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Liu M, Ye L, Chen L, Korpelainen H, Niinemets Ü, Li C. Sex-specific phosphorus acquisition strategies and cycling in dioecious Populus euphratica forests along a natural water availability gradient. PLANT, CELL & ENVIRONMENT 2024; 47:3266-3281. [PMID: 38742574 DOI: 10.1111/pce.14951] [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: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
Soil phosphorus (P) availability affects plant growth and distribution. However, it is still unknown how sex-specific variation in functional traits affects plants' P acquisition and soil P transformation. On wet sites, female poplars had a greater specific root length (SRL), and a higher diversity of arbuscular mycorrhizal fungi (AMF) and phosphate-solubilizing bacteria (PSB). Male poplars living on wet sites increased the abundance of AMF and PSB communities and enhanced moderately labile and highly resistant organic P mineralisation via increased phosphatase activity. In contrast, on the dry site, the abundance and diversity of AMF and PSB communities increased in females, enhancing moderately labile and highly resistant organic P mineralisation via elevating phosphatase activities. Males maintained greater SRL and promoted Ca-P mobilisation via the release of root carboxylic acids and rhizosphere acidification on the dry site. The AMF community diversity followed a similar pattern as that of the PSB community when altering the P availability of different-sex plants. Our results indicated that organic P and Ca-P are the major sources of plant-available P in natural P. euphratica forests. Seasonal shifts and geographic locations affected the share of organic and inorganic P pools, and AMF and PSB diversities, ultimately altering sex-specific P acquisition strategies of plants.
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Affiliation(s)
- Miao Liu
- Department of Ecology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Department of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Liyun Ye
- Department of Ecology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Liangliang Chen
- Department of Ecology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ülo Niinemets
- Department of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Chunyang Li
- Department of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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Zhang C, Ndungu CN, Feng L, Huang J, Ba S, Liu W, Cai M. Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121509. [PMID: 38897088 DOI: 10.1016/j.jenvman.2024.121509] [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: 02/18/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.
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Affiliation(s)
- Caifang Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caroline Njambi Ndungu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lian Feng
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Jieya Huang
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Sang Ba
- School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Wenzhi Liu
- Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China.
| | - Miaomiao Cai
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China.
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Zhang Y, Gan G, Li Y, Li W, Jiang Y, Wang P, Hu J, Wang N, Quan X, Liu J, Raza W, Xu Y, Hohmann P, Jousset A, Wang Y, Shen Q, Jiang G, Wei Z. Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants. iScience 2024; 27:110319. [PMID: 39055957 PMCID: PMC11269921 DOI: 10.1016/j.isci.2024.110319] [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: 03/31/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.
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Affiliation(s)
- Yuling Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Yarong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Jie Hu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Ningqi Wang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowen Quan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jialin Liu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Waseem Raza
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Pierre Hohmann
- Department of Biology, Healthcare and the Environment, Universitat de Barcelona, 08028 Barcelona, Spain
- BonaPlanta, 08241 Manresa, Spain
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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Tyborski N, Koehler T, Steiner FA, Tung SY, Wild AJ, Carminati A, Mueller CW, Vidal A, Wolfrum S, Pausch J, Lueders T. Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations. Front Microbiol 2024; 15:1386476. [PMID: 39091306 PMCID: PMC11292614 DOI: 10.3389/fmicb.2024.1386476] [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: 02/15/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and β-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.
