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Zhang D, Liu F, Al MA, Yang Y, Yu H, Li M, Wu K, Niu M, Wang C, He Z, Yan Q. Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172518. [PMID: 38631637 DOI: 10.1016/j.scitotenv.2024.172518] [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: 02/14/2024] [Revised: 04/13/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4+, NO2- and SO42, while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.
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Affiliation(s)
- Dandan Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Mamun Abdullah Al
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuchun Yang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Huang Yu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; School of Resources Environment and Safety Engineering, Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang 421001, China
| | - Mingyue Li
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Kun Wu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Mingyang Niu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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Zhang L, Yuan L, Wen Y, Zhang M, Huang S, Wang S, Zhao Y, Hao X, Li L, Gao Q, Wang Y, Zhang S, Huang S, Liu K, Yu X, Li D, Xu J, Zhao B, Zhang L, Zhang H, Zhou W, Ai C. Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices. THE NEW PHYTOLOGIST 2024; 242:1275-1288. [PMID: 38426620 DOI: 10.1111/nph.19653] [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: 06/06/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.
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Affiliation(s)
- Liyu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Liang Yuan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanchen Wen
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Meiling Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shuyu Huang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Shiyu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yuanzheng Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Xiangxiang Hao
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Lujun Li
- Hailun National Observation and Research Station of Agroecosystems, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Qiang Gao
- Jilin Agricultural University, Changchun, 130118, China
| | - Yin Wang
- Jilin Agricultural University, Changchun, 130118, China
| | - Shuiqing Zhang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Shaomin Huang
- Institute of Plant Nutrition, Resource and Environment, Henan Academy of Agricultural Sciences, 116 Garden Road, Zhengzhou, 450002, China
| | - Kailou Liu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Xichu Yu
- Jiangxi Institute of Red Soil, National Engineering and Technology Research Center for Red Soil Improvement, Nanchang, 330046, China
| | - Dongchu Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiukai Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Bingqiang Zhao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Lu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huimin Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Chao Ai
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
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Wang A, Zhang S, Liang Z, Zeng Z, Ma Y, Zhang Z, Yang Y, He Z, Yu G, Liang Y. Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment. ENVIRONMENTAL RESEARCH 2024; 248:118137. [PMID: 38295972 DOI: 10.1016/j.envres.2024.118137] [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: 11/27/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024]
Abstract
Since nitrate nitrogen (NO3--N) input has proved an effective approach for the treatment of black and odorous river waterbody, it was controversial whether the total nitrogen concentration standard should be raised when the effluent from the sewage treatment plant is discharged into the polluted river. To reveal the effect of exogenous nitrate (NO3--N) on black odorous waterbody, sediments with different features from contaminated rivers were collected, and the changes of physical and chemical characteristics and microbial community structure in sediments before and after the addition of exogenous NO3--N were investigated. The results showed that after the input of NO3--N, reducing substances such as acid volatile sulfide (AVS) in the sediment decreased by 80 % on average, ferrous (Fe2+) decreased by 50 %, yet the changing trend of ammonia nitrogen (NH4+-N) in some sediment samples increased while others decreased. High-throughput sequencing results showed that the abundance of Thiobacillus at most sites increased significantly, becoming the dominant genus in the sediment, and the abundance of functional genes in the metabolome increased, such as soxA, soxX, soxY, soxZ. Network analysis showed that sediment microorganisms evolved from a single sulfur oxidation ecological function to diverse ecological functions, such as nitrogen cycle nirB, nirD, nirK, nosZ, and aerobic decomposition. In summary, inputting an appropriate amount of exogenous NO3--N is beneficial for restoring and maintaining the oxidation states of river sediment ecosystems.
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Affiliation(s)
- Ao Wang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Shengrui Zhang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ziyang Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zhanqin Zeng
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yingshi Ma
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiang Zhang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Yang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zihao He
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Guangwei Yu
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China.
| | - Yuhai Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China.
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4
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Peng Z, Qian X, Liu Y, Li X, Gao H, An Y, Qi J, Jiang L, Zhang Y, Chen S, Pan H, Chen B, Liang C, van der Heijden MGA, Wei G, Jiao S. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nat Commun 2024; 15:3624. [PMID: 38684659 PMCID: PMC11058813 DOI: 10.1038/s41467-024-47348-8] [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: 09/16/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.
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Affiliation(s)
- Ziheng Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xiaomeng Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Hang Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yining An
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Jiejun Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Lan Jiang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Shi Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Haibo Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Beibei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Chunling Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
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Rafie SAA, Blentlinger LR, Putt AD, Williams DE, Joyner DC, Campa MF, Schubert MJ, Hoyt KP, Horn SP, Franklin JA, Hazen TC. Impact of prescribed fire on soil microbial communities in a Southern Appalachian Forest clear-cut. Front Microbiol 2024; 15:1322151. [PMID: 38741734 PMCID: PMC11090169 DOI: 10.3389/fmicb.2024.1322151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.
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Affiliation(s)
- S. A. A. Rafie
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - L. R. Blentlinger
- Department of Geography, University of Tennessee, Knoxville, TN, United States
| | - A. D. Putt
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
| | - D. E. Williams
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - D. C. Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - M. F. Campa
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Bredesen Center—Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
| | - M. J. Schubert
- Forest Resources AgResearch and Education Center, Knoxville, TN, United States
| | - K. P. Hoyt
- Forest Resources AgResearch and Education Center, Knoxville, TN, United States
| | - S. P. Horn
- Department of Geography, University of Tennessee, Knoxville, TN, United States
| | - J. A. Franklin
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States
| | - T. C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
- Bredesen Center—Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
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Huang H, Zan S, Shao K, Chen H, Fan J. Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170511. [PMID: 38309352 DOI: 10.1016/j.scitotenv.2024.170511] [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: 08/30/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.
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Affiliation(s)
- Huiling Huang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Shuaijun Zan
- Groundwater Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Kuishuang Shao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Hanjun Chen
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
| | - Jingfeng Fan
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China.
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7
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Wang H, Pijl A, Liu B, Wamelink W, Korthals GW, Costa OYA, Kuramae EE. A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil. Microorganisms 2024; 12:760. [PMID: 38674704 PMCID: PMC11051824 DOI: 10.3390/microorganisms12040760] [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: 02/28/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil ("MP kit") and the DNeasy PowerSoil Pro Kit ("PowerSoil kit"). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642-37,805 16S rRNA gene sequence reads and 30,380-42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.
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Affiliation(s)
- Han Wang
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Binbin Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China;
| | - Wieger Wamelink
- Biodiversity and Policy, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Gerard W. Korthals
- Bioindications and Plant Health, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Ohana Y. A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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8
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Ho PY, Huang KC. Challenges in quantifying functional redundancy and selection in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586891. [PMID: 38586050 PMCID: PMC10996602 DOI: 10.1101/2024.03.26.586891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Microbiomes can exhibit large variations in species abundances but high reproducibility in abundances of functional units, an observation often considered evidence for functional redundancy. Based on such reduction in functional variability, selection is hypothesized to act on functional units in these ecosystems. However, the link between functional redundancy and selection remains unclear. Here, we show that reduction in functional variability does not always imply selection on functional profiles. We propose empirical null models to account for the confounding effects of statistical averaging and bias toward environment-independent beneficial functions. We apply our models to existing data sets, and find that the abundances of metabolic groups within microbial communities from bromeliad foliage do not exhibit any evidence of the previously hypothesized functional selection. By contrast, communities of soil bacteria or human gut commensals grown in vitro are selected for metabolic capabilities. By separating the effects of averaging and functional bias on functional variability, we find that the appearance of functional selection in gut microbiome samples from the Human Microbiome Project is artifactual, and that there is no evidence of selection for any molecular function represented by KEGG orthology. These concepts articulate a basic framework for quantifying functional redundancy and selection, advancing our understanding of the mapping between microbiome taxonomy and function.
