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He L, Sun X, Li S, Zhou W, Yu J, Zhao G, Chen Z, Bai X, Zhang J. Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169905. [PMID: 38190904 DOI: 10.1016/j.scitotenv.2024.169905] [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: 07/24/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain. Our results showed significant altitudinal distribution patterns concerning bacterial diversity and structure in the surface soil. The bacterial diversity exhibited a consistent decrease, while specific taxa demonstrated unique patterns along the altitudinal gradient. However, no altitudinal dependence was observed for bacterial diversity and community structure in the subsurface soil. Additionally, a shift in bacterial ecological groups is evident with changing soil depth. Copiotrophic taxa thrive in surface soils characterized by higher carbon and nutrient content, while oligotrophic taxa dominate in subsurface soils with more limited resources. Bacterial community characteristics exhibited strong correlations with soil organic carbon in both soil layers, followed by pH in the surface soil and soil moisture in the subsurface soil. With increasing depth, there is an observable increase in taxa-taxa interaction complexity and network structure within bacterial communities. The surface soil exhibits greater sensitivity to environmental perturbations, leading to increased modularity and an abundance of positive relationships in its community networks compared to the subsurface soil. Furthermore, the bacterial community at different depths was influenced by combining deterministic and stochastic processes, with stochasticity (homogenizing dispersal and undominated) decreasing and determinism (heterogeneous selection) increasing with soil depth.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jiantao Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Guanyu Zhao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jinshuo Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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Ji M, Xu J, Gao L, Li L, Liu H, Hao B. Effect of long-term in-row branch covering on soil microorganisms in pear orchards. Open Life Sci 2024; 19:20220807. [PMID: 38299010 PMCID: PMC10828664 DOI: 10.1515/biol-2022-0807] [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: 07/28/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 02/02/2024] Open
Abstract
Branches covering (BC) is a way to reuse the pruned branches and save the cost of ground cloth. This study investigated the effects of BC and ground-cloth covering on the soil microcosm environment by measuring the chemical properties and microbial communities at different soil depths for 6 years. The results revealed that BC significantly improved soil chemical properties, increased the abundance of bacterial microbial communities and the diversity and homogeneity of bacteria and fungi, while decreased the abundance of fungal microbial communities. There was a threshold value for the regulation of microbial communities by BC, which decreased the high-abundance communities (Proteobacteria, Ascomycota, etc.) and increased the low-abundance communities (Acidobacteriota, Basidiomycota, etc.). Fungi were more sensitive to BC than bacteria. The stability and homogeneity of microorganisms were stronger in the 15-25 cm soil layer. The bacterial phyla were dominated by Proteobacteria, with the top 10 phyla accounting for more than 80% of the relative abundance; the genera were dominated by MND1, with the top 10 genera accounting for about 10%. The fungal phyla were dominated by Ascomycota, with the top 10 phyla accounting for 50-90%; the genera were dominated by unidentified Pyronemataceae sp., with the top 10 genera accounting for 30-60%. The phyla that differed significantly between treatments were mainly Proteobacteria, Ascomycota, Acidobacteriota, and Basidiomycota. In addition, metabolism was the predominant function in bacteria, while Saprotroph was the predominant function in fungi. Bacteroidota correlated strongly with soil chemical properties and bacterial functions, while Chytridiomycota correlated strongly with soil chemical properties and Pathogen-Saprotroph-Symbiotroph. In conclusion, BC can improve soil nutrient content and optimize microbial community structure and function. Through initially assessing the effects of BC on soil nutrients and microorganisms in pear orchard rows, this study provides a reference for excavating key microorganisms and updating the soil row management model.
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Affiliation(s)
- Minghui Ji
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Jintao Xu
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Lijuan Gao
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Longfei Li
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Huan Liu
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Baofeng Hao
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
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3
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Bandla A, Akhtar H, Lupascu M, Sukri RS, Swarup S. Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly. NPJ Biofilms Microbiomes 2024; 10:8. [PMID: 38253600 PMCID: PMC10803758 DOI: 10.1038/s41522-024-00478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Fires in tropical peatlands extend to depth, transforming them from carbon sinks into methane sources and severely limit forest recovery. Peat microbiomes influence carbon transformations and forest recovery, yet our understanding of microbiome shifts post-fire is currently limited. Our previous study highlighted altered relationships between the peat surface, water table, aboveground vegetation, and methane flux after fire in a tropical peatland. Here, we link these changes to post-fire shifts in peat microbiome composition and assembly processes across depth. We report kingdom-specific and depth-dependent shifts in alpha diversity post-fire, with large differences at deeper depths. Conversely, we found shifts in microbiome composition across all depths. Compositional shifts extended to functional groups involved in methane turnover, with methanogens enriched and methanotrophs depleted at mid and deeper depths. Finally, we show that community shifts at deeper depths result from homogeneous selection associated with post-fire changes in hydrology and aboveground vegetation. Collectively, our findings provide a biological basis for previously reported methane fluxes after fire and offer new insights into depth-dependent shifts in microbiome assembly processes, which ultimately underlie ecosystem function predictability and ecosystem recovery.