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Affiliation(s)
- Nicolas Tyborski
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tina Koehler
- Root-Soil Interaction, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Franziska A. Steiner
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Shu-Yin Tung
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas J. Wild
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Andrea Carminati
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Carsten W. Mueller
- Soil Science, Institute of Ecology, Technical University of Berlin, Berlin, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Alix Vidal
- Soil Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Sebastian Wolfrum
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
| | - Johanna Pausch
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tillmann Lueders
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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5
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Wang D, He X, Baer M, Lami K, Yu B, Tassinari A, Salvi S, Schaaf G, Hochholdinger F, Yu P. Lateral root enriched Massilia associated with plant flowering in maize. MICROBIOME 2024; 12:124. [PMID: 38982519 PMCID: PMC11234754 DOI: 10.1186/s40168-024-01839-4] [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: 09/19/2023] [Accepted: 05/16/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND Beneficial associations between plants and soil microorganisms are critical for crop fitness and resilience. However, it remains obscure how microorganisms are assembled across different root compartments and to what extent such recruited microbiomes determine crop performance. Here, we surveyed the root transcriptome and the root and rhizosphere microbiome via RNA sequencing and full-length (V1-V9) 16S rRNA gene sequencing from genetically distinct monogenic root mutants of maize (Zea mays L.) under different nutrient-limiting conditions. RESULTS Overall transcriptome and microbiome display a clear assembly pattern across the compartments, i.e., from the soil through the rhizosphere to the root tissues. Co-variation analysis identified that genotype dominated the effect on the microbial community and gene expression over the nutrient stress conditions. Integrated transcriptomic and microbial analyses demonstrated that mutations affecting lateral root development had the largest effect on host gene expression and microbiome assembly, as compared to mutations affecting other root types. Cooccurrence and trans-kingdom network association analysis demonstrated that the keystone bacterial taxon Massilia (Oxalobacteraceae) is associated with root functional genes involved in flowering time and overall plant biomass. We further observed that the developmental stage drives the differentiation of the rhizosphere microbial assembly, especially the associations of the keystone bacteria Massilia with functional genes in reproduction. Taking advantage of microbial inoculation experiments using a maize early flowering mutant, we confirmed that Massilia-driven maize growth promotion indeed depends on flowering time. CONCLUSION We conclude that specific microbiota supporting lateral root formation could enhance crop performance by mediating functional gene expression underlying plant flowering time in maize. Video Abstract.
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Affiliation(s)
- Danning Wang
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Xiaoming He
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Marcel Baer
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Klea Lami
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Baogang Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Alberto Tassinari
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, 40127, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, 40127, Italy
| | - Gabriel Schaaf
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany.
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53113, Germany.
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Wang W, Guo Y, Yang L, Adams JM. Methanogen-methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane. Mol Ecol 2024; 33:e17416. [PMID: 38801181 DOI: 10.1111/mec.17416] [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: 01/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high-throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross-feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance-decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities.
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Affiliation(s)
- Wenqi Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Lin Yang
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
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Sun RZ, Wang YY, Liu XQ, Yang ZL, Deng X. Structure and dynamics of microbial communities associated with the resurrection plant Boea hygrometrica in response to drought stress. PLANTA 2024; 260:24. [PMID: 38858226 DOI: 10.1007/s00425-024-04459-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
MAIN CONCLUSION The resurrection plant Boea hygrometrica selectively recruits and assembles drought-specific microbial communities across the plant-soil compartments, which may benefit plant growth and fitness under extreme drought conditions. Plant-associated microbes are essential for facilitating plant growth and fitness under drought stress. The resurrection plant Boea hygrometrica in natural habitats with seasonal rainfall can survive rapid desiccation, yet their interaction with microbiomes under drought conditions remains unexplored. This study examined the bacterial and fungal microbiome structure and drought response across plant-soil compartments of B. hygrometrica by high-throughput amplicon sequencing of 16S rRNA gene and internal transcribed spacer. Our results demonstrated that the diversity, composition, and functional profile of the microbial community varied considerably across the plant-soil compartments and were strongly affected by drought stress. Bacterial and fungal diversity was significantly reduced from soil to endosphere and belowground to aboveground compartments. The compartment-specific enrichment of the dominant bacteria phylum Cyanobacteriota and genus Methylorubrum in leaf endosphere, genera Pseudonocardia in rhizosphere soil and Actinoplanes in root endosphere, and fungal phylum Ascomycota in the aboveground compartments and genera Knufia in root endosphere and Cladosporium in leaf endosphere composed part of the core microbiota with corresponding enrichment of beneficial functions for plant growth and fitness. Moreover, the recruitment of dominant microbial genera Sphingosinicella and Plectosphaerella, Ceratobasidiaceae mycorrhizal fungi, and numerous plant growth-promoting bacteria involving nutrient supply and auxin regulation was observed in desiccated B. hygrometrica plants. Our results suggest that the stable assembled drought-specific microbial community of B. hygrometrica may contribute to plant survival under extreme environments and provide valuable microbial resources for the microbe-mediated drought tolerance enhancement in crops.