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9
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Li Q, Hu H, Tan X, Wang J, Mei R, Jiang F, Ling Y, Li X. Effects of Storage in an Active and Spontaneous Controlled O 2/CO 2 Atmosphere on Volatile Flavor Components and the Microbiome of Truffles. ACS OMEGA 2024; 9:9331-9347. [PMID: 38434872 PMCID: PMC10905597 DOI: 10.1021/acsomega.3c08375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024]
Abstract
This study explored the potential to improve the storage quality and prolong the shelf life of truffles by storing them in a modified atmosphere fresh-keeping box with sealed gas components of Active Modified Atmosphere Packaging (AMAP, 40% O2 + 60% CO2) at 4 °C. During the storage period, a total of 63 volatile components in 10 categories were detected, with aldehydes being the most abundant and the relative content of ethers being the highest. The relative odor activity value and principal component analysis revealed that isovaleraldehyde, 1-octen-3-ol, 1-octen-3-one, and dimethyl sulfide were the characteristic flavor components of fresh truffles. However, 3-methylthiopropionaldehyde and (E, E)-2,4-nonadienal were the components that caused the deterioration of truffle flavor and could potentially serve as markers of truffle decay characteristics. 16S rDNA high-throughput sequencing showed that Leuconostoc and Lactococcus were dominant in the truffle samples stored for 14 days, but the abundance of putrefactive pathogenic bacteria showed an increasing trend in the truffle samples stored for 28 days. During the whole storage period, the common fungi detected in the different treatment groups were Candida and Aspergillus. The relative abundance of the former decreased, while the relative abundance of the latter decreased initially and then increased. The correlation between volatile components and the microbial flora was further analyzed, which indicated that Lactococcus and Lactobacillus had the same contributions to the same flavor, while Pseudomonas and Glutamicibacter had the opposite contributions to the same flavor. The results provide a reference for the storage and preservation of truffles.
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Affiliation(s)
- Qiang Li
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Haiyang Hu
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Xingyi Tan
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Jianhui Wang
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Ruhuai Mei
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Fangguo Jiang
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Yunkun Ling
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Xiang Li
- School of Food and Biological
Engineering, Chengdu University, Chengdu, Sichuan 610106, China
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10
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Zhang X, Lan T, Jiang H, Ye K, Dai Z. Bacterial community driven nitrogen cycling in coastal sediments of intertidal transition zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168299. [PMID: 37926266 DOI: 10.1016/j.scitotenv.2023.168299] [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: 08/01/2023] [Revised: 10/14/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Microorganisms inhabiting in coastal sediments significantly affect the nitrogen cycling in coastal waters and ecosystems. However, the bacterial community that related to the key active nitrogen transformation processes in intertidal transition zone are still not understood. Across a long flat intertidal zone at depths from 0 to 3 m in Daya Bay, China, the bacterial communities in sediments and their driven nitrogen cycling potential were evaluated with environmental factors and 16S rRNA sequencing. The results showed that the intertidal zone is a divide for environmental factors as pH, salinity and C/N ratio, instead of an average shift from freshwater to salt water. At the same time, the environmental factors influenced the abundance of bacterial community related to nitrogen cycling. Across the intertidal zone, the dominant nitrogen transformation processes were different. At the high tide and middle tide sites, the primary nitrogen cycling process was nitrification that worked with Nitrosomonadaceae, Nitrospiraceae, 0319-6A21, and wb1-A12. At the low tide sites, nitrogen fixation was the dominant function conducted by Bradyrhizobiaceae. The reduction of nitrate was carried out with the help of Xanthomonadales but relatively weak in all sampling sites especially for low tide sites. This was mostly because the richness and evenness of bacterial community were the lowest at the low tide sites. Meanwhile, the pH, Cl-, salinity, NH4+, NO3- and C/N ratio were the important factors that shaped the composition of local bacterial community. Further, the nonmetric multidimensional scaling results indicated that there were significant statistical differences in the composition of bacterial community among samples at different layers. The dominant nitrogen cycling processes in coastal sediments at different tide levels were revealed in this study, which offered an extended concept of nitrogen transformation along the groundwater discharge path in the intertidal transition zone. The distributions and compositions of bacterial communities and predicted functions provided a new insight for coastal environment and ecosystem management.
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Affiliation(s)
- Xiaoying Zhang
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China; College of Construction Engineering, Jilin University, Changchun 130026, China
| | - Tianshan Lan
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China.
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Kexin Ye
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China
| | - Zhenxue Dai
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China; College of Construction Engineering, Jilin University, Changchun 130026, China.
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11
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Wang T, Li L, Figeys D, Liu YY. Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes. ISME COMMUNICATIONS 2024; 4:ycae063. [PMID: 38808120 PMCID: PMC11131966 DOI: 10.1093/ismeco/ycae063] [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: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024]
Abstract
The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed in vitro cultures of a human gut microbiome sample and investigated how oversupplying various sugars involved in ecological niches influences the community structure and protein abundance. The presented results demonstrate the performance of our pipeline in identifying proteins' metabolic and ecological roles, as well as its potential to help us design nutrient interventions to modulate the human microbiome.
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Affiliation(s)
- Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Leyuan Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61820, United States
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12
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McGuinness AJ, Stinson LF, Snelson M, Loughman A, Stringer A, Hannan AJ, Cowan CSM, Jama HA, Caparros-Martin JA, West ML, Wardill HR. From hype to hope: Considerations in conducting robust microbiome science. Brain Behav Immun 2024; 115:120-130. [PMID: 37806533 DOI: 10.1016/j.bbi.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/14/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023] Open
Abstract
Microbiome science has been one of the most exciting and rapidly evolving research fields in the past two decades. Breakthroughs in technologies including DNA sequencing have meant that the trillions of microbes (particularly bacteria) inhabiting human biological niches (particularly the gut) can be profiled and analysed in exquisite detail. This microbiome profiling has profound impacts across many fields of research, especially biomedical science, with implications for how we understand and ultimately treat a wide range of human disorders. However, like many great scientific frontiers in human history, the pioneering nature of microbiome research comes with a multitude of challenges and potential pitfalls. These include the reproducibility and robustness of microbiome science, especially in its applications to human health outcomes. In this article, we address the enormous promise of microbiome science and its many challenges, proposing constructive solutions to enhance the reproducibility and robustness of research in this nascent field. The optimisation of microbiome science spans research design, implementation and analysis, and we discuss specific aspects such as the importance of ecological principals and functionality, challenges with microbiome-modulating therapies and the consideration of confounding, alternative options for microbiome sequencing, and the potential of machine learning and computational science to advance the field. The power of microbiome science promises to revolutionise our understanding of many diseases and provide new approaches to prevention, early diagnosis, and treatment.
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Affiliation(s)
- Amelia J McGuinness
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Matthew Snelson
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia.
| | - Amy Loughman
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Andrea Stringer
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
| | | | - Hamdi A Jama
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia
| | | | - Madeline L West
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Hannah R Wardill
- Supportive Oncology Research Group, Precision Medicine (Cancer), South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide, Adelaide, South Australia, Australia
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13
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Hayashi I, Fujita H, Toju H. Deterministic and stochastic processes generating alternative states of microbiomes. ISME COMMUNICATIONS 2024; 4:ycae007. [PMID: 38415200 PMCID: PMC10897905 DOI: 10.1093/ismeco/ycae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such "alternative states" of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the "stability landscapes" of ecological community compositions.
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Affiliation(s)
- Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan
| | - Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
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14
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Goyal A, Flamholz AI, Petroff AP, Murugan A. Closed ecosystems extract energy through self-organized nutrient cycles. Proc Natl Acad Sci U S A 2023; 120:e2309387120. [PMID: 38127977 PMCID: PMC10756307 DOI: 10.1073/pnas.2309387120] [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: 06/04/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
Our planet is a self-sustaining ecosystem powered by light energy from the sun, but roughly closed to matter. Many ecosystems on Earth are also approximately closed to matter and recycle nutrients by self-organizing stable nutrient cycles, e.g., microbial mats, lakes, open ocean gyres. However, existing ecological models do not exhibit the self-organization and dynamical stability widely observed in such planetary-scale ecosystems. Here, we advance a conceptual model that explains the self-organization, stability, and emergent features of closed microbial ecosystems. Our model incorporates the bioenergetics of metabolism into an ecological framework. By studying this model, we uncover a crucial thermodynamic feedback loop that enables metabolically diverse communities to almost always stabilize nutrient cycles. Surprisingly, highly diverse communities self-organize to extract [Formula: see text]10[Formula: see text] of the maximum extractable energy, or [Formula: see text]100 fold more than randomized communities. Further, with increasing diversity, distinct ecosystems show strongly correlated fluxes through nutrient cycles. However, as the driving force from light increases, the fluxes of nutrient cycles become more variable and species-dependent. Our results highlight that self-organization promotes the efficiency and stability of complex ecosystems at extracting energy from the environment, even in the absence of any centralized coordination.
