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Liu Z, Cao F, Wan J, Chen X, Kong B, Li D, Zhang XH, Jiang Y, Shi X. Stable microbial community diversity across large-scale Antarctic water masses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174559. [PMID: 38992373 DOI: 10.1016/j.scitotenv.2024.174559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
The distinctive environmental attributes of the Southern Ocean underscore the indispensability of microorganisms in this region. We analyzed 208 samples obtained from four separate layers (Surface, Deep Chlorophyll Maximum, Middle, and Bottom) in the neighboring seas of the Antarctic Peninsula and the Cosmonaut Sea to explore variations in microbial composition, interactions and community assembly processes. The results demonstrated noteworthy distinctions in alpha and beta diversity across diverse communities, with the increase in water depth, a gradual rise in community diversity was observed. In particular, the co-occurrence network analysis exposed pronounced microbial interactions within the same water mass, which are notably stronger than those observed between different water masses. Co-occurrence network complexity was higher in the surface water mass than in the bottom water mass. Yet, the surface water mass exhibited greater network stability. Moreover, in the phylogenetic-based β-nearest taxon distance analyses, deterministic processes were identified as the primary factors influencing community assembly in Antarctic microorganisms. This study contributes to exploring diversity and assembly processes under the complex hydrological conditions of Antarctica.
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Affiliation(s)
- Zhengang Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Furong Cao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jiyuan Wan
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Bin Kong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Dong Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Xiaochong Shi
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Gago JF, Viver T, Urdiain M, Ferreira E, Robledo P, Rossello-Mora R. Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode. Syst Appl Microbiol 2024; 47:126506. [PMID: 38640749 DOI: 10.1016/j.syapm.2024.126506] [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: 12/05/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024]
Abstract
Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Elaine Ferreira
- The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain
| | - Pedro Robledo
- Unit of Geological and Mining Institute of Spain in Balearic Islands (IGME-CSIC), Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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Li Y, Zhang R, Ma G, Shi M, Xi Y, Li X, Wang S, Zeng X, Jia Y. Bacterial community in the metal(loid)-contaminated marine vertical sediments of Jinzhou Bay: Impacts and adaptations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171180. [PMID: 38402990 DOI: 10.1016/j.scitotenv.2024.171180] [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: 01/06/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Metal(loid) discharge has led to severe coastal contamination; however, there remains a significant knowledge gap regarding its impact on sediment profiles and depth-resolved bacterial communities. In this study, geochemical measurements (pH, nutrient elements, total and bioavailable metal(loid) content) consistently revealed decreasing nitrogen, phosphorus, and metal(loid) levels with sediment depth, accompanied by reduced alpha diversity. Principal coordinate analysis indicated distinct community compositions with varying sediment depths, suggesting a geochemical influence on diversity. Ecological niche width expanded with depth, favoring specialists over generalists, but both groups decreased in abundance. Taxonomic shifts emerged, particularly in phyla and families, correlated with sediment depth. Microbe-microbe interactions displayed intricate dynamics, with keystone taxa varying by sediment layer. Zinc and arsenic emerged as key factors impacting community diversity and composition using random forest, network analysis, and Mantel tests. Functional predictions revealed shifts in potential phenotypes related to mobile elements, biofilm formation, pathogenicity, N/P/S cycles, and metal(loid) resistance along sediment profiles. Neutral and null models demonstrated a transition from deterministic to stochastic processes with sediment layers. This study provides insights into the interplay between sediment geochemistry and bacterial communities across sediment depths, illuminating the factors shaping these ecosystems.
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Affiliation(s)
- Yongbin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Rui Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Guoqing Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Mingyi Shi
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yimei Xi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Xiaojun Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Shaofeng Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiangfeng Zeng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China.
| | - Yongfeng Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
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Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol 2024; 9:490-501. [PMID: 38212658 DOI: 10.1038/s41564-023-01573-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
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Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yajiao Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jianjun Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel J Curtis
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Lauren Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew W Fields
- Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Paul D Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Adam P Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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Jiang H, Luo J, Liu Q, Ogunyemi SO, Ahmed T, Li B, Yu S, Wang X, Yan C, Chen J, Li B. Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation. Microbiol Spectr 2023; 11:e0105923. [PMID: 37846986 PMCID: PMC10715139 DOI: 10.1128/spectrum.01059-23] [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: 03/09/2023] [Accepted: 08/27/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera Streptomyces, Chitinophaga, Sphingomonas, and Bacillus increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.