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Affiliation(s)
- Run-Ze Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
| | - Yuan-Yuan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiao-Qiang Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhao-Lin Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xin Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
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8
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Wang M, Zhao X, Li F, Wu L, Li Y, Tang R, Yao J, Lin S, Zheng Y, Ling Y, Ren K, Chen Z, Yin X, Wang Z, Gao Z, Zhang X. Using sustained vowels to identify patients with mild Parkinson's disease in a Chinese dataset. Front Aging Neurosci 2024; 16:1377442. [PMID: 38765774 PMCID: PMC11102047 DOI: 10.3389/fnagi.2024.1377442] [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: 01/27/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Introduction Parkinson's disease (PD) is the second most common neurodegenerative disease and affects millions of people. Accurate diagnosis and subsequent treatment in the early stages can slow down disease progression. However, making an accurate diagnosis of PD at an early stage is challenging. Previous studies have revealed that even for movement disorder specialists, it was difficult to differentiate patients with PD from healthy individuals until the average modified Hoehn-Yahr staging (mH&Y) reached 1.8. Recent researches have shown that dysarthria provides good indicators for computer-assisted diagnosis of patients with PD. However, few studies have focused on diagnosing patients with PD in the early stages, specifically those with mH&Y ≤ 1.5. Method We used a machine learning algorithm to analyze voice features and developed diagnostic models for differentiating between healthy controls (HCs) and patients with PD, and for differentiating between HCs and patients with mild PD (mH&Y ≤ 1.5). The models were independently validated using separate datasets. Results Our results demonstrate that, a remarkable diagnostic performance of the model in identifying patients with mild PD (mH&Y ≤ 1.5) and HCs, with area under the ROC curve 0.93 (95% CI: 0.851.00), accuracy 0.85, sensitivity 0.95, and specificity 0.75. Conclusion The results of our study are helpful for screening PD in the early stages in the community and primary medical institutions where there is a lack of movement disorder specialists and special equipment.
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Affiliation(s)
- Miao Wang
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Xingli Zhao
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Fengzhu Li
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Lingyu Wu
- Gyenno Science Co., Ltd., Shenzhen, China
- HUST-GYENNO CNS Intelligent Digital Medicine Technology Center, Wuhan, China
| | - Yifan Li
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Ruonan Tang
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Jiarui Yao
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Shinuan Lin
- Gyenno Science Co., Ltd., Shenzhen, China
- HUST-GYENNO CNS Intelligent Digital Medicine Technology Center, Wuhan, China
| | - Yuan Zheng
- Gyenno Science Co., Ltd., Shenzhen, China
- HUST-GYENNO CNS Intelligent Digital Medicine Technology Center, Wuhan, China
| | - Yun Ling
- Gyenno Science Co., Ltd., Shenzhen, China
- HUST-GYENNO CNS Intelligent Digital Medicine Technology Center, Wuhan, China
| | - Kang Ren
- Gyenno Science Co., Ltd., Shenzhen, China
- HUST-GYENNO CNS Intelligent Digital Medicine Technology Center, Wuhan, China
| | - Zhonglue Chen
- Gyenno Science Co., Ltd., Shenzhen, China
- HUST-GYENNO CNS Intelligent Digital Medicine Technology Center, Wuhan, China
| | - Xi Yin
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Zhenfu Wang
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Zhongbao Gao
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Xi Zhang
- Department of Geriatric Neurology, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
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9
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [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: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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10
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Jiang L, Ke D, Sun B, Zhang J, Lyu S, Yu H, Chen P, Mao X, Liu Q, Chen W, Fan Z, Huang L, Yin S, Deng Y, Li C. Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process. Microbiol Spectr 2024; 12:e0333023. [PMID: 38470483 PMCID: PMC10986595 DOI: 10.1128/spectrum.03330-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.