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Affiliation(s)
- Akshit Goyal
- Department of Physics, Massachusetts Insitute of Technology, Cambridge, MA02139
| | - Avi I. Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA91125
| | | | - Arvind Murugan
- Department of Physics, University of Chicago, Chicago, IL60637
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15
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Khan T, Song W, Nappi J, Marzinelli EM, Egan S, Thomas T. Functional guilds and drivers of diversity in seaweed-associated bacteria. FEMS MICROBES 2023; 5:xtad023. [PMID: 38213395 PMCID: PMC10781435 DOI: 10.1093/femsmc/xtad023] [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: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.
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Affiliation(s)
- Tahsin Khan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Jadranka Nappi
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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16
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Hosoda K, Seno S, Kamiura R, Murakami N, Kondoh M. Biodiversity and Constrained Information Dynamics in Ecosystems: A Framework for Living Systems. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1624. [PMID: 38136504 PMCID: PMC10742641 DOI: 10.3390/e25121624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023]
Abstract
The increase in ecosystem biodiversity can be perceived as one of the universal processes converting energy into information across a wide range of living systems. This study delves into the dynamics of living systems, highlighting the distinction between ex post adaptation, typically associated with natural selection, and its proactive counterpart, ex ante adaptability. Through coalescence experiments using synthetic ecosystems, we (i) quantified ecosystem stability, (ii) identified correlations between some biodiversity indexes and the stability, (iii) proposed a mechanism for increasing biodiversity through moderate inter-ecosystem interactions, and (iv) inferred that the information carrier of ecosystems is species composition, or merged genomic information. Additionally, it was suggested that (v) changes in ecosystems are constrained to a low-dimensional state space, with three distinct alteration trajectories-fluctuations, rapid environmental responses, and long-term changes-converging into this state space in common. These findings suggest that daily fluctuations may predict broader ecosystem changes. Our experimental insights, coupled with an exploration of living systems' information dynamics from an ecosystem perspective, enhance our predictive capabilities for natural ecosystem behavior, providing a universal framework for understanding a broad spectrum of living systems.
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Affiliation(s)
- Kazufumi Hosoda
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; (R.K.); (N.M.)
- Center for Information and Neural Networks (CiNet), National Institute of Information and Communications Technology (NICT), Osaka 565-0871, Japan
- Institute for Transdisciplinary Graduate Degree Programs, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Life and Medical Sciences Area, Health Sciences Discipline, Kobe University, Tomogaoka 7-10-2, Suma-ku, Kobe, Hyogo 654-0142, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Rikuto Kamiura
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; (R.K.); (N.M.)
| | - Naomi Murakami
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; (R.K.); (N.M.)
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan;
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17
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Zhou J, Qin W, Lu X, Yang Y, Stahl D, Jiao N, Zhou J, Liu J, Tu Q. The diversity and ecological significance of microbial traits potentially involved in B 12 biosynthesis in the global ocean. MLIFE 2023; 2:416-427. [PMID: 38818271 PMCID: PMC10989127 DOI: 10.1002/mlf2.12095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/21/2023] [Accepted: 10/04/2023] [Indexed: 06/01/2024]
Abstract
Cobalamin (B12), an essential nutrient and growth cofactor for many living organisms on Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related to B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional assemblages. By anchoring microbial traits potentially involved in B12 biosynthesis, we depict the biogeographic patterns of B12 biosynthesis genes and the taxa harboring them in the global ocean, despite the limitations of detecting de novo B12 synthesizers via metagenomes alone. Both the taxonomic and functional composition of B12 biosynthesis genes were strongly shaped by depth, differentiating the epipelagic zones from the mesopelagic layers. Functional genes related to B12 biosynthesis were relatively stably distributed across different oceans, but the taxa harboring them varied considerably, showing clear functional redundancy among microbial systems. Microbial taxa carrying B12 biosynthesis genes in the surface water were influenced by environmental factors such as temperature, oxygen, and nitrate. However, the composition of functional genes was only weakly associated with these environmental factors. Null model analyses demonstrated that determinism governed the variations in B12 biosynthesis genes, whereas a higher degree of stochasticity was associated with taxonomic variations. Significant associations were observed between the chlorophyll a concentration and B12 biosynthesis, confirming its importance in primary production in the global ocean. The results of this study reveal an essential ecological mechanism governing the assembly of microbes in nature: the environment selects for function rather than taxonomy; functional redundancy underlies stochastic community assembly.
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Affiliation(s)
- Jiayin Zhou
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
| | - Wei Qin
- School of Biological SciencesUniversity of OklahomaNormanOklahomaUSA
| | - Xinda Lu
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
DermBiont Inc.BostonMassachusettsUSA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - David Stahl
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Nianzhi Jiao
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Institute of Marine Microbes and EcospheresXiamen UniversityXiamenChina
| | - Jizhong Zhou
- School of Biological SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Institute for Environmental Genomics, University of OklahomaNormanOklahomaUSA
- School of Civil Engineering and Environmental Sciences, University of OklahomaNormanOklahomaUSA
- School of Computer Sciences, University of OklahomaNormanOklahomaUSA
| | - Jihua Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
| | - Qichao Tu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
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Shan X, Liu C, Song L, Huan H, Chen H. Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122575. [PMID: 37742860 DOI: 10.1016/j.envpol.2023.122575] [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: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/26/2023]
Abstract
Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.
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Affiliation(s)
- Xin Shan
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Liuting Song
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Huan Huan
- Technical Centre for Soil, Agricultural and Rural Ecology and Environment, Ministry of Ecology and Environment of the People's Republic of China, Beijing, 100012, China
| | - Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China.
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Ding Y, Geng Y, Zhou W, Li D. Habitat-specific environmental factors regulate the spatial variability of biological soil crust microbial communities on the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165937. [PMID: 37532035 DOI: 10.1016/j.scitotenv.2023.165937] [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: 05/30/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/04/2023]
Abstract
Biological soil crusts (BSCs) are an important biological component of the soil surface, covering approximately 12 % of the Earth's land surface. Although BSCs are closely related to habitats, the microbial diversity and spatial variability of BSCs in different ecosystems are still unclear, especially on the Qinghai-Tibet Plateau (QTP), where climate is changeable and habitats are complex. Here, we investigated the diversity, assembly processes, spatial distribution pattern and driving factors of prokaryotic and eukaryotic microbial communities in BSCs in four habitats on the QTP. It was found that habitat-specific environmental factors regulated the composition, diversity and spatial variability of BSC microbial communities. Soil organic carbon and soil water content were the most important factors (R2 = 0.9024, P = 0.001; R2 = 0.8004, P = 0.001) affecting the spatial differences in prokaryotes and eukaryotes, respectively. Under the specific climate of the QTP, the spatial pattern of microbial communities in BSCs was controlled by precipitation rather than temperature. In addition, ecological processes further explained the effects of habitat specificity, and environmental filtering explained microbial community differences better than dispersal limitation. The results of the neutral community model and the normalized stochastic ratio index revealed that the assembly of prokaryotic communities was determined by deterministic processes at the regional scale, and at the local scale, the assembly process was mainly determined by habitat type, while the assembly of eukaryotic communities was determined by stochastic processes at both the regional and local scales. This study provided a scientific reference for the prediction of BSC distribution and resource conservation under future climate change scenarios.