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Affiliation(s)
- Hubiao Jiang
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, China
| | - Quanhong Liu
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Bing Li
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
| | - Shanhong Yu
- Taizhou Academy of Agricultural Sciences, Taizhou, China
| | - Xiao Wang
- Ningbo Jiangbei District Agricultural Technology Extension Service Station, Ningbo , China
| | - Chenqi Yan
- Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou , China
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Balcha ES, Gómez F, Gemeda MT, Bekele FB, Abera S, Cavalazzi B, Woldesemayat AA. Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region. Antibiotics (Basel) 2023; 12:1697. [PMID: 38136731 PMCID: PMC10740858 DOI: 10.3390/antibiotics12121697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.
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Affiliation(s)
- Ermias Sissay Balcha
- School of Medical Laboratory Science, College of Medicine and Health Sciences, Hawassa University, Hawassa P.O. Box 1560, Ethiopia;
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
| | - Felipe Gómez
- Centro de Astrobiología (INTA-CSIC) Crtera, Ajalvir km 4 Torrejón de Ardoz, P.O. Box 28850 Madrid, Spain;
| | - Mesfin Tafesse Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
| | - Fanuel Belayneh Bekele
- School of Public Health, College of Medicine and Health Sciences, Hawassa University, Hawassa P.O. Box 1560, Ethiopia;
| | - Sewunet Abera
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands;
- Institute of Biology, Leiden University, P.O. Box 9500, 2300 RA Leiden, The Netherlands
- Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa P.O. Box 2003, Ethiopia
| | - Barbara Cavalazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, 40100 Bologna, Italy;
- Department of Geology, University of Johannesburg, Johannesburg P.O. Box 524, South Africa
| | - Adugna Abdi Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
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Wang J, Zhang F, Yao T, Li Y, Wei N. Risk assessment of mycotoxins, the identification and environmental influence on toxin-producing ability of Alternaria alternate in the main Tibetan Plateau Triticeae crops. Front Microbiol 2023; 13:1115592. [PMID: 36824588 PMCID: PMC9942522 DOI: 10.3389/fmicb.2022.1115592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/30/2022] [Indexed: 02/10/2023] Open
Abstract
In order to find out the contamination of mycotoxins in Triticeae crops of Qinghai-Tibet Plateau, a total of 153 Triticeae crop fruits were collected as target samples, and 22 mycotoxins were tested. High detection rate was found in the Alternaria mycotoxins, including tentoxin (TEN), tenuazonic acid (TEA) and alternariol (AOH) toxins. To further clarify the production rules of Alternaria mycotoxins. A number of 9 high yield toxic strains were selected from 65 bacterial strains and the gene sequences of each were determined. The nine selected Alternaria alternate were cultured under specific pH of the culture medium, temperature and ultraviolet (UV) irradiation, and their growth and toxicity were analyzed. The results showed that the toxic capacity of most A. alternate increased with the increase of culture environment temperature and decreased with the increase of UV irradiation. However, the production of some toxins did not meet this principle, or even met the principle of relativity. In the culture experiments, a total of five Alternaria toxins were detected as positive, which were TEN, AOH, alternariol monomethyl ether (AME), TEA, and Alternaria (ALT). The altenusin (ALS) toxin was not detected in the metabolites of the nine Alternaria strains. It indicated that the TEN, AOH, AME, TEA, and ALT toxins should be particularly valued in the future risk assessments. This finding provided comprehensive information of mycotoxins contamination in the Tibetan Plateau Triticeae crops, it pointed out a direction to the Tibetan Plateau food crops' quality control.
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Affiliation(s)
- Jun Wang
- Zhang Zhong-jing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, China
| | - Feilong Zhang
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Ting Yao
- Zhang Zhong-jing School of Chinese Medicine, Nanyang Institute of Technology, Nanyang, China
| | - Ying Li
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Na Wei
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China,*Correspondence: Na Wei, ✉
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Groult B, Bredin P, Lazar CS. Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada). Environ Microbiol 2022; 24:5898-5910. [PMID: 36135934 DOI: 10.1111/1462-2920.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023]
Abstract
Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km2 in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.
