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Zhou X, Liu X, Liu M, Liu W, Xu J, Li Y. Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management. Front Microbiol 2024; 15:1424795. [PMID: 39077744 PMCID: PMC11284604 DOI: 10.3389/fmicb.2024.1424795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/01/2024] [Indexed: 07/31/2024] Open
Abstract
Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments.
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Affiliation(s)
- Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
| | - Xiaoyin Liu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
| | - Meiyu Liu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
| | - Weixuan Liu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
| | - Junzeng Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, China
| | - Yawei Li
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
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Li C, Liao H, Xu L, Wang C, Yao M, Wang J, Li X. Comparative genomics reveals the adaptation of ammonia-oxidising Thaumarchaeota to arid soils. Environ Microbiol 2024; 26:e16601. [PMID: 38454574 DOI: 10.1111/1462-2920.16601] [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: 06/08/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024]
Abstract
Thaumarchaeota are predominant in oligotrophic habitats such as deserts and arid soils, but their adaptations to these arid conditions are not well understood. In this study, we assembled 23 Thaumarchaeota genomes from arid and semi-arid soils collected from the Inner Mongolia Steppe and the Qinghai-Tibet Plateau. Using a comparative genomics approach, integrated with 614 Thaumarchaeota genomes from public databases, we identified the traits and evolutionary forces that contribute to their adaptations to aridity. Our results showed that the newly assembled genomes represent an early diverging group within the lineage of ammonia-oxidising Thaumarchaeota. While the genomic functions previously identified in arid soil lineages were conserved across terrestrial, shallow-ocean and deep-ocean lineages, several traits likely contribute to Thaumarchaeota's adaptation to aridity. These include chlorite dismutase, arsenate reductase, V-type ATPase and genes dealing with oxidative stresses. The acquisition and loss of traits at the last common ancestor of arid soil lineages may have facilitated the specialisation of Thaumarchaeota in arid soils. Additionally, the acquisition of unique adaptive traits, such as a urea transporter, Ca2+ :H+ antiporter, mannosyl-3-phosphoglycerate synthase and phosphatase, DNA end-binding protein Ku and phage shock protein A, further distinguishes arid soil Thaumarchaeota. This study provides evidence for the adaptations of Thaumarchaeota to arid soil, enhancing our understanding of the nitrogen and carbon cycling driven by Thaumarchaeota in drylands.
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Affiliation(s)
- Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Haijun Liao
- Engineering Research Center of Chuanxibei RHS Construction at Mianyang Normal University of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Changting Wang
- Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, China
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junming Wang
- Section of Climate Science, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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Ni Y, Xu T, Yan S, Chen L, Wang Y. Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle-shaped viruses that putatively infect mesophilic ammonia-oxidizing archaea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13230. [PMID: 38263861 PMCID: PMC10866085 DOI: 10.1111/1758-2229.13230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
The genome of a putative Nitrosopumilaceae virus with a hypothetical spindle-shaped particle morphology was identified in the Yangshan Harbour metavirome from the East China Sea through protein similarity comparison and structure analysis. This discovery was accompanied by a set of 10 geographically dispersed close relatives found in the environmental virus datasets from typical locations of ammonia-oxidizing archaeon distribution. Its host prediction was supported by iPHoP prediction and protein sequence similarity. The structure of the predicted major capsid protein, together with the overall N-glycosylation site, the transmembrane helices prediction, the hydrophilicity profile, and the docking simulation of the major capsid proteins, indicate that these viruses resemble spindle-shaped viruses. It suggests a similarly assembled structure and, consequently, a possibly spindle-shaped morphology of these newly discovered archaeal viruses.
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Affiliation(s)
- Yimin Ni
- College of Food Science and TechnologyShanghai Ocean UniversityShanghaiChina
| | - Tianqi Xu
- College of Food Science and TechnologyShanghai Ocean UniversityShanghaiChina
| | - Shuling Yan
- Entwicklungsgenetik und Zellbiologie der TierePhilipps‐Universität MarburgMarburgGermany
| | - Lanming Chen
- College of Food Science and TechnologyShanghai Ocean UniversityShanghaiChina
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai)Ministry of AgricultureShanghaiChina
| | - Yongjie Wang
- College of Food Science and TechnologyShanghai Ocean UniversityShanghaiChina
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai)Ministry of AgricultureShanghaiChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler MKH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W, Qin W. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. THE ISME JOURNAL 2024; 18:wrad002. [PMID: 38365232 PMCID: PMC10811736 DOI: 10.1093/ismejo/wrad002] [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: 10/20/2023] [Revised: 11/03/2023] [Accepted: 10/28/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.