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Affiliation(s)
- Yuang Ding
- School of Ecology and Environment, Tibet University, Lhasa 850001, PR China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuchen Geng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Weicheng Zhou
- School of Chemistry and Environmental Science, Xiangnan University, Chenzhou 423000, PR China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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20
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Alsholi DM, Yacoub GS, Rehman AU, Ullah H, Khan AI, Deng T, Siddiqui NZ, Alioui Y, Farooqui NA, Elkharti M, Li Y, Wang L, Xin Y. Lactobacillus rhamnosus Attenuates Cisplatin-Induced Intestinal Mucositis in Mice via Modulating the Gut Microbiota and Improving Intestinal Inflammation. Pathogens 2023; 12:1340. [PMID: 38003804 PMCID: PMC10674506 DOI: 10.3390/pathogens12111340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/26/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Lactobacillus rhamnosus (LBS) is a well-documented probiotic strain in oncology and has a pivotal role in clinical applications. Here, we have investigated the protective effect of Lactobacillus rhamnosus on intestinal mucositis induced by cisplatin (CP) and explored the underlying mechanisms targeting inflammatory proteins, as well as the histological changes in the intestinal tissue of mice, in addition, the bacterial strains that may be related to the health-enhancing properties. BALB/c mice were pre-treated with or without LBS via oral gavage, followed by mucositis induction with cisplatin. Our results revealed that the LBS-treated groups significantly attenuated proinflammatory cytokine levels (IL-1β, IL-6, and TNF-α) compared to the CP group. Furthermore, LBS mitigated the damaged tight junction integrity caused by CP via up-regulating the levels of claudin, occludin, ZO-1, and mucin-2 protein (MUC-2). Finally, the 16S rRNA fecal microbiome genomic analysis showed that LBS administration enhanced the growth of beneficial bacteria, i.e., Firmicutes and Lachnospiraceae, while the relative abundance of the opportunistic bacteria Bacteroides and Proteobacteria decreased. Collectively, LBS was found to beneficially modulate microbial composition structure and functions and enrich the ecological diversity in the gut.
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Affiliation(s)
- Duaa M. Alsholi
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Ghazi Suleiman Yacoub
- Department of Dermatology, The First Affiliated Hospital of Dalian Medical University, 222 Zhongshan Lu, Dalian 116011, China;
| | - Ata Ur Rehman
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Hidayat Ullah
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Asif Iqbal Khan
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Ting Deng
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Nimra Zafar Siddiqui
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Yamina Alioui
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Nabeel Ahmed Farooqui
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
| | - Maroua Elkharti
- Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China;
| | - Yanxia Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Liang Wang
- Stem Cell Clinical Research Center, National Joint Engineering Laboratory, Regenerative Medicine Center, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Yi Xin
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; (D.M.A.); (A.U.R.); (H.U.); (A.I.K.); (T.D.); (N.Z.S.); (Y.A.); (N.A.F.)
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21
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Xu L, Tang Y, Liu S, Chen X, Wang Y, Liu Z, Qin Q, Fu D, Xu Y. Short-chain fatty acids facilitated long-term dechlorination of PCBs in Taihu Lake sediment microcosms: Evidence from PCB congener and microbial community analyses. CHEMOSPHERE 2023; 340:139935. [PMID: 37619750 DOI: 10.1016/j.chemosphere.2023.139935] [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: 03/30/2023] [Revised: 07/12/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Microbial reductive dechlorination hosts great promise as an in situ bioremediation strategy for polychlorinated biphenyls (PCBs) contamination. However, the slow dechlorination in sediments limits natural attenuation. Short-chain fatty acids, as preferred carbon sources and electron donors for dechlorinating microorganisms, might stimulate PCB dechlorination. Herein, two sets of short-chain fatty acids, sole acetate and a fatty acid mixture (acetate, propionate, and butyrate), were amended periodically into Taihu Lake (China) sediment microcosms containing nine PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170) after 24 weeks of incubation. Short-chain fatty acids facilitated the long-term PCB dechlorination and the promoting effect of the fatty acid mixture compared favorably with that of sole acetate. By the end of 108 weeks, the total PCB mass concentrations in acetate amended and fatty acid mixture amended microcosms significantly declined by 7.6% and 10.3% compared with non-amended microcosms (P < 0.05), respectively. Short-chain fatty acids selectively favored the removal of flanked meta and single-flanked para chlorines. Notably, a rare ortho dechlorination pathway, PCB25 (24-3-CB) to PCB13 (3-4-CB), was enhanced. Supplementary fatty acids significantly increased reductive dehalogenases (RDase) gene pcbA5 instead of improving the growth of Dehalococcoides. These findings highlight the merits of low cost short-chain fatty acids on in situ biostimulation in treating PCBs contamination.
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Affiliation(s)
- Lei Xu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yanqiang Tang
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Sha Liu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Xi Chen
- Water Affairs Bureau of Nanjing Pukou District, Nanjing, 211899, China
| | - Ying Wang
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Zheming Liu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Qingdong Qin
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Dafang Fu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yan Xu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China.
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22
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Sun J, Zhou H, Cheng H, Chen Z, Yang J, Wang Y, Jing C. Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts. MICROBIAL ECOLOGY 2023; 86:3027-3042. [PMID: 37792089 DOI: 10.1007/s00248-023-02305-8] [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: 05/17/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023]
Abstract
Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, Shandong, People's Republic of China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, People's Republic of China.
- Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, People's Republic of China.
| | - Chunlei Jing
- National Deepsea Center, Ministry of Natural Resources, Qingdao, 266237, Shandong, People's Republic of China.
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Lin Q, Li L, De Vrieze J, Li C, Fang X, Li X. Functional conservation of microbial communities determines composition predictability in anaerobic digestion. THE ISME JOURNAL 2023; 17:1920-1930. [PMID: 37666974 PMCID: PMC10579369 DOI: 10.1038/s41396-023-01505-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Lingjuan Li
- Department of Biology, University of Antwerp, 2610, Wilrijk, Belgium
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoyu Fang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Deng T, He Z, Xu M, Dong M, Guo J, Sun G, Huang H. Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning. mBio 2023; 14:e0156723. [PMID: 37702500 PMCID: PMC10653917 DOI: 10.1128/mbio.01567-23] [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: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE Understanding the processes and mechanisms governing microbial community assembly and their linkages to ecosystem functioning has long been a core issue in microbial ecology. An in-depth insight still requires combining with analyses of species' functional traits and microbial interactions. Our study showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using high-throughput sequencing and culture-dependent technologies. The results provided solid evidences that species' functional traits and interactions were the intrinsic factors determining community structure and function. More importantly, our study established quantitative links between community structure and function based on species' functional traits and interactions, which would have important implications for the design and synthesis of microbiomes with expected functions.
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Affiliation(s)
- Tongchu Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Meijun Dong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Jun Guo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Guoping Sun
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
| | - Haobin Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, Guangdong, China
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Colette M, Guentas L, Della Patrona L, Ansquer D, Callac N. Suaeda australis and its associated rhizosphere microbiota: a comparison of the nutrient removal potential between different shrimp farm sediments in New Caledonia. Front Microbiol 2023; 14:1260585. [PMID: 37876780 PMCID: PMC10591223 DOI: 10.3389/fmicb.2023.1260585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Shrimp rearing generate organic waste that is trapped in the pond sediment. In excess, these wastes may impair aquaculture ecosystem and shrimps' health. To promote the biological oxidation of accumulated organic waste, the pond is drained and dried at the end of each production cycle. However, this practice is not always conducive to maintaining microbial decomposition activities in sediments. Shrimp production in New Caledonia is no exception to this problem of pollution of pond bottoms. One promising way of treating this waste would be bioremediation, using a native halophyte plant and its microbiota. Thus, this study explored the nutrient removal potential of Suaeda australis and its microbiota on sediments from four shrimp farms. Suaeda australis was grown in an experimental greenhouse for 6 months. In order to mimic the drying out of the sediments, pots containing only sediments were left to dry in the open air without halophytes. An analysis of the chemical composition and active microbiota was carried out initially and after 6 months in the sediments of the halophyte cultures and in the dry sediments for each farm, respectively. In the initial state, the chemical parameters and the microbial diversity of the sediment varied considerably from one farm to another. Growing Suaeda australis reduced the nitrogen, phosphorus and sulfur content in all type of sediment. However, this reduction varied significantly from one sediment to another. The rhizosphere of Suaeda australis is mainly composed of micro-organisms belonging to the Alphaproteobacteria class. However, the families recruited from this class vary depending on the farm in question. Depending on the sediment, the variation in microbiota leads to different putative biochemical functions. For two of the farms, a similar reduction in nitrogen concentration was observed in both dry and cultivated sediments. This suggests that certain initial chemical characteristics of the sediments influence the nutrient removal efficiency of Suaeda australis. Our study therefore highlights the need to control the pH of sediments before cultivation or in dry sediments in order to ensure optimal microbial decomposition of organic waste and nutrient cycling.