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Affiliation(s)
- Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Da Ke
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lyu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Li Huang
- Healthtimegene Institute, Shenzhen, China
| | - Sanjun Yin
- Healthtimegene Institute, Shenzhen, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
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11
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Argiroff WA, Carrell AA, Klingeman DM, Dove NC, Muchero W, Veach AM, Wahl T, Lebreux SJ, Webb AB, Peyton K, Schadt CW, Cregger MA. Seasonality and longer-term development generate temporal dynamics in the Populus microbiome. mSystems 2024; 9:e0088623. [PMID: 38421171 PMCID: PMC10949431 DOI: 10.1128/msystems.00886-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.
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Affiliation(s)
- William A. Argiroff
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Nicholas C. Dove
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Allison M. Veach
- Department of Integrative Biology, The University of Texas, San Antonio, Texas, USA
| | - Toni Wahl
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steven J. Lebreux
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Amber B. Webb
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kellie Peyton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Melissa A. Cregger
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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12
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Zhang T, Yan L, Wei M, Su R, Qi J, Sun S, Song Y, Li X, Zhang D. Bioaerosols in the coastal region of Qingdao: Community diversity, impact factors and synergistic effect. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170246. [PMID: 38246385 DOI: 10.1016/j.scitotenv.2024.170246] [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: 10/19/2023] [Revised: 12/26/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Atmospheric bioaerosols are influenced by multiple factors, including physical, chemical, and biotic interactions, and pose a significant threat to the public health and the environment. The nonnegligible truth however is that the primary driver of the changes in bioaerosol community diversity remains unknown. In this study, putative biological association (PBA) was obtained by constructing an ecological network. The relationship between meteorological conditions, atmospheric pollutants, water-soluble inorganic ions, PBA and bioaerosol community diversity was analyzed using random forest regression (RFR)-An ensemble learning algorithm based on a decision tree that performs regression tasks by constructing multiple decision trees and integrating the predicted results, and the contribution of different rich species to PBA was predicted. The species richness, evenness and diversity varied significantly in different seasons, with the highest in summer, followed by autumn and spring, and was lowest in winter. The RFR suggested that the explanation rate of alpha diversity increased significantly from 73.74 % to 85.21 % after accounting for the response of the PBA to diversity. The PBA, temperature, air pollution, and marine source air masses were the most crucial factors driving community diversity. PBA, particularly putative positive association (PPA), had the highest significance in diversity. We found that under changing external conditions, abundant taxa tend to cooperate to resist external pressure, thereby promoting PPA. In contrast, rare taxa were more responsive to the putative negative association because of their sensitivity to environmental changes. The results of this research provided scientific advance in the understanding of the dynamic and temporal changes in bioaerosols, as well as support for the prevention and control of microbial contamination of the atmosphere.
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Affiliation(s)
- Ting Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, PR China
| | - Lingchong Yan
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, PR China
| | - Mingming Wei
- Laoshan District Meteorological Bureau, Qingdao 266107, PR China
| | - Rongguo Su
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, PR China
| | - Jianhua Qi
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, PR China
| | - Shaohua Sun
- Laoshan District Meteorological Bureau, Qingdao 266107, PR China
| | - Yongzhong Song
- Jufeng Peak Tourist Management Service Center of Laoshan Scenic Spot, Qingdao 266100, PR China
| | - Xianguo Li
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, PR China
| | - Dahai Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, PR China.
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13
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Paina C, Fois M, Asp T, Jensen J, Hansen PB, Rohde PD. The soil microbiome of Lolium perenne L. depends on host genotype, is modified by nitrogen level and varies across season. Sci Rep 2024; 14:5767. [PMID: 38459164 PMCID: PMC10923896 DOI: 10.1038/s41598-024-56353-2] [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: 06/01/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
Genotype by environment interactions (G × E) are frequently observed in herbage production. Understanding the underlying biological mechanisms is important for achieving stable and predictive outputs across production environments. The microbiome is gaining increasing attention as a significant contributing factor to G × E. Here, we focused on the soil microbiome of perennial ryegrass (Lolium perenne L.) grown under field conditions and investigated the soil microbiome variation across different ryegrass varieties to assess whether environmental factors, such as seasonality and nitrogen levels, affect the microbial community. We identified bacteria, archaea, and fungi operational taxonomic units (OTUs) and showed that seasonality and ryegrass variety were the two factors explaining the largest fraction of the soil microbiome diversity. The strong and significant variety-by-treatment-by-seasonal cut interaction for ryegrass dry matter was associated with the number of unique OTUs within each sample. We identified seven OTUs associated with ryegrass dry matter variation. An OTU belonging to the Solirubrobacterales (Thermoleophilales) order was associated with increased plant biomass, supporting the possibility of developing engineered microbiomes for increased plant yield. Our results indicate the importance of incorporating different layers of biological data, such as genomic and soil microbiome data to improve the prediction accuracy of plant phenotypes grown across heterogeneous environments.