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Affiliation(s)
- Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Bu Xu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University , Qingdao 266101, China
| | - Daliang Ning
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qian Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, United States
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Department of Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, United States
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
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Zhang RY, Wang YR, Liu RL, Rhee SK, Zhao GP, Quan ZX. Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment. MICROBIOME 2024; 12:7. [PMID: 38191433 PMCID: PMC10773090 DOI: 10.1186/s40168-023-01728-2] [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: 07/01/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. RESULTS In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways. CONCLUSIONS One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.
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Affiliation(s)
- Ru-Yi Zhang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan-Ren Wang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Ru-Long Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Guo-Ping Zhao
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhe-Xue Quan
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
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Hao Z, Wang Q, Wang J, Deng Y, Yan Z, Tian L, Jiang H. Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains. MICROBIAL ECOLOGY 2023; 87:24. [PMID: 38159125 DOI: 10.1007/s00248-023-02331-6] [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: 07/30/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.
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Affiliation(s)
- Zheng Hao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qianhong Wang
- Changjiang Nanjing Waterway Engineering Bureau, Nanjing, 210011, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Linqi Tian
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
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Liu Z, Jin Y, Yu Z, Liu Z, Zhang B, Chi T, Cheng D, Zhu L, Hu B. Vertical migration and dissipation of oxytetracycline induces the recoverable shift in microbial community and antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167162. [PMID: 37730066 DOI: 10.1016/j.scitotenv.2023.167162] [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: 06/12/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
Antibiotic resistance gene (ARG) spread in anthropogenic polluted soils is believed to be accelerated by the incidental inputs of antibiotics via fertilizing and irrigation, and endangering food and human health. However, due to the complex nature of substrates and uncertain microbial responses, the primary drivers of ARG dissemination remain unclear. To address this concern, the effects of antibiotic inputs on soil microbes and antibiotic resistance under simulated natural conditions was investigated in this study. Specifically, four flow-through reactors with gravity flow were established, and the oxytetracycline (OTC) a typical antibiotic in agricultural soils was studied at environmental concentrations (i.e. 0.1, 1 and 10 mg/kg) for 31 days. The vertical distribution and dissipation of OTC were profiled by measuring the residuals in layers over time. Correspondingly, the effects of antibiotic exposure on microbial communities and ARG abundances were studied. The results showed that the average exposure intensity of OTC in different soil layers ranged in 0.03-6.45 mg/kg, and resulted in different dissipation kinetics. In addition, top layer was found to be the main site of OTC reduction, where OTC dissipated at magnitude of 74.0-96.6 %, depending on the initial OTC concentration. OTC migration and dissipation resulted in the shift of community composition to the extent of 0.25-0.33 in terms of Bray-Curtis distance, which partially recovered over time. And the achievement of alternative community compositions was supposed to be largely affected by the microbial interaction. Along with the community changes, a short-term accumulation of resistance genes was detected, while the relative abundance of indicator ARGs, i.e. tetG and mexB, rising up to 10-fold higher than the initial, although eventually decayed. Collective findings of this study indicated that antibiotics at environmental concentrations might trigger extra microbial interactions and thereby reducing the demand for ARGs accumulation. It provided valuable understandings in the risk of antibiotic spillage, especially for the incident exposure at the environmentally relevant concentrations.
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Affiliation(s)
- Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Yihao Jin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhendi Yu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Zhengzheng Liu
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China.
| | - Baofeng Zhang
- Hangzhou Ecological and Environmental Monitoring Center, Hangzhou 310007, China.
| | - Taolue Chi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310058, China.