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Affiliation(s)
- Marie Colette
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
- Institute of Exact and Applied Sciences (ISEA), University of New Caledonia, Nouméa, New Caledonia
| | - Linda Guentas
- Institute of Exact and Applied Sciences (ISEA), University of New Caledonia, Nouméa, New Caledonia
| | - Luc Della Patrona
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Dominique Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Nolwenn Callac
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
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26
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Li S, Liao Y, Jiang Z, Ji G. Life strategies and metabolic interactions of core microbes during thiosulphate-based denitrification. Environ Microbiol 2023; 25:1925-1939. [PMID: 37231629 DOI: 10.1111/1462-2920.16430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 05/13/2023] [Indexed: 05/27/2023]
Abstract
Sulphur-driven denitrification is a low-cost process for the treatment of nitrate-contaminated water. However, a comprehensive understanding of core populations and microbial interactions of a sulphur-based denitrifying system is lacking. This study presents results from three replicated denitrifying systems amended with thiosulphate and operated under a low C/N ratio. Amplicon sequencing revealed gradual enrichments of a few abundant denitrifiers. Based on genome-centred metagenomics and metatranscriptomics, a core set of microbes was identified in the systems, with Pseudomonas 1 and Thauera 2 being the most abundant ones. Although the replicates showed different enrichments, generalized observations were summarized. Most core populations conserved energy from denitrification coupled with sulphur. Pseudomonas 1 and Thauera 2 were able to finish complete denitrification. Surprisingly, they were also able to synthesize almost all amino acids and vitamins. In contrast, less abundant members, including Pseudomonas 2, were relatively auxotrophic and required an exogenous supply of amino acids and vitamins. The high expression of enzymes involved in biosynthesis and transport systems indicated their syntrophic relationships. The genomic findings suggested life strategies and interactions of the core thiosulphate-based denitrifying microbiome, with implications for nitrate-polluted water remediation.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| | - Zhuo Jiang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
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Palanisamy V, Bosilevac JM, Barkhouse DA, Velez SE, Chitlapilly Dass S. Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants. Front Cell Infect Microbiol 2023; 13:1240138. [PMID: 37743870 PMCID: PMC10515220 DOI: 10.3389/fcimb.2023.1240138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/08/2023] [Indexed: 09/26/2023] Open
Abstract
Background Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments. Methods This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, & Grind room) of three beef-processing plants (Plant A, B & C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing. Results Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms. Conclusion This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.
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Affiliation(s)
- Vignesh Palanisamy
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Joseph M. Bosilevac
- U. S. Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Lincoln, NE, United States
| | - Darryll A. Barkhouse
- Molecular Center of Excellence, Invisible Sentinel, bioMerieux Inc., Philadelphia, PA, United States
| | - Sarah E. Velez
- Molecular Center of Excellence, Invisible Sentinel, bioMerieux Inc., Philadelphia, PA, United States
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Berdan EL, Roger F, Wellenreuther M, Kinnby A, Cervin G, Pereyra R, Töpel M, Johannesson K, Butlin RK, André C. A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea-Baltic Sea transition zone. Environ Microbiol 2023; 25:1659-1673. [PMID: 37032322 DOI: 10.1111/1462-2920.16379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/18/2023] [Indexed: 04/11/2023]
Abstract
Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Fabian Roger
- Lund University, Centre for Environmental and Climate Science, Sölvegatan 37, 223 62, Lund, Sweden
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alexandra Kinnby
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Gunnar Cervin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Ricardo Pereyra
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Mats Töpel
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Roger K Butlin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Carl André
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
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Reynolds R, Hyun S, Tully B, Bien J, Levine NM. Identification of microbial metabolic functional guilds from large genomic datasets. Front Microbiol 2023; 14:1197329. [PMID: 37455725 PMCID: PMC10348482 DOI: 10.3389/fmicb.2023.1197329] [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: 03/30/2023] [Accepted: 05/26/2023] [Indexed: 07/18/2023] Open
Abstract
Heterotrophic microbes play an important role in the Earth System as key drivers of major biogeochemical cycles. Specifically, the consumption rate of organic matter is set by the interaction between diverse microbial communities and the chemical and physical environment in which they reside. Modeling these dynamics requires reducing the complexity of microbial communities and linking directly with biogeochemical functions. Microbial metabolic functional guilds provide one approach for reducing microbial complexity and incorporating microbial biogeochemical functions into models. However, we lack a way to identify these guilds. In this study, we present a method for defining metabolic functional guilds from annotated genomes, which are derived from both uncultured and cultured organisms. This method utilizes an Aspect Bernoulli (AB) model and was tested on three large genomic datasets with 1,733-3,840 genomes each. Ecologically relevant microbial metabolic functional guilds were identified including guilds related to DMSP degradation, dissimilatory nitrate reduction to ammonia, and motile copiotrophy. This method presents a way to generate hypotheses about functions co-occurring within individual microbes without relying on cultured representatives. Applying the concept of metabolic functional guilds to environmental samples will provide new insight into the role that heterotrophic microbial communities play in setting rates of carbon cycling.
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Affiliation(s)
- Ryan Reynolds
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Sangwon Hyun
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Benjamin Tully
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
- Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Jacob Bien
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Naomi M. Levine
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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Qiu S, Zhang X, Xia W, Li Z, Wang L, Chen Z, Ge S. Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162702. [PMID: 36898547 DOI: 10.1016/j.scitotenv.2023.162702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 05/06/2023]
Abstract
The control of pH is effective for inhibiting methanogenesis in the chain elongation fermentation (CEF) system. However, obscure conclusions exist especially with regard to the underlying mechanism. This study comprehensively explored the responses of methanogenesis in granular sludge at various pH levels, ranging from 4.0 to 10.0, from multiple aspects including methane production, methanogenesis pathway, microbial community structure, energy metabolism and electron transport. Results demonstrated that compared with that at pH 7.0, pH at 4.0, 5.5, 8.5 and 10.0 triggered a 100%, 71.7%, 23.8% and 92.1% suppression on methanogenesis by the end of 3 cycles lasting 21 days. This might be explained by the remarkably inhibited metabolic pathways and intracellular regulations. To be more specific, extreme pH conditions decreased the abundance of the acetoclastic methanogens. However, obligate hydrogenotrophic and facultative acetolactic/hydrogenotrophic methanogens were significantly enriched by 16.9%-19.5 fold. pH stress reduced the gene abundance and/or activity of most enzymes involved in methanogenesis such as acetate kinase (by 81.1%-93.1%), formylmethanofuran dehydrogenase (by 10.9%-54.0%) and tetrahydromethanopterin S-methyltransferase (by 9.3%-41.5%). Additionally, pH stress suppressed electron transport via improper electron carriers and decreased electron amount as evidenced by 46.3%-70.4% reduced coenzyme F420 content and diminished abundance of CO dehydrogenase (by 15.5%-70.5%) and NADH:ubiquinone reductase (by 20.2%-94.5%). pH stress also regulated energy metabolism with inhibited ATP synthesis (e.g., ATP citrate synthase level reduced by 20.1%-95.3%). Interestingly, the protein and carbohydrate content secreted in EPS failed to show consistent responses to acidic and alkaline conditions. Specifically, when compared with pH 7.0, the acidic condition remarkably reduced the levels of total EPS and EPS protein while both levels were enhanced in the alkaline condition. However, the EPS carbohydrate content at pH 4.0 and 10.0 both decreased. This study is expected to promote the understanding of the pH control-induced methanogenesis inhibition in the CEF system.
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Affiliation(s)
- Shuang Qiu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Xingchen Zhang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Wenhao Xia
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zimu Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Lingfeng Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zhipeng Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China.