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Affiliation(s)
- Aditya Bandla
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Hasan Akhtar
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
- School of Liberal Arts and Sciences, RV University, Bengaluru, Karnataka, India
| | - Massimo Lupascu
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Rahayu Sukmaria Sukri
- Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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4
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Radujković D, Vicca S, van Rooyen M, Wilfahrt P, Brown L, Jentsch A, Reinhart KO, Brown C, De Gruyter J, Jurasinski G, Askarizadeh D, Bartha S, Beck R, Blenkinsopp T, Cahill J, Campetella G, Canullo R, Chelli S, Enrico L, Fraser L, Hao X, Henry HAL, Hohn M, Jouri MH, Koch M, Lawrence Lodge R, Li FY, Lord JM, Milligan P, Minggagud H, Palmer T, Schröder B, Szabó G, Zhang T, Zimmermann Z, Verbruggen E. Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency. Mol Ecol 2023; 32:6924-6938. [PMID: 37873915 DOI: 10.1111/mec.17178] [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: 07/01/2022] [Revised: 08/26/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023]
Abstract
Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine (i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and (ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs. high). Our results revealed that bacteria were associated with particular soil properties (such as base saturation) and both bacteria and fungi were associated with plant community composition across sites and within the majority of sites. Moreover, a discernible microbial community signal emerged, clearly distinguishing high and low-productivity soils across different grasslands independent of their location in the world. Hence, regional productivity differences may be typified by characteristic soil microbial communities across the grassland biome. These results could encourage future research aiming to predict the general effects of global changes on soil microbial community composition in grasslands and to discriminate fertile from infertile systems using generally applicable microbial indicators.
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Affiliation(s)
- Dajana Radujković
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Sara Vicca
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Margaretha van Rooyen
- Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
| | - Peter Wilfahrt
- Department of Disturbance Ecology, University of Bayreuth, Bayreuth, Germany
- Department of Ecology, Evolution, and Behavior, University Minnesota, Saint Paul, Minnesota, USA
| | - Leslie Brown
- Applied Behavioural Ecology & Ecosystem Research Unit, Dept. Environmental Sciences, University of South Africa, Florida, South Africa
| | - Anke Jentsch
- Department of Disturbance Ecology, University of Bayreuth, Bayreuth, Germany
| | - Kurt O Reinhart
- United States Department of Agriculture-Agricultural Research Service (or USDA-ARS), Fort Keogh Livestock& Range Research Laboratory, Miles City, Montana, USA
| | - Charlotte Brown
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Desert Laboratory on Tumamoc Hill, University of Arizona, Tucson, Arizona, USA
| | - Johan De Gruyter
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Gerald Jurasinski
- Landscape Ecology, University of Rostock, Rostock, Germany
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Diana Askarizadeh
- Department of Rehabilitation of Arid and Mountainous Regions, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Sandor Bartha
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Ryan Beck
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Theodore Blenkinsopp
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - James Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Giandiego Campetella
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Roberto Canullo
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Stefano Chelli
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Lucas Enrico
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC) and FCEFyN, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Lauchlan Fraser
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Xiying Hao
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Hugh A L Henry
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Maria Hohn
- Department of Botany, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | | | - Marian Koch
- Soil Physics, University of Rostock, Rostock, Germany
| | | | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Janice M Lord
- Department of Botany - Te Tari Huaota, University of Otago, Dunedin, New Zealand
| | - Patrick Milligan
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Hugjiltu Minggagud
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Todd Palmer
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | - Gábor Szabó
- Environmental Sciences Doctoral School, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Tongrui Zhang
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zita Zimmermann
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Erik Verbruggen
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
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5
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Miao Z, Bai Y, Wang X, Han C, Wang B, Li Z, Sun J, Zheng F, Zhang Y, Sun B. Unravelling Metabolic Heterogeneity of Chinese Baijiu Fermentation in Age-Gradient Vessels. Foods 2023; 12:3425. [PMID: 37761135 PMCID: PMC10530105 DOI: 10.3390/foods12183425] [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: 08/14/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Fermentation vessels affect the characteristics of food fermentation; however, we lack an approach to identify the biomarkers indicating fermentation. In this study, we applied metabolomics and high-throughput sequencing analysis to reveal the dynamic of metabolites and microbial communities in age-gradient fermentation vessels for baijiu production. Furthermore, we identified 64 metabolites during fermentation, and 19 metabolites significantly varied among the three vessels (p < 0.05). Moreover, the formation of these 19 metabolites were positively correlated with the core microbiota (including Aspergillus, Saccharomyces, Lactobacillus, and Bacillus). In addition, ethyl lactate or ethyl acetate were identified as the biomarkers for indicating the metabolism among age-gradient fermentation vessels by BP-ANN (R2 > 0.40). Therefore, this study combined the biological analysis and predictive model to identify the biomarkers indicating metabolism in different fermentation vessels, and it also provides a potential approach to assess the profiling of food fermentations.