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8
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Liu S, Hu R, Peng N, Zhou Z, Chen R, He Z, Wang C. Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments. THE ISME JOURNAL 2023; 17:2313-2325. [PMID: 37880540 PMCID: PMC10689504 DOI: 10.1038/s41396-023-01544-4] [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: 04/24/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Nenglong Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruihan Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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9
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Yu B, Zeng Q, Li J, Li J, Tan X, Gao X, Huang P, Wu S. Vertical variation in prokaryotic community composition and co-occurrence patterns in sediments of the Three Gorges Reservoir, China. ENVIRONMENTAL RESEARCH 2023; 237:116927. [PMID: 37604225 DOI: 10.1016/j.envres.2023.116927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Archaea and bacteria are distributed throughout the sediment; however, our understanding of their biodiversity patterns, community composition, and interactions is primarily limited to the surface horizons (0-20 cm). In this research, sediment samples were collected from three vertical sediment profiles (depths of 0-295 cm) in the Three Gorges Reservoir (TGR), one of the largest reservoirs in the world. Through 16S rRNA sequencing, it was shown that sediment microbial diversity did not significantly vary across the sediment. Nevertheless, a decline in the similarity of archaeal and bacterial communities over distance along sediment vertical profiles was noted. Nonmetric multidimensional scaling (NMDS) analysis revealed that archaeal and bacterial communities could be clearly separated into two groups, located in the upper sediments (0-135 cm) and deep sediments (155-295 cm). Meanwhile, at the fine-scale of the vertical section, noteworthy variations were observed in the relative abundance of prominent archaea (e.g., Euryarchaeota) and bacteria (e.g., Proteobacteria). The linear discriminant analysis effect size (LEfSe) demonstrated that twenty-four bacterial and twenty-six archaeal biomarker microbes exist in the upper and deep sediment layers. Each layer exhibited distinctive microbial divisions, suggesting that microbes with diverse biological functions are capable of thriving and propagating along the sediment profile. Co-occurrence network analysis further indicated that the microbial network in the upper sediments was more complex than that in the deep sediments. Additionally, the newly discovered anaerobic methanotrophic archaeon Candidatus Methanoperedens was identified as the most abundant keystone archaeal taxon in both sediment layers, highlighting the significance of methane oxidation in material cycling within the TGR ecosystem. In summary, our study examined the biodiversity and coexistence patterns of benthic microbial communities throughout the vertical sediment profile, providing detailed insights into the vertical geography of archaeal and bacterial communities in typical deep-water reservoir ecosystems.
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Affiliation(s)
- Baohong Yu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Quanchao Zeng
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China.
| | - Jinlin Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Jun Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Xun Tan
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Xin Gao
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Ping Huang
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Shengjun Wu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
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10
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Zhao J, Huang L, Chakrabarti S, Cooper J, Choi E, Ganan C, Tolchinsky B, Triplett EW, Daroub SH, Martens-Habbena W. Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. THE ISME JOURNAL 2023; 17:1839-1850. [PMID: 37596409 PMCID: PMC10579303 DOI: 10.1038/s41396-023-01493-y] [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: 08/02/2022] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Laibin Huang
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - EunKyung Choi
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Carolina Ganan
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Bryn Tolchinsky
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA.
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11
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Huang L, Levintal E, Erikson CB, Coyotl A, Horwath WR, Dahlke HE, Mazza Rodrigues JL. Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37467434 PMCID: PMC10399200 DOI: 10.1021/acs.est.3c01356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Nitrate (NO3-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15N-NO3- and 18O-NO3- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.
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Affiliation(s)
- Laibin Huang
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Elad Levintal
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Christian Bernard Erikson
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Adolfo Coyotl
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - William R Horwath
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Helen E Dahlke
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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12
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Chen C, Deng Y, Zhou H, Jiang L, Deng Z, Chen J, Han X, Zhang D, Zhang C. Revealing the response of microbial communities to polyethylene micro(nano)plastics exposure in cold seep sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163366. [PMID: 37044349 DOI: 10.1016/j.scitotenv.2023.163366] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023]
Abstract
To date, multiple studies have shown that the accumulation of microplastics (MPs)/nanoplastics (NPs) in the environment may lead to various problems. However, the effects of MPs/NPs on microbial communities and biogeochemical processes, particularly methane metabolism in cold seep sediments, have not been well elucidated. In this study, an indoor microcosm experiment for a period of 120 days exposure of MPs/NPs was conducted. The results showed that MPs/NPs addition did not significantly influence bacterial and archaeal richness in comparison with the control (p > 0.05), whereas higher levels of NPs (1 %, w/w) had a significant adverse effect on bacterial diversity (p < 0.05). Moreover, the bacterial community was more sensitive to the addition of MPs/NPs than the archaea, and Epsilonbacteraeota replaced Proteobacteria as the dominant phylum in the MPs/NPs treatments (except 0.2 % NPs). With respect to the co-occurrence relationships, network analysis showed that the presence of NPs, in comparison with MPs, reduced microbial network complexity. Finally, the presence of MPs/NPs decreased the abundance of mcrA, while promoting the abundance of pmoA. This study will help elucidate the responses of microbial communities to MPs/NPs and evaluate their effects on methane metabolism in cold seep ecosystems.