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Li B, Wang H, Lai A, Xue J, Wu Q, Yu C, Xie K, Mao Z, Li H, Xing P, Wu QL. Hydrogenotrophic pathway dominates methanogenesis along the river-estuary continuum of the Yangtze River. WATER RESEARCH 2023; 240:120096. [PMID: 37229838 DOI: 10.1016/j.watres.2023.120096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
Rivers are considered as an important source of methane (CH4) to the atmosphere, but our understanding for the methanogenic pathway in rivers and its linkage with CH4 emission is very limited. Here, we investigated the diffusive flux of CH4 and its stable carbon isotope signature (δ13C-CH4) along the river-estuary continuum of the Yangtze River. The diffusive CH4 flux was estimated to 27.9 ± 11.4 μmol/m2/d and 36.5 ± 24.4 μmol/m2/d in wet season and dry season, respectively. The δ13C-CH4 values were generally lower than -60‰, with the fractionation factor (αc) higher than 1.055 and the isotope separation factor (εc) ranged from 55 to 100. In situ microbial composition showed that hydrogenotrophic methanogens accounts for over 70% of the total reads. Moreover, the incubation test showed that the headspace CH4 concentration by adding CO2/H2 to the sediment was orders of magnitude higher than that by adding trimethylamine and sodium acetate. These results jointly verified the river-estuary continuum is a minor CH4 source and dominated by hydrogenotrophic pathway. Based on the methanogenic pathway here and previous reported data in the same region, the historical variation of diffusive CH4 flux was calculated and results showed that CH4 emission has reduced 82.5% since the construction of Three Gorges Dam (TGD). Our study verified the dominant methanogenic pathway in river ecosystems and clarified the effect and mechanism of dam construction on riverine CH4 emission.
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Affiliation(s)
- Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hongwei Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Anxing Lai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jingya Xue
- School of Geographical Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qiong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Yu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ke Xie
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China.
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32
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Schultz CR, Johnson M, Wallace JG. Effects of Inbreeding on Microbial Community Diversity of Zea mays. Microorganisms 2023; 11:microorganisms11040879. [PMID: 37110300 PMCID: PMC10145435 DOI: 10.3390/microorganisms11040879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.
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33
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Liu H, Li FY, Liu J, Shi C, Tang K, Yang Q, Liu Y, Fu Q, Gao X, Wang N, Guo W. The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland. Front Microbiol 2023; 14:1113157. [PMID: 37007478 PMCID: PMC10060659 DOI: 10.3389/fmicb.2023.1113157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no “decoupling” in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the “monopoly” of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.
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Affiliation(s)
- Huaiqiang Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Hohhot, China
- *Correspondence: Frank Yonghong Li,
| | - Jiayue Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Chunjun Shi
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Kuanyan Tang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qianhui Yang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yu Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qiang Fu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiaotian Gao
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ning Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wei Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Saha A, Gupta A, Sar P. Metagenome based analysis of groundwater from arsenic contaminated sites of West Bengal revealed community diversity and their metabolic potential. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2023; 58:91-106. [PMID: 36852697 DOI: 10.1080/10934529.2023.2173919] [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: 03/17/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The study of microbial community in groundwater systems is considered to be essential to improve our understanding of arsenic (As) biogeochemical cycling in aquifers, mainly as it relates to the fate and transport of As. The present study was conducted to determine the microbial community composition and its functional potential using As-contaminated groundwater from part of the Bengal Delta Plain (BDP) in West Bengal, India. Geochemical analyses indicated low to moderate dissolved oxygen (0.42-3.02 mg/L), varying As (2.5-311 µg/L) and Fe (0.19-1.2 mg/L) content, while low concentrations of total organic carbon (TOC), total inorganic carbon (TIC), nitrate, and sulfate were detected. Proteobacteria was the most abundant phylum, while the indiscriminate presence of an array of archaeal phyla, Euryarchaeota, Crenarchaeota, Nanoarchaeota, etc., was noteworthy. The core community members were affiliated to Sideroxydans, Acidovorax, Pseudoxanthomonas, Brevundimonas, etc. However, diversity assessed over multiple seasons indicated a shift from Sideroxydans to Pseudomonas or Brevundimonas dominant community, suggestive of microbial response to seasonally fluctuating geochemical stimuli. Taxonomy-based functional potential showed prospects for As biotransformation, methanogenesis, sulfate respiration, denitrification, etc. Thus, this study strengthened existing reports from this region by capturing the less abundant or difficult-to-culture taxa collectively forming a major fraction of the microbial community.
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Affiliation(s)
- Anumeha Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, Xiao X, Li J, Jia K, Greening C, Shao Z, Hubert CRJ. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun 2023; 14:1127. [PMID: 36854684 PMCID: PMC9974965 DOI: 10.1038/s41467-023-36877-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Muhua Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Laura Woods
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Wenxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510075, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Sanchez A, Bajic D, Diaz-Colunga J, Skwara A, Vila JCC, Kuehn S. The community-function landscape of microbial consortia. Cell Syst 2023; 14:122-134. [PMID: 36796331 DOI: 10.1016/j.cels.2022.12.011] [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: 06/28/2022] [Revised: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Quantitatively linking the composition and function of microbial communities is a major aspiration of microbial ecology. Microbial community functions emerge from a complex web of molecular interactions between cells, which give rise to population-level interactions among strains and species. Incorporating this complexity into predictive models is highly challenging. Inspired by a similar problem in genetics of predicting quantitative phenotypes from genotypes, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.
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Affiliation(s)
- Alvaro Sanchez
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA; Department of Microbial Biotechnology, CNB-CSIC, Campus de Cantoblanco, Madrid, Spain.
| | - Djordje Bajic
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Abigail Skwara
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, The Unviersity of Chicago, Chicago, IL, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
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Li X, Meng Z, Chen K, Hu F, Liu L, Zhu T, Yang D. Comparing diversity patterns and processes of microbial community assembly in water column and sediment in Lake Wuchang, China. PeerJ 2023; 11:e14592. [PMID: 36627922 PMCID: PMC9826614 DOI: 10.7717/peerj.14592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
The study compare the diversity patterns and processes of microbial community assembly in the water and sediment of Lake Wuchang (China) using high-throughput sequencing of 16S rRNA gene amplicons. A higher microbial α-diversity in the sediment was revealed (P < 0.01), and the most common bacterial phyla in water column were Proteobacteria, Cyanobacteria and Actinobacteria, while Proteobacteria, Acidobacteria, Chloroflexi and Nitrospirae were dominant in sediment. Functions related to phototrophy and nitrogen metabolism primarily occurred in the water column and sediment, respectively. The microbial communities in water column from different seasons were divided into three groups, while no such dispersion in sediment based on PCoA and ANOSIM. According to Pearson correlation analysis, water temperature, dissolved oxygen, water depth, total nitrogen, ammonium, and nitrite were key factors in determining microbial community structure in water column, while TN in sediment, conductivity, and organic matter were key factors in sediment. However, the stochastic processes (|βNTI| < 2) dominated community assembly in both the water column and sediment of Lake Wuchang. These data will provide a foundation for microbial development and utilization in lake water column and sediment under the circumstances of increasing tendency of lake ecological fishery in China.
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Gil JC, Hird SM. Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes. Microbiol Spectr 2022; 10:e0238422. [PMID: 36318011 PMCID: PMC9769641 DOI: 10.1128/spectrum.02384-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022] Open
Abstract
16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using "simulated metagenomes" (shotgun metagenomes simulated from 16S rRNA amplicons using a database of full genomes closely related to the amplicons) in nonmodel systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a nonmodel organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing. We found significant differences between the metagenomes, metatranscriptomes, and simulated metagenomes when comparing enzymes, KEGG orthologies (KO), and metabolic pathways. The simulated metagenomes accurately identified the majority (>70%) of the total enzymes, KOs, and pathways. The simulated metagenomes accurately identified the majority of the short-chain fatty acid metabolic pathways crucial to folivores. When narrowed in scope to specific genes of interest, the simulated metagenomes overestimated the number of antimicrobial resistance genes and underestimated the number of genes related to the breakdown of plant matter. Our results suggest that simulated metagenomes should not be used in lieu of empirical sequencing when studying the functional potential of a nonmodel organism's microbiome. Regarding the function of the Canada goose microbiome, we found unexpected amounts of fermentation pathways, and we found that a few taxa are responsible for large portions of the functional potential of the microbiome. IMPORTANCE The taxonomic composition of a microbiome is predominately identified using amplicon sequencing of 16S rRNA genes, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive. Therefore, computational methods have been developed to generate simulated metagenomes derived from 16S rRNA sequences and databases of full-length genomes. Simulated metagenomes can be an effective alternative to empirical sequencing, but accuracy depends on the genomic database used and whether the database contains organisms closely related to the 16S sequences. These tools are effective in well-studied systems, but the accuracy of these predictions in a nonmodel system is less known. Using a nonmodel bird species, we characterized the function of the microbiome and compared the accuracy of 16S-derived simulated metagenomes to sequenced metagenomes. We found that the simulated metagenomes reflect most but not all functions of empirical metagenome sequencing.