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Affiliation(s)
- Benjamin Groult
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
| | - Pascal Bredin
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
| | - Cassandre Sara Lazar
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
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9
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Wen T, Xie P, Penton CR, Hale L, Thomashow LS, Yang S, Ding Z, Su Y, Yuan J, Shen Q. Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin. MICROBIOME 2022; 10:177. [PMID: 36271396 PMCID: PMC9587672 DOI: 10.1186/s40168-022-01375-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning. RESULTS Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.
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Affiliation(s)
- Tao Wen
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Penghao Xie
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - C Ryan Penton
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- Faculty of Science and Mathematics, College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, USA
| | - Lauren Hale
- Agricultural Research Service, USDA, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Linda S Thomashow
- Agricultural Research Service, US Department of Agriculture, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164, USA
| | - Shengdie Yang
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhexu Ding
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaqi Su
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- The Key Laboratory of Plant ImmunityJiangsu Provincial Key Lab for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
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10
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Merino N, Jackson TR, Campbell JH, Kersting AB, Sackett J, Fisher JC, Bruckner JC, Zavarin M, Hamilton-Brehm SD, Moser DP. Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156768. [PMID: 35738377 DOI: 10.1016/j.scitotenv.2022.156768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa-Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat-Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.
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Affiliation(s)
- Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States.
| | - Tracie R Jackson
- Nevada Water Science Center, U.S. Geological Survey, Boulder City, NV 89005, United States
| | - James H Campbell
- Department of Natural Sciences, Northwest Missouri State University, Maryville, MO 64468, United States
| | - Annie B Kersting
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Joshua Sackett
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV 89119, United States; Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV 89119, United States; School of Life Sciences, University of Nevada, Las Vegas, NV 89154, United States
| | - Jenny C Fisher
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV 89119, United States; Biology Department, Indiana University Northwest, Gary, IN 46408, United States
| | - James C Bruckner
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV 89119, United States
| | - Mavrik Zavarin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Scott D Hamilton-Brehm
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV 89119, United States; Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL 62901, United States
| | - Duane P Moser
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV 89119, United States; Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV 89119, United States.
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11
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Zhang H, Yan Y, Lin T, Xie W, Hu J, Hou F, Han Q, Zhu X, Zhang D. Disentangling the Mechanisms Shaping the Prokaryotic Communities in a Eutrophic Bay. Microbiol Spectr 2022; 10:e0148122. [PMID: 35638815 PMCID: PMC9241920 DOI: 10.1128/spectrum.01481-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/08/2022] [Indexed: 11/24/2022] Open
Abstract
Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters. IMPORTANCE A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters. In this study, we built a conceptual model that links seasonal microbial interactions to ecological processes, which has not been reported before. The model showed that heterogeneous selection plays an important role in driving community assembly during low-temperature seasons, resulting in higher β-diversity and more tightly connected networks. In contrast, drift became a dominant force during high-temperature seasons, leading to declines in the β-diversity and network associations. This model could function as a new framework to predict how prokaryotic communities respond to intensified eutrophication induced by climate change in coastal environment.
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Affiliation(s)
- Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Yi Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Tenghui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Weijuan Xie
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Jian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Fanrong Hou
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Qingxi Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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12
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Korbel KL, Greenfield P, Hose GC. Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150870. [PMID: 34627912 DOI: 10.1016/j.scitotenv.2021.150870] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.
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Affiliation(s)
- K L Korbel
- Department of Biological Sciences, Macquarie University, Australia.