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Affiliation(s)
- Chunlei Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Yinan Deng
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Guangzhou Marine Geological Survey, Guangzhou 510075, China
| | - Hanghai Zhou
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Lijia Jiang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Jiawang Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Xiqiu Han
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Key Laboratory of Submarine Geosciences & The Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China.
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13
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Lai JL, Li ZG, Wang Y, Xi HL, Luo XG. Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5305-5316. [PMID: 36952228 DOI: 10.1021/acs.est.3c00422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The potential ecological risks caused by entering radioactive wastewater containing tritium and carbon-14 into the sea require careful evaluation. This study simulated seawater's tritium and carbon-14 pollution and analyzed the effects on the seawater and sediment microenvironments. Tritium and carbon-14 pollution primarily altered nitrogen and phosphorus metabolism in the seawater environment. Analysis by 16S rRNA sequencing showed changes in the relative abundance of microorganisms involved in carbon, nitrogen, and phosphorus metabolism and organic matter degradation in response to tritium and carbon-14 exposure. Metabonomics and metagenomic analysis showed that tritium and carbon-14 exposure interfered with gene expression involving nucleotide and amino acid metabolites, in agreement with the results seen for microbial community structure. Tritium and carbon-14 exposure also modulated the abundance of functional genes involved in carbohydrate, phosphorus, sulfur, and nitrogen metabolic pathways in sediments. Tritium and carbon-14 pollution in seawater adversely affected microbial diversity, metabolic processes, and the abundance of nutrient-cycling genes. These results provide valuable information for further evaluating the risks of tritium and carbon-14 in marine environments.
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Affiliation(s)
- Jin-Long Lai
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Zhan-Guo Li
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Yi Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Hai-Ling Xi
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Xue-Gang Luo
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
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14
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Nelkner J, Huang L, Lin TW, Schulz A, Osterholz B, Henke C, Blom J, Pühler A, Sczyrba A, Schlüter A. Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis. ENVIRONMENTAL MICROBIOME 2023; 18:26. [PMID: 36998097 PMCID: PMC10064710 DOI: 10.1186/s40793-023-00479-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess-Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes. RESULTS Taxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO[Formula: see text]) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus. CONCLUSIONS On a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.
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Affiliation(s)
- Johanna Nelkner
- Genome Research of Industrial Microorganisms, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Liren Huang
- Genome Research of Industrial Microorganisms, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Timo W. Lin
- Nucleic Acids Core Facility, Faculty of Biology, Johannes Gutenberg University Mainz, Germany Mainz
| | - Alexander Schulz
- Machine Learning Group, CITEC - Cognitive Interaction Technology, Bielefeld University, Bielefeld, Germany
| | - Benedikt Osterholz
- Genome Research of Industrial Microorganisms, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christian Henke
- Computational Metagenomics Group, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Alexander Sczyrba
- Genome Research of Industrial Microorganisms, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, CeBiTec - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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15
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Fang GY, Mu XJ, Huang BW, Jiang YJ. Monitoring Longitudinal Trends and Assessment of the Health Risk of Shigella flexneri Antimicrobial Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4971-4983. [PMID: 36929874 DOI: 10.1021/acs.est.2c08766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Shigella flexneri infection is the main cause of diarrhea in humans worldwide. The emergence of antimicrobial resistance (AMR) of S. flexneri is a growing public health threat worldwide, while large-scale studies monitoring the longitudinal AMR trends of isolates remain scarce. Here, the AMR gene (ARG) profiles of 717 S. flexneri isolates from 1920 to 2020 worldwide were determined. The results showed that the average number of ARGs in isolates has increased significantly, from 19.2 ± 2.4 before 1970 to 29.6 ± 5.3 after 2010. In addition, mobile genetic elements were important contributors to ARGs in S. flexneri isolates. The results of the structural equation model showed that the human development index drove the consumption of antibiotics and indirectly promoted the antibiotic resistance. Finally, a machine learning algorithm was used to predict the antibiotic resistance risk of global terrestrial S. flexneri isolates and successfully map the antibiotic resistance threats in global land habitats with over 80% accuracy. Collectively, this study monitored the longitudinal AMR trends, quantitatively surveilled the health risk of S. flexneri AMR, and provided a theoretical basis for mitigating the threat of antibiotic resistance.