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Affiliation(s)
- Joshua C. Gil
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sarah M. Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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Jurburg SD, Buscot F, Chatzinotas A, Chaudhari NM, Clark AT, Garbowski M, Grenié M, Hom EFY, Karakoç C, Marr S, Neumann S, Tarkka M, van Dam NM, Weinhold A, Heintz-Buschart A. The community ecology perspective of omics data. MICROBIOME 2022; 10:225. [PMID: 36510248 PMCID: PMC9746134 DOI: 10.1186/s40168-022-01423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Narendrakumar M Chaudhari
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Adam T Clark
- Institute of Biology, University of Graz, Graz, Austria
| | - Magda Garbowski
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Botany, University of Wyoming, Wyoming, USA
| | - Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Erik F Y Hom
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, Oxford, Mississippi, USA
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology, Indiana University, Indiana, USA
| | - Susanne Marr
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle Wittenberg, Halle, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Mika Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome. MICROBIOME 2022; 10:217. [PMID: 36482420 PMCID: PMC9733318 DOI: 10.1186/s40168-022-01383-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND From a theoretical ecology point of view, microbiomes are far more complex than expected. Besides competition and competitive exclusion, cooperative microbe-microbe interactions have to be carefully considered. Metabolic dependencies among microbes likely explain co-existence in microbiota. METHODOLOGY In this in silico study, we explored genome-scale metabolic models (GEMs) of 193 bacteria isolated from Arabidopsis thaliana roots. We analyzed their predicted producible metabolites under simulated nutritional constraints including "root exudate-mimicking growth media" and assessed the potential of putative metabolic exchanges of by- and end-products to avoid those constraints. RESULTS We found that the genome-encoded metabolic potential is quantitatively and qualitatively clustered by phylogeny, highlighting metabolic differentiation between taxonomic groups. Random, synthetic combinations of increasing numbers of strains (SynComs) indicated that the number of producible compounds by GEMs increased with average phylogenetic distance, but that most SynComs were centered around an optimal phylogenetic distance. Moreover, relatively small SynComs could reflect the capacity of the whole community due to metabolic redundancy. Inspection of 30 specific end-product metabolites (i.e., target metabolites: amino acids, vitamins, phytohormones) indicated that the majority of the strains had the genetic potential to produce almost all the targeted compounds. Their production was predicted (1) to depend on external nutritional constraints and (2) to be facilitated by nutritional constraints mimicking root exudates, suggesting nutrient availability and root exudates play a key role in determining the number of producible metabolites. An answer set programming solver enabled the identification of numerous combinations of strains predicted to depend on each other to produce these targeted compounds under severe nutritional constraints thus indicating a putative sub-community level of functional redundancy. CONCLUSIONS This study predicts metabolic restrictions caused by available nutrients in the environment. By extension, it highlights the importance of the environment for niche potential, realization, partitioning, and overlap. Our results also suggest that metabolic dependencies and cooperation among root microbiota members compensate for environmental constraints and help maintain co-existence in complex microbial communities. Video Abstract.
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Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35000, Rennes, France
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | - Nathan Vannier
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | | | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany.
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Qi Q, Zhao J, Tian R, Zeng Y, Xie C, Gao Q, Dai T, Wang H, He JS, Konstantinidis KT, Yang Y, Zhou J, Guo X. Microbially enhanced methane uptake under warming enlarges ecosystem carbon sink in a Tibetan alpine grassland. GLOBAL CHANGE BIOLOGY 2022; 28:6906-6920. [PMID: 36191158 DOI: 10.1111/gcb.16444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/10/2022] [Accepted: 09/02/2022] [Indexed: 05/25/2023]
Abstract
The alpine grasslands of the Tibetan Plateau store 23.2 Pg soil organic carbon, which becomes susceptible to microbial degradation with climate warming. However, accurate prediction of how the soil carbon stock changes under future climate warming is hampered by our limited understanding of belowground complex microbial communities. Here, we show that 4 years of warming strongly stimulated methane (CH4 ) uptake by 93.8% and aerobic respiration (CO2 ) by 11.3% in the soils of alpine grassland ecosystem. Due to no significant effects of warming on net ecosystem CO2 exchange (NEE), the warming-stimulated CH4 uptake enlarged the carbon sink capacity of whole ecosystem. Furthermore, precipitation alternation did not alter such warming effects, despite the significant effects of precipitation on NEE and soil CH4 fluxes were observed. Metagenomic sequencing revealed that warming led to significant shifts in the overall microbial community structure and the abundances of functional genes, which contrasted to no detectable changes after 2 years of warming. Carbohydrate utilization genes were significantly increased by warming, corresponding with significant increases in soil aerobic respiration. Increased methanotrophic genes and decreased methanogenic genes were observed under warming, which significantly (R2 = .59, p < .001) correlated with warming-enhanced CH4 uptakes. Furthermore, 212 metagenome-assembled genomes were recovered, including many populations involved in the degradation of various organic matter and a highly abundant methylotrophic population of the Methyloceanibacter genus. Collectively, our results provide compelling evidence that specific microbial functional traits for CH4 and CO2 cycling processes respond to climate warming with differential effects on soil greenhouse gas emissions. Alpine grasslands may play huge roles in mitigating climate warming through such microbially enhanced CH4 uptake.
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Affiliation(s)
- Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jianshu Zhao
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Changyi Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tianjiao Dai
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Hao Wang
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, China
| | - Jin-Sheng He
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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Naya-Català F, Piazzon MC, Torrecillas S, Toxqui-Rodríguez S, Calduch-Giner JÀ, Fontanillas R, Sitjà-Bobadilla A, Montero D, Pérez-Sánchez J. Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream ( Sparus aurata) Production Cycle. BIOLOGY 2022; 11:1744. [PMID: 36552254 PMCID: PMC9774573 DOI: 10.3390/biology11121744] [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: 10/10/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Fish genetically selected for growth (GS) and reference (REF) fish were fed with CTRL (15% FM, 5-7% FO) or FUTURE (7.5% FM, 10% poultry meal, 2.2% poultry oil + 2.5% DHA-algae oil) diets during a 12-months production cycle. Samples from initial (t0; November 2019), intermediate (t1; July 2020) and final (t2; November 2020) sampling points were used for Illumina 16S rRNA gene amplicon sequencing of the adherent microbiota of anterior intestine (AI). Samples from the same individuals (t1) were also used for the gene expression profiling of AI by RNA-seq, and subsequent correlation analyses with microbiota abundances. Discriminant analyses indicated the gut bacterial succession along the production cycle with the proliferation of some valuable taxa for facing seasonality and different developmental stages. An effect of genetic background was evidenced along time, decreasing through the progression of the trial, namely the gut microbiota of GS fish was less influenced by changes in diet composition. At the same time, these fish showed wider transcriptomic landmarks in the AI to cope with these changes. Our results highlighted an enhanced intestinal sphingolipid and phospholipid metabolism, epithelial turnover and intestinal motility in GS fish, which would favour their improved performance despite the lack of association with changes in gut microbiota composition. Furthermore, in GS fish, correlation analyses supported the involvement of different taxa with the down-regulated expression of pro-inflammatory markers and the boosting of markers of extracellular remodelling and response to bacterium. Altogether, these findings support the combined action of the gut microbiome and host transcriptionally mediated effects to preserve and improve gut health and function in a scenario of different growth performance and potentiality.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Socorro Toxqui-Rodríguez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Josep À Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | | | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Canary Islands, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain
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Liu Q, Yang J, Wang B, Liu W, Hua Z, Jiang H. Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments. Front Microbiol 2022; 13:1019010. [PMID: 36519167 PMCID: PMC9742235 DOI: 10.3389/fmicb.2022.1019010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Zhengshuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
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Tang Q, Huang J, Zhang S, Qin H, Dong Y, Wang C, Li D, Zhou R. Characterizing the correlation between species/strain-specific starter with community assembly and metabolic regulation in Xiaoqu Pei. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100170. [DOI: 10.1016/j.crmicr.2022.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Wang T, Weiss A, Aqeel A, Wu F, Lopatkin AJ, David LA, You L. Horizontal gene transfer enables programmable gene stability in synthetic microbiota. Nat Chem Biol 2022; 18:1245-1252. [PMID: 36050493 PMCID: PMC10018779 DOI: 10.1038/s41589-022-01114-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/15/2022] [Indexed: 11/09/2022]
Abstract
The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have been commonly hypothesized to explain such decoupling. Here, we proposed that dynamic mechanisms, mediated by horizontal gene transfer (HGT), also enable the independence of functions from the compositions of microbial communities. We combined theoretical analysis with numerical simulations to illustrate that HGT rates can determine the stability of gene abundance in microbial communities. We further validated these predictions using engineered microbial consortia of different complexities transferring one or more than a dozen clinically isolated plasmids, as well as through the reanalysis of data from the literature. Our results demonstrate a generalizable strategy to program the gene stability of microbial communities.