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Affiliation(s)
- Cristiana Paina
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mattia Fois
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus University, C. F. Møllers Allé 3, Bldg. 1130, 8000, Aarhus, Denmark.
| | - Pernille Bjarup Hansen
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Palle Duun Rohde
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Selma Lagerløfs Vej 249, 9260, Gistrup, Denmark
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14
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Ni Z, Gong Z, Song L, Jia C, Zhang X. Adaptation strategies and functional transitions of microbial community in pyrene-contaminated soils promoted by lead with Pseudomonas veronii and its extracellular polymeric substances. CHEMOSPHERE 2024; 351:141139. [PMID: 38185422 DOI: 10.1016/j.chemosphere.2024.141139] [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: 07/18/2023] [Revised: 12/25/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
Pyrene was designated as a remediation target in this study, and low contamination of lead (Pb) was set to induce heavy metal stress. Pseudomonas veronii and its extracellular polymeric substances (EPSs) were chosen for biofortification, with the aim of elucidating the structural, metabolic, and functional responses of soil microbial communities. Community analysis of soil microorganisms using high-throughput sequencing showed that the co-addition of P. veronii and EPSs resulted in an increase in relative abundance of phyla associated with pyrene degradation, and formed a symbiotic system dominated by Firmicutes and Proteobacteria, which involved in pyrene metabolism. Co-occurrence network analysis revealed that the module containing P. veronii was the only one exhibiting a positive correlation between bacterial abundance and pyrene removal, indicating the potential of bioaugmentation in enriching functional taxa. Biofortification also enhanced the abundance of functional gene linked to EPS production (biofilm formation-Pseudomonas aeruginosa) and pyrene degradation. Furthermore, 17 potential functional bacteria were screened out using random forest algorithm. Lead contamination further promoted the growth of Proteobacteria, intensified cooperative associations among bacteria, and increased the abundance of bacteria with positive correlation with pyrene degradation. The results offer novel perspectives on alterations in microbial communities resulting from the synergistic impact of heavy metal stress and biofortification.
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Affiliation(s)
- Zijun Ni
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zongqiang Gong
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Lei Song
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chunyun Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Xiaorong Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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15
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Wang M, Ge AH, Ma X, Wang X, Xie Q, Wang L, Song X, Jiang M, Yang W, Murray JD, Wang Y, Liu H, Cao X, Wang E. Dynamic root microbiome sustains soybean productivity under unbalanced fertilization. Nat Commun 2024; 15:1668. [PMID: 38395981 PMCID: PMC10891064 DOI: 10.1038/s41467-024-45925-5] [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: 05/25/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.
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Affiliation(s)
- Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An-Hui Ge
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xingzhu Ma
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, China
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiujin Xie
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Like Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengchen Jiang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weibing Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jeremy D Murray
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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16
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Wang J, Liu Z, Ren J, Zhang M, Guan Z, Zhao X, Gao C, Zhang G. A preliminary study characterizing temporal changes in soil bacterial communities after dismembered bones were buried. Electrophoresis 2024. [PMID: 38332582 DOI: 10.1002/elps.202300274] [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: 10/18/2023] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
Determining the burial time of skeletal remains is one of the most important issues of forensic medicine. We speculated that the microbiome of gravesoil may be a promising method to infer burial time by virtue of time-dependent. As we know, forensic scientists have established various models to predict the postmortem interval of a decedent based on the changes in body and soil microbiome communities. However, limited data are available on the burial time prediction for bones, especially dismembered bones. In this exploratory study, we initially conducted 16S rRNA amplicon high-throughput sequencing on the burial soil of 10 porcine femurs within a 120-day period and analyzed the changes in soil microbial communities. Compared with the control soil, a higher Shannon index in the microbial diversity of burial soil containing bones was observed. Correlation analysis identified 61 time-related bacterial families and the best subset selection method obtained best subset, containing Thermomonosporaceae, Clostridiaceae, 0319-A21, and Oxalobacteraceae, which were used to construct a simplified multiple linear regression model with a mean absolute error (MAE) of 56.69 accumulated degree day (ADD). An additional random forest model was established based on indicators for the minimum cross-validation error of Thermomonosporaceae, Clostridiaceae, 0319-A21, Oxalobacteraceae, and Syntrophobacteraceae, with an MAE of 55.65 ADD. The produced empirical data in this pilot study provided the evidence of feasibility that the microbial successional changes of burial soil will predict the burial time of dismembered bones and may also expand the current knowledge of the effects of bone burial on soil bacterial communities.