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Affiliation(s)
- Guan-Yu Fang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
- Suzhou Precision Biotech Co., Ltd, Suzhou 215000, P. R. China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
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16
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Abstract
Coronavirus disease 2019 (COVID-19) severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples from 300 in-hospital COVID-19 patients, collected at the time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), redundancy analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Co-abundance network analysis determined that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Based on average abundance difference between the two guilds, the guild-level microbiome index (GMI) classified patients from different severity groups (average AUROC [area under the receiver operating curve] = 0.83). Moreover, age-adjusted partial Spearman's correlation showed that GMIs at admission were correlated with 8 clinical parameters, which are predictors for COVID-19 prognosis, on day 7 in hospital. In addition, GMI at admission was associated with death/discharge outcome of the critical patients. We further validated that GMI was able to consistently classify patients with different COVID-19 symptom severities in different countries and differentiated COVID-19 patients from healthy subjects and pneumonia controls in four independent data sets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission. IMPORTANCE Previous reports on the associations between COVID-19 and gut microbiome have been constrained by taxonomic-level analysis and overlook the interaction between microbes. By applying a genome-resolved, reference-free, guild-based metagenomic analysis, we demonstrated that the relationship between gut microbiota and COVID-19 is genome-specific instead of taxon-specific or even species-specific. Moreover, the COVID-19-associated genomes were not independent but formed two competing guilds, with Guild 1 potentially beneficial and Guild 2 potentially more detrimental to the host based on comparative genomic analysis. The dominance of Guild 2 over Guild 1 at time of admission was associated with hospitalized COVID-19 patients at high risk for more severe outcomes. Moreover, the guild-level microbiome signature is not only correlated with the symptom severity of COVID-19 patients, but also differentiates COVID-19 patients from pneumonia controls and healthy subjects across different studies. Here, we showed the possibility of using genome-resolved and guild-level microbiome signatures to identify hospitalized COVID-19 patients with a high risk of more severe outcomes at the time of admission.
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Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, Wollard J, Vyshenska D, Riley R, Tomatsu A, Hestrin R, Malmstrom RR, Firestone M, Pett-Ridge J. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. MICROBIOME 2022; 10:199. [PMID: 36434737 PMCID: PMC9700909 DOI: 10.1186/s40168-022-01391-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. RESULTS Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera. CONCLUSIONS Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.
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Affiliation(s)
- Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Marissa Lafler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Ashley N. Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Anne Kakouridis
- Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | | | | | | | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA USA
| | | | - Mary Firestone
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA USA
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Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales. mSphere 2022; 7:e0022322. [PMID: 36069437 PMCID: PMC9599434 DOI: 10.1128/msphere.00223-22] [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] [Indexed: 11/20/2022] Open
Abstract
Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.
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Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of
Clostridium
in an Artificial Ecosystem for Liquor Production. mSystems 2022; 7:e0029722. [PMID: 35491831 PMCID: PMC9238394 DOI: 10.1128/msystems.00297-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pit mud is a typical artificial ecosystem for Chinese liquor production.
Clostridium
inhabiting pit mud plays essential roles in the flavor formation of strong-flavor baijiu. The relative abundance of
Clostridium
increased with pit mud quality, further influencing the quality of baijiu.
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High Abundance of Thaumarchaeota Found in Deep Metamorphic Subsurface in Eastern China. Microorganisms 2022; 10:microorganisms10030542. [PMID: 35336118 PMCID: PMC8950554 DOI: 10.3390/microorganisms10030542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Members of the Thaumarchaeota phylum play a key role in nitrogen cycling and are prevalent in a variety of environments including soil, sediment, and seawater. However, few studies have shown the presence of Thaumarchaeota in the terrestrial deep subsurface. Using high-throughput 16S rRNA gene sequencing, this study presents evidence for the high relative abundance of Thaumarchaeota in a biofilm sample collected from the well of Chinese Continental Scientific Drilling at a depth of 2000 m. Phylogenetic analysis showed a close relationship of these thaumarchaeotal sequences with known ammonia-oxidizing archaea (AOA) isolates, suggesting the presence of AOA in the deep metamorphic environment of eastern China which is believed to be oxic. Based on fluid geochemistry and FAProTax functional prediction, a pathway of nitrogen cycling is proposed. Firstly, heterotrophic nitrogen fixation is executed by diazotrophic bacteria coupled with methane oxidation. Then, ammonia is oxidized to nitrite by AOA, and nitrite is further oxidized to nitrate by bacteria within the phylum Nitrospirae. Denitrification and anaerobic ammonia oxidation occur slowly, leading to nitrate accumulation in the subsurface. With respect to biogeochemistry, the reaction between downward diffusing O2 and upward diffusing CH4 potentially fuels the ecosystem with a high relative abundance of Thaumarchaeota.
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