| | | | - G C Hose
- Department of Biological Sciences, Macquarie University, Australia
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13
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Huang Y, Li XT, Jiang Z, Liang ZL, Wang P, Liu ZH, Li LZ, Yin HQ, Jia Y, Huang ZS, Liu SJ, Jiang CY. Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3). Front Microbiol 2021; 12:761579. [PMID: 34917049 PMCID: PMC8670003 DOI: 10.3389/fmicb.2021.761579] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO42−, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg2+ and SO42− were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg2+ and SO42−, Ca2+, temperature, and Fe2+, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg2+ and SO42− concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Hua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liang-Zhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yan Jia
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zhong-Sheng Huang
- Zijin Mining Group Company Limited, Fujian, China.,School of Metallurgy and Environment, Central South University, Changsha, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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14
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Osburn ED, Aylward FO, Barrett JE. Historical land use has long-term effects on microbial community assembly processes in forest soils. ISME COMMUNICATIONS 2021; 1:48. [PMID: 37938278 PMCID: PMC9723674 DOI: 10.1038/s43705-021-00051-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 05/04/2023]
Abstract
Land use change has long-term effects on the structure of soil microbial communities, but the specific community assembly processes underlying these effects have not been identified. To investigate effects of historical land use on microbial community assembly, we sampled soils from several currently forested watersheds representing different historical land management regimes (e.g., undisturbed reference, logged, converted to agriculture). We characterized bacterial and fungal communities using amplicon sequencing and used a null model approach to quantify the relative importance of selection, dispersal, and drift processes on bacterial and fungal community assembly. We found that bacterial communities were structured by both selection and neutral (i.e., dispersal and drift) processes, while fungal communities were structured primarily by neutral processes. For both bacterial and fungal communities, selection was more important in historically disturbed soils compared with adjacent undisturbed sites, while dispersal processes were more important in undisturbed soils. Variation partitioning identified the drivers of selection to be changes in vegetation communities and soil properties (i.e., soil N availability) that occur following forest disturbance. Overall, this study casts new light on the effects of historical land use on soil microbial communities by identifying specific environmental factors that drive changes in community assembly.
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Affiliation(s)
- Ernest D Osburn
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - J E Barrett
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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15
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Dong Y, Sanford RA, Connor L, Chee-Sanford J, Wimmer BT, Iranmanesh A, Shi L, Krapac IG, Locke RA, Shao H. Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL. WATER RESEARCH 2021; 202:117431. [PMID: 34320445 DOI: 10.1016/j.watres.2021.117431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput FluidigmTM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.
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Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, USA
| | | | | | | | | | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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16
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Michel C, Baran N, André L, Charron M, Joulian C. Side Effects of Pesticides and Metabolites in Groundwater: Impact on Denitrification. Front Microbiol 2021; 12:662727. [PMID: 34054765 PMCID: PMC8155494 DOI: 10.3389/fmicb.2021.662727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/30/2021] [Indexed: 01/16/2023] Open
Abstract
The impact of two pesticides (S-metolachlor and propiconazole) and their respective main metabolites (ESA-metolachlor and 1,2,4-triazole) on bacterial denitrification in groundwater was studied. For this, the denitrification activity and the bacterial diversity of a microbial community sampled from a nitrate-contaminated groundwater were monitored during 20 days in lab experiments in the presence or absence of pesticides or metabolites at 2 or 10 μg/L. The kinetics of nitrate reduction along with nitrite and N2O production all suggested that S-metolachlor had no or only little impact, whereas its metabolite ESA-metolachlor inhibited denitrification by 65% at 10 μg/L. Propiconazole and 1,2,4-triazole also inhibited denitrification at both concentrations, but to a lesser extent (29–38%) than ESA-metolachlor. When inhibition occurred, pesticides affected the reduction of nitrate into nitrite step. However, no significant differences were detected on the abundance of nitrate reductase narG and napA genes, suggesting an impact of pesticides/metabolites at the protein level rather than on denitrifying bacteria abundance. 16S rRNA gene Illumina sequencing indicated no major modification of bacterial diversity in the presence or absence of pesticides/metabolites, except for ESA-metolachlor and propiconazole at 10 μg/L that tended to increase or decrease Shannon and InvSimpson indices, respectively. General growth parameters suggested no impact of pesticides, except for propiconazole at 10 μg/L that partially inhibited acetate uptake and induced a decrease in microbial biomass. In conclusion, pesticides and metabolites can have side effects at environmental concentrations on microbial denitrification in groundwater and may thus affect ecosystem services based on microbial activities.