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Affiliation(s)
- Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jianbo Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Mingming Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zimeng Guan
- Department of Biotechnology, Biomedical Sciences College, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, P. R. China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Cairong Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
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17
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Gao M, Xiong C, Tsui CKM, Cai L. Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome. Mol Ecol 2024; 33:e17228. [PMID: 38037712 DOI: 10.1111/mec.17228] [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: 07/07/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.
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Affiliation(s)
- Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Chao Xiong
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Clement K M Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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18
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Wang W, Chen J, Fang L, A Y, Ren S, Men J, Wang G. Remote sensing retrieval and driving analysis of phytoplankton density in the large storage freshwater lake: A study based on random forest and Landsat-8 OLI. JOURNAL OF CONTAMINANT HYDROLOGY 2024; 261:104304. [PMID: 38244425 DOI: 10.1016/j.jconhyd.2024.104304] [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: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/22/2024]
Abstract
Remote sensing monitoring of seasonal changes in phytoplankton density and analyses of the driving factors of phytoplankton densities are necessary for assessing the health of aquatic ecosystems, controlling lake eutrophication, and formulating ecological restoration policies. Building upon the satellite-ground synchronization experiment that involves the in situ aquatic ecological monitoring conducted in Nansi Lake, which is the largest storage lake situated along the eastern route of the South-to-North Water Diversion Project, we developed a phytoplankton density retrieval model utilizing the random forest (RF) method and Landsat-8 OLI data. On this basis, we mapped the seasonal fluctuations and spatial disparities in the phytoplankton densities from 2013 to 2023. Subsequently, we conducted a detailed analysis of the driving factors and considered both the natural and anthropogenic aspects. The results indicate that (1) the RF model, when utilizing three band combinations, yielded favorable results with R2, RMSE and MAE values of 0.67, 1.31 × 106 cells/L and 1.18 × 106 cells/L, respectively. (2) The phytoplankton densities exhibited both seasonal and spatial variations, with higher concentrations in summer and autumn than in spring and winter. Significantly, the northwestern region of Zhaoyang Lake and the southeastern region of Weishan Lake had substantially greater phytoplankton densities than did the other areas. Furthermore, overarching upward trends were observed from 2013 to 2023, reflecting an annual rate of increase of 3.32%. (3) An analysis of the causal factors indicated that temperatures and gross agricultural production levels are the primary drivers influencing the seasonal variations and distributions of phytoplankton densities. In the future, we will delve into the potential of deep learning and utilize various satellite sensors to explore the intricacies of phytoplankton monitoring, as well as the complex mechanisms that influence aquatic ecological health.
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Affiliation(s)
- Wanting Wang
- Academician Workstation for Big Data in Ecology and Environment, Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jinyue Chen
- Academician Workstation for Big Data in Ecology and Environment, Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Lei Fang
- Academician Workstation for Big Data in Ecology and Environment, Environment Research Institute, Shandong University, Qingdao 266237, China.