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Affiliation(s)
- Zijian Miao
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Yu Bai
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Xinlei Wang
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Chao Han
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Bowen Wang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Zexia Li
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Jinyuan Sun
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Fuping Zheng
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Yuhang Zhang
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Baoguo Sun
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
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Liu X, Nie Y, Wu XL. Predicting microbial community compositions in wastewater treatment plants using artificial neural networks. MICROBIOME 2023; 11:93. [PMID: 37106397 PMCID: PMC10142226 DOI: 10.1186/s40168-023-01519-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Activated sludge (AS) of wastewater treatment plants (WWTPs) is one of the world's largest artificial microbial ecosystems and the microbial community of the AS system is closely related to WWTPs' performance. However, how to predict its community structure is still unclear. RESULTS Here, we used artificial neural networks (ANN) to predict the microbial compositions of AS systems collected from WWTPs located worldwide. The predictive accuracy R21:1 of the Shannon-Wiener index reached 60.42%, and the average R21:1 of amplicon sequence variants (ASVs) appearing in at least 10% of samples and core taxa were 35.09% and 42.99%, respectively. We also found that the predictability of ASVs was significantly positively correlated with their relative abundance and occurrence frequency, but significantly negatively correlated with potential migration rate. The typical functional groups such as nitrifiers, denitrifiers, polyphosphate-accumulating organisms (PAOs), glycogen-accumulating organisms (GAOs), and filamentous organisms in AS systems could also be well recovered using ANN models, with R21:1 ranging from 32.62% to 56.81%. Furthermore, we found that whether industry wastewater source contained in inflow (IndConInf) had good predictive abilities, although its correlation with ASVs in the Mantel test analysis was weak, which suggested important factors that cannot be identified using traditional methods may be highlighted by the ANN model. CONCLUSIONS We demonstrated that the microbial compositions and major functional groups of AS systems are predictable using our approach, and IndConInf has a significant impact on the prediction. Our results provide a better understanding of the factors affecting AS communities through the prediction of the microbial community of AS systems, which could lead to insights for improved operating parameters and control of community structure. Video Abstract.
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Affiliation(s)
- Xiaonan Liu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, 100871, China.
- Institute of Ocean Research, Peking University, Beijing, 100871, China.
- Institute of Ecology, Peking University, Beijing, 100871, China.
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7
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Busato S, Gordon M, Chaudhari M, Jensen I, Akyol T, Andersen S, Williams C. Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102326. [PMID: 36538837 PMCID: PMC9925409 DOI: 10.1016/j.pbi.2022.102326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
The plant-associated microbiome is a key component of plant systems, contributing to their health, growth, and productivity. The application of machine learning (ML) in this field promises to help untangle the relationships involved. However, measurements of microbial communities by high-throughput sequencing pose challenges for ML. Noise from low sample sizes, soil heterogeneity, and technical factors can impact the performance of ML. Additionally, the compositional and sparse nature of these datasets can impact the predictive accuracy of ML. We review recent literature from plant studies to illustrate that these properties often go unmentioned. We expand our analysis to other fields to quantify the degree to which mitigation approaches improve the performance of ML and describe the mathematical basis for this. With the advent of accessible analytical packages for microbiome data including learning models, researchers must be familiar with the nature of their datasets.
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Affiliation(s)
- Sebastiano Busato
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA
| | - Max Gordon
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA
| | - Meenal Chaudhari
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA
| | - Ib Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Turgut Akyol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Stig Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, USA; NC Plant Sciences Initiative, North Carolina State University, Raleigh, USA; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA.