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Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ammara Aqeel
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Allison J Lopatkin
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA
| | - Lawrence A David
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
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Divergent Changes in Bacterial Functionality as Affected by Root-Zone Ecological Restoration in an Aged Peach Orchard. Microorganisms 2022; 10:microorganisms10112127. [DOI: 10.3390/microorganisms10112127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
Soil restoration is a crucial approach to improving plant productivity in orchards with soil degradation, yield reduction, and fruit quality declination in China. A self-invented root-zone ecological restoration practice (RERP) with soil conditioner, or organic fertilizer, was employed in a degraded peach orchard in Beijing in 2020 to investigate the consequent impacts on soil bacterial composition and functionality at soil depths of 0–20 cm and 20–40 cm. Bacterial diversity was sensitive to RERP, especially in subsurface soil. RERP with soil conditioner significantly increased bacterial diversity, and affected abundances of certain genera, such as a significantly increased amount of Bacillus in surface soil and Blastococcus, Microvirga, Nocardioides, and Sphingomonas in subsurface soil. It also significantly affected abundances of bacterial functions related to metabolism in subsurface soil, particularly those with low abundance such as decreased transcription abundance and increased amino acid metabolism abundance. Soil bacterial functions were observably affected by bacterial diversity and composition, particularly in the deep soil layer. RERP affected bacterial functionality via responses of soil bacteria and bacteria-mediated alterations to the changed soil property. Correlation analysis between soil properties, bacterial taxonomy, and bacterial functions revealed that RERP affected bacterial functionality by altering the soil microenvironment with ample nutrients and water supply in root zone. Consequently, shifted bacterial functionality could have a potential in orchard ecosystem services in view of fruit yield and quality. Taken together, RERP had notably positive impacts on soil bacterial diversity and functions, and a prospect of increased plant productivity in the degrade orchard ecosystem.
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47
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Mawarda PC, Mallon CA, Le Roux X, van Elsas JD, Salles JF. Interactions between Bacterial Inoculants and Native Soil Bacterial Community: the Case of Spore-forming Bacillus spp. FEMS Microbiol Ecol 2022; 98:6776013. [PMID: 36302145 PMCID: PMC9681130 DOI: 10.1093/femsec/fiac127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/21/2022] [Accepted: 10/25/2022] [Indexed: 01/21/2023] Open
Abstract
Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities' niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities' niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.
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Affiliation(s)
| | - Cyrus A Mallon
- Microbial Community Ecology Cluster, expertise group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Xavier Le Roux
- INRAE, CNRS, Université Lyon 1, Université de Lyon, VetAgroSup, Laboratoire d'Ecologie Microbienne LEM, UMR 1418 INRAE, UMR 5557 CNRS, 69622 Villeurbanne Cedex, France
| | - Jan Dirk van Elsas
- Microbial Community Ecology Cluster, expertise group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Joana Falcão Salles
- Microbial Community Ecology Cluster, expertise group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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48
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Aguilar-Cruz Y, Milke F, Leinberger J, Poehlein A, Zotz G, Brinkhoff T. Diversity and putative metabolic function of prokaryotic communities in tank bromeliads along an elevation gradient in tropical Mexico. Front Microbiol 2022; 13:945488. [PMID: 36312956 PMCID: PMC9608151 DOI: 10.3389/fmicb.2022.945488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/13/2022] [Indexed: 12/02/2022] Open
Abstract
Tank bromeliads are unique canopy microhabitats that offer freshwater and organic nutrient-rich substrates in the Neotropics. In them it is possible to thoroughly characterize environmental factors and species composition of terrestrial and aquatic biota. Therefore, these plants have been used as natural models to study how communities are distributed and assembled. Here we used amplicon sequencing of the 16S rRNA gene and their functional annotations to study the diversity and metabolic potential of prokaryotic communities in tank bromeliads in five different forests along an elevation gradient in tropical Mexico. Furthermore, we analyzed the effects of vegetation type and environmental factors inside the tanks on prokaryotic composition. We found a high prokaryotic diversity in tank bromeliads along the elevation gradient. Prokaryotes commonly observed in acidic environments rich in organic carbon, and the potential pathogen Pasteurella multocida, were present in all samples, but few amplicon sequence variants were shared between forests. The prokaryotic composition was affected by forest type, and comparisons against null models suggest that it was shaped by non-neutral processes. Furthermore, prokaryotic community changes significantly covaried with tank water temperature, pH, and inorganic carbon. We found a high diversity of putative metabolic groups dominated by chemoheterotrophs and fermenters, but taxonomic groups involved in nitrogen and sulfur cycling were also present in all samples. These results suggest that tank bromeliads promote taxonomic and metabolic diversity of the prokaryotic community at a local and regional scale and play an important role in the biogeochemistry of forest canopies in the Neotropics.
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Affiliation(s)
- Yonatan Aguilar-Cruz
- Functional Ecology of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- *Correspondence: Yonatan Aguilar-Cruz, ; Felix Milke,
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- *Correspondence: Yonatan Aguilar-Cruz, ; Felix Milke,
| | - Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Gerhard Zotz
- Functional Ecology of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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49
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Frey B, Rast BM, Qi W, Stierli B, Brunner I. Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance. Front Microbiol 2022; 13:1034138. [PMID: 36274742 PMCID: PMC9581213 DOI: 10.3389/fmicb.2022.1034138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg–1 dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg–1 dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg–1 dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
| | - Basil M. Rast
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- FGCZ Functional Genomics Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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50
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Qi H, Huang D, Wang F, Ye M, Jiang X. Spatial dynamics of prokaryotic microbial communities in sediments of the Yellow Sea: Assembly process, co-occurrence relationships, and environmental implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115645. [PMID: 35797911 DOI: 10.1016/j.jenvman.2022.115645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Marine sediment microorganisms play an important role in the biogeochemical cycle of elements and the transformation of exogenous pollutants; therefore, it is important to study the microbial assembly process and inter taxa associations. In this study, we investigated the profiles and assembly processes of microbial communities of sediments collected from 19 points in the Yellow Sea. As revealed by 16S rRNA sequencing, Proteobacteria (43.11%-65.54%) was the dominant phylum in marine sediment. Further, the physicochemical properties of sediments were significantly influenced by depth (P < 0.05), and the effects of homogeneous selection became greater with increasing depth. The microbial species located in marine sediment at 35°N had a significantly higher co-occurrence relationship (82.76%) than those at 34°N (57.99%) and 36°N (54.07%). Additionally, the microbial community structure of the sediments changed significantly at the genus level with strong fluctuations in the physicochemical properties. By contrast, the carbon, nitrogen, and sulfur associated functional gene diversity and abundance showed no clear variation among different locations, indicating the probable functional redundancy and a potential functional gene pool of the microbes in marine sediments. This study could provide new insights into the composition of microorganisms in sediments in the Yellow Sea, the driving force of microbial diversity, the assembly process, the modes of species' co-occurrence, and their ecological functions.
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Affiliation(s)
- Huiyuan Qi
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Fenghe Wang
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
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