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Affiliation(s)
- Caroline Michel
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Nicole Baran
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Laurent André
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France.,Université d'Orléans, CNRS, BRGM, UMR 7327 Institut des Sciences de la Terre d'Orléans, Orléans, France
| | - Mickael Charron
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Catherine Joulian
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
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17
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Knobloch S, Klonowski AM, Tómasdóttir S, Kristjánsson BR, Guðmundsson S, Marteinsson VÞ. Microbial intrusion and seasonal dynamics in the groundwater microbiome of a porous basaltic rock aquifer used as municipal water reservoir. FEMS Microbiol Ecol 2021; 97:6122586. [PMID: 33507241 DOI: 10.1093/femsec/fiab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/26/2021] [Indexed: 01/04/2023] Open
Abstract
Groundwater is a key resource for safe drinking water supply. Yet unconfined aquifers can be vulnerable to microbial contamination during extreme weather events that lead to surface runoff. The current study characterises the groundwater microbiome of a porous basaltic rock aquifer in South-West Iceland used for drinking water extraction and analyses the microbial community dynamics during surface runoff. The groundwater microbial community sampled from 12 wells across the extraction area contained over 745 prokaryotic genera and was phylogenetically similar between wells and most seasons, representing a diverse but homogenous ecosystem. The largest seasonal variation in the microbial community composition was detected during a period of concurrent snow melt and high precipitation leading to surface runoff. This period was characterised by an increased abundance of soil-associated taxa in the groundwater microbiome and specifically of taxa assigned to Aeromonas and Bacillus. A field experiment simulating high surface runoff around a groundwater well confirmed the increased abundance of surface soil microorganisms in the well water, indicating vulnerability of groundwater towards surface microbial intrusion during extreme weather events. As such events are likely to increase due to climate change, novel water management tools such as microbial community analysis could help ensure drinking water safety.
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Affiliation(s)
- Stephen Knobloch
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
| | | | - Sigrún Tómasdóttir
- Department of Research and Innovation, Reykjavik Energy, Bæjarháls 1, 110 Reykjavík, Iceland
| | | | | | - Viggó Þór Marteinsson
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland.,Faculty of Food Science and Nutrition, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland
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18
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Ruiz-González C, Rodellas V, Garcia-Orellana J. The microbial dimension of submarine groundwater discharge: current challenges and future directions. FEMS Microbiol Rev 2021; 45:6128669. [PMID: 33538813 PMCID: PMC8498565 DOI: 10.1093/femsre/fuab010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC). Passeig Marítim de la Barceloneta 37-49, E08003 Barcelona, Spain
| | - Valentí Rodellas
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
| | - Jordi Garcia-Orellana
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain.,Departament de Física, Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
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19
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Fillinger L, Hug K, Griebler C. Aquifer recharge viewed through the lens of microbial community ecology: Initial disturbance response, and impacts of species sorting versus mass effects on microbial community assembly in groundwater during riverbank filtration. WATER RESEARCH 2021; 189:116631. [PMID: 33217664 DOI: 10.1016/j.watres.2020.116631] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Riverbank filtration has gained increasing importance for balancing rising groundwater demands and securing drinking water supplies. While microbial communities are the pillar of vital ecosystem functions in groundwater, the impact of riverbank filtration on these communities has been understudied so far. Here, we followed changes in microbial community composition based on 16S rRNA gene amplicon sequence variants (ASVs) in an initially pristine shallow porous aquifer in response to surface water intrusion during the early stages of induced riverbank filtration over a course of seven weeks. We further analyzed sediment cores for imprints of river-derived ASVs after seven weeks of riverbank filtration. The onset of the surface water intrusion caused loss of taxa and significant changes in community composition, revealing low disturbance resistance of the initial aquifer microbial communities. SourceTracker analysis revealed that proportions of river-derived ASVs in the groundwater were generally <25%, but locally could reach up to 62% during a period of intense precipitation. However, variation partitioning showed that the impact of dispersal of river-derived ASVs on changes in aquifer microbial community composition was overall outweighed by species sorting due to changes in environmental conditions caused by the infiltrating river water. Proportions of river-derived ASVs on aquifer sediments were <0.5%, showing that taxa transported from the river into the aquifer over the course of the study mainly resided as planktonic microorganisms in the groundwater. Our study demonstrates that groundwater microbial communities react sensitively to changes in environmental conditions caused by surface water intrusion, whereas mass effects resulting from the influx of river-derived taxa play a comparatively minor role.
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Affiliation(s)
- Lucas Fillinger
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Katrin Hug
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Christian Griebler
- Helmholtz Zentrum München, Institute of Groundwater Ecology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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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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