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8
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Liu KL, Chen BY, Zhang B, Wang RH, Wang CS. Understory vegetation diversity, soil properties and microbial community response to different thinning intensities in Cryptomeria japonica var. sinensis plantations. Front Microbiol 2023; 14:1117384. [PMID: 36925469 PMCID: PMC10011715 DOI: 10.3389/fmicb.2023.1117384] [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: 12/06/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Soil microorganisms are the key factors in elucidating the effects of thinning on tree growth performance, but the effects of vegetation and soil on the species composition and function of soil microorganisms after thinning are still not well elaborated. Methods The effects of thinning on understory vegetation diversity, soil physicochemical properties and soil microbial community composition were investigated in a thinning trial plantation of Cryptomeria japonica var. sinensis, including four thinning intensities (control: 0%, LIT: 20%, MIT: 30% and HIT: 40%), and the relationships of the microbial community structure with the understory vegetation diversity and soil properties were assessed. Results The results showed that thinning had a greater effect on the diversity of the shrub layer than the herb layer. The soil bulk density and the contents of soil organic matter, total potassium and nitrogen increased with increasing thinning intensities. The Shannon and Chao indices of soil bacteria and fungi were significantly lower in the LIT, MIT and HIT treatments than in the control. Thinning can significantly increase the abundance of Proteobacteria and Actinobacteria, and higher thinning intensities led to a higher relative abundance of Ascomycota and a lower relative abundance of Basidiomycota, Rozellomycota, and Mortierellomycota. Redundancy analysis indicated that soil physicochemical properties rather than understory vegetation diversity were the main drivers of microbial communities, and fungi were more sensitive to soil properties than bacteria. Functional prediction showed that thinning significantly reduced the potential risk of human diseases and plant pathogens, and the nitrogen fixation capacity of bacteria was the highest in the HIT treatment. Thinning significantly increased the relative abundance of cellulolysis and soil saprotrophs in bacteria and fungi. Conclusion The findings provide important insights into the effects of thinning on C. japonica var. sinensis plantation ecosystems, which is essential for developing thinning strategies to promote their ecological and economic benefits.
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Affiliation(s)
- Kai-Li Liu
- College of Forestry, Central South University of Forestry & Technology, Changsha, China.,Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China.,National Long-term Scientific Research Base of Central and Subtropical Forestry, Changsha, China
| | - Bo-Yao Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Bin Zhang
- College of Forestry, Central South University of Forestry & Technology, Changsha, China.,National Long-term Scientific Research Base of Central and Subtropical Forestry, Changsha, China
| | - Rui-Hui Wang
- College of Forestry, Central South University of Forestry & Technology, Changsha, China.,National Long-term Scientific Research Base of Central and Subtropical Forestry, Changsha, China
| | - Chun-Sheng Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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9
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Merino‐Martín L, Hernández‐Cáceres D, Reverchon F, Angeles‐Alvarez G, Zhang G, Dunoyer de Segonzac D, Dezette D, Stokes A. Habitat partitioning of soil microbial communities along an elevation gradient: from plant root to landscape scale. OIKOS 2022. [DOI: 10.1111/oik.09034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis Merino‐Martín
- Depto de Biología y Geología, Física y Química inorgánica, ESCET, Univ. Rey Juan Carlos Madrid Spain
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Univ. Paul Valéry Montpellier 3 Montpellier France
| | | | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Inst. de Ecología, A.C. Pátzcuaro Michoacán México
| | | | - Guangqi Zhang
- Univ. Montpellier, AMAP, INRAE, CIRAD, CNRS, IRD Montpellier France
| | | | - Damien Dezette
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro Montpellier France
| | - Alexia Stokes
- Univ. Montpellier, AMAP, INRAE, CIRAD, CNRS, IRD Montpellier France
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10
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Higgins E, Parr TB, Vaughn CC. Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds. Front Microbiol 2022; 12:790554. [PMID: 35095802 PMCID: PMC8793333 DOI: 10.3389/fmicb.2021.790554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.
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Affiliation(s)
- Edward Higgins
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Edward Higgins,
| | - Thomas B. Parr
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- National Park Service, Great Lakes Inventory and Monitoring Network, Ashland, WI, United States
| | - Caryn C. Vaughn
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
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11
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Werbin ZR, Hackos B, Lopez-Nava J, Dietze MC, Bhatnagar JM. The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis. F1000Res 2021; 10:299. [PMID: 35707452 PMCID: PMC9178279 DOI: 10.12688/f1000research.51494.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 11/20/2022] Open
Abstract
The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON's shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.
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Affiliation(s)
- Zoey R. Werbin
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Briana Hackos
- Department of Mathematics, University of Colorado, Boulder, Boulder, CO, 80309, USA
| | - Jorge Lopez-Nava
- Department of Mathematics, Swarthmore College, Swarthmore, PA 19081, USA
| | - Michael C. Dietze
- Department of Earth & Environment, Boston University, Boston, MA, 02215, USA
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