| | - Yinglan A
- Innovation Research Center of Satellite Application, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
| | - Shilong Ren
- Academician Workstation for Big Data in Ecology and Environment, Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jilin Men
- Academician Workstation for Big Data in Ecology and Environment, Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Guoqiang Wang
- Academician Workstation for Big Data in Ecology and Environment, Environment Research Institute, Shandong University, Qingdao 266237, China; Innovation Research Center of Satellite Application, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
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19
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Liu HB, Sun HX, Du LQ, Jiang LL, Zhang LA, Qi YY, Cai J, Yu F. Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice. THE ISME JOURNAL 2024; 18:wrae006. [PMID: 38366198 PMCID: PMC10900889 DOI: 10.1093/ismejo/wrae006] [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: 11/06/2023] [Revised: 12/22/2023] [Accepted: 01/20/2024] [Indexed: 02/18/2024]
Abstract
Oxygen is one of the determinants of root microbiome formation. However, whether plants regulate rhizosphere oxygen levels to affect microbiota composition and the underlying molecular mechanisms remain elusive. The receptor-like kinase (RLK) family member FERONIA modulates the growth-defense tradeoff in Arabidopsis. Here, we established that rice FERONIA-like RLK 7 (FLR7) controls rhizosphere oxygen levels by methylene blue staining, oxygen flux, and potential measurements. The formation of oxygen-transporting aerenchyma in roots is negatively regulated by FLR7. We further characterized the root microbiota of 11 FLR mutants including flr7 and wild-type Nipponbare (Nip) grown in the field by 16S ribosomal RNA gene profiling and demonstrated that the 11 FLRs are involved in regulating rice root microbiome formation. The most abundant anaerobic-dependent genus Anaeromyxobacter in the Nip root microbiota was less abundant in the root microbiota of all these mutants, and this contributed the most to the community differences between most mutants and Nip. Metagenomic sequencing revealed that flr7 increases aerobic respiration and decreases anaerobic respiration in the root microbiome. Finally, we showed that a representative Anaeromyxobacter strain improved submergence tolerance in rice via FLR7. Collectively, our findings indicate that FLR7 mediates changes in rhizosphere oxygen levels and enriches the beneficial dominant genus Anaeromyxobacter and may provide insights for developing plant flood prevention strategies via the use of environment-specific functional soil microorganisms.
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Affiliation(s)
- Hong-Bin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
- Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha 410082, P.R. China
- Interdisciplinary and Intelligent Seed Industry Equipment Research Department, Yuelushan Laboratory, Changsha 410082, P.R. China
| | - Hong-Xia Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Li-Qiong Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Ling-Li Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Lin-An Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Yin-Yao Qi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Jun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, P.R. China
- Interdisciplinary and Intelligent Seed Industry Equipment Research Department, Yuelushan Laboratory, Changsha 410082, P.R. China
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20
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Gao AX, Chen C, Gao ZY, Zhai ZQ, Wang P, Zhang SY, Zhao FJ. Soil redox status governs within-field spatial variation in microbial arsenic methylation and rice straighthead disease. THE ISME JOURNAL 2024; 18:wrae057. [PMID: 38564256 PMCID: PMC11031232 DOI: 10.1093/ismejo/wrae057] [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: 01/23/2024] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024]
Abstract
Microbial arsenic (As) methylation in paddy soil produces mainly dimethylarsenate (DMA), which can cause physiological straighthead disease in rice. The disease is often highly patchy in the field, but the reasons remain unknown. We investigated within-field spatial variations in straighthead disease severity, As species in rice husks and in soil porewater, microbial composition and abundance of arsM gene encoding arsenite S-adenosylmethionine methyltransferase in two paddy fields. The spatial pattern of disease severity matched those of soil redox potential, arsM gene abundance, porewater DMA concentration, and husk DMA concentration in both fields. Structural equation modelling identified soil redox potential as the key factor affecting arsM gene abundance, consequently impacting porewater DMA and husk DMA concentrations. Core amplicon variants that correlated positively with husk DMA concentration belonged mainly to the phyla of Chloroflexi, Bacillota, Acidobacteriota, Actinobacteriota, and Myxococcota. Meta-omics analyses of soil samples from the disease and non-disease patches identified 5129 arsM gene sequences, with 71% being transcribed. The arsM-carrying hosts were diverse and dominated by anaerobic bacteria. Between 96 and 115 arsM sequences were significantly more expressed in the soil samples from the disease than from the non-disease patch, which were distributed across 18 phyla, especially Acidobacteriota, Bacteroidota, Verrucomicrobiota, Chloroflexota, Pseudomonadota, and Actinomycetota. This study demonstrates that even a small variation in soil redox potential within the anoxic range can cause a large variation in the abundance of As-methylating microorganisms, thus resulting in within-field variation in rice straighthead disease. Raising soil redox potential could be an effective way to prevent straighthead disease.
