (POT) increased in the 2500 m. Additionally, nutrient-cycling functions and the genera of Anaeromyxobacter, Roseiflexus, and Geobacter related to PHO, POT at 2500 m were significantly greater than those of other transects. Carbon cycling functions within Carbohydrates (CHO) also differed significantly across transects. These research results demonstrated that the relative abundance of metagenomic microorganisms and their functional genes were significantly separated across the three transects. The vegetation type, salinity, and soil properties might be among the influencing factors.
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Affiliation(s)
- Jiannan Yangyao
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Huaihai Chen
- School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China; State Key Laboratory of Biocontrol, Sun Yat-sen University, Shenzhen 518107, China
| | - Yuanfang Wang
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China
| | - Peiying Kan
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China
| | - Jiafeng Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - WeiWei Sun
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China; Department of Geography and Spatial Information Techniques, Ningbo University, Ningbo 315211, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China.
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Zhang J, Fu Q, Huang Y, Fan Y, Liang M, Chen H, Yu S. Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156087. [PMID: 35605852 DOI: 10.1016/j.scitotenv.2022.156087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/07/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.
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Affiliation(s)
- Juanjuan Zhang
- School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China; Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
| | - Qi Fu
- School of Ecology/State Key Laboratory of Biocontrol, Sun Yat-sen University, Shenzhen 518107, China
| | - Yu Huang
- School of Ecology/State Key Laboratory of Biocontrol, Sun Yat-sen University, Shenzhen 518107, China
| | - Yuxuan Fan
- School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China; Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
| | - Minxia Liang
- School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China; School of Ecology/State Key Laboratory of Biocontrol, Sun Yat-sen University, Shenzhen 518107, China
| | - Huaihai Chen
- School of Ecology/State Key Laboratory of Biocontrol, Sun Yat-sen University, Shenzhen 518107, China.
| | - Shixiao Yu
- School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China; Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China.
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Chen H, Ma K, Lu C, Fu Q, Qiu Y, Zhao J, Huang Y, Yang Y, Schadt CW, Chen H. Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe. Front Microbiol 2022; 13:878978. [PMID: 35586865 PMCID: PMC9108720 DOI: 10.3389/fmicb.2022.878978] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022] Open
Abstract
Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.
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Affiliation(s)
- Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Kayan Ma
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Caiyan Lu
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Key Lab of Conservation Tillage and Ecological Agriculture, Shenyang, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | | | - Hao Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
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