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Affiliation(s)
- A-Xiang Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Chuan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Zi-Yu Gao
- School of Ecological and Environmental Sciences, East China Normal University, NO. 500 Dongchuan Street, Minghang, Shanghai 200241, China
| | - Zhi-Qiang Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Si-Yu Zhang
- School of Ecological and Environmental Sciences, East China Normal University, NO. 500 Dongchuan Street, Minghang, Shanghai 200241, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
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21
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Blakney AJC, St-Arnaud M, Hijri M. Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages? ISME COMMUNICATIONS 2024; 4:ycae019. [PMID: 38500702 PMCID: PMC10944699 DOI: 10.1093/ismeco/ycae019] [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: 01/17/2024] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/20/2024]
Abstract
Soil history has been shown to condition future rhizosphere microbial communities. However, previous experiments have also illustrated that mature, adult plants can "re-write," or mask, different soil histories through host plant-soil community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Thus, here we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere, and roots of the B. napus hosts at different growth stages-the initial seeding conditions, seedling, rosette, bolting, and flower-from all three soil history plots. We compared composition and diversity of the B. napus soil bacterial communities, as estimated using 16S rRNA gene metabarcoding, to identify any changes associated with soil history and growth stages. We found that soil history remained significant across each growth stage in structuring the bacterial bulk soil and rhizosphere communities, but not the bacterial root communities. This suggests that the host plant's capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil history's identity remain present, such that the previously established soil history continues to impact the bacterial rhizosphere communities, but not the root communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.
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Affiliation(s)
- Andrew J C Blakney
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- Present address: Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Ontario, M1C 1A4, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
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22
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Wang YX, Liu XY, Di HH, He XS, Sun Y, Xiang S, Huang ZB. The mechanism of microbial community succession and microbial co-occurrence network in soil with compost application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167409. [PMID: 37769744 DOI: 10.1016/j.scitotenv.2023.167409] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
The application of organic and chemical fertilizer into soil can regulate microbial communities. However, the response mechanism of microbial communities in soil to compost and chemical fertilizer application remain unclear. In this study, compost made of tobacco leaves individually and combined with chemical fertilizer was applied, respectively, to investigate their effect on soil microorganisms during the pot-culture process. High-throughput sequence, neutral community model and null model were employed to clarify how soil microbial community respond to the application of compost and chemical fertilizer. Furthermore, random forest model was applied to predict the relationships between the plant agronomical traits and the soil microorganism during the pot-culture process. The results demonstrated that the simultaneous application of compost and chemical fertilizer increased significantly the richness and diversity of the microorganisms in soil (p < 0.05), groups C and D led to a significant reduction in the number of nodes and edges in the microbial network (77.78 %-96.57 %). The dominant bacteria in the application of 50 g fertilizer accounted for the highest proportion (40 %) and organic matter was the main factors driving the change in bacterial communities. Compared to the tilled soil, the microbial communities of the soil with the simultaneous application of compost and chemical fertilizer were more susceptible to stochastic processes, and soil microorganisms had less influence on the growth of crops during pot-culture. In conclusion, the simultaneous application of compost and fertilizer altered the ecological functions of soil microbial communities, leading to an enhanced stochastic process of community formation.
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Affiliation(s)
- Yu-Xin Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xie-Yang Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Hui-Hui Di
- Enshi Tobacco Company of Hubei Province Corporation, Enshi 445000, China
| | - Xiao-Song He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yue Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Song Xiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Zhan-Bin Huang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
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23
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Dong W, Ricker N, Holman DB, Johnson TA. Meta-analysis reveals the predictable dynamic development of the gut microbiota in commercial pigs. Microbiol Spectr 2023; 11:e0172223. [PMID: 37815394 PMCID: PMC10715009 DOI: 10.1128/spectrum.01722-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/24/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The swine gut microbiome undergoes an age-dependent assembly pattern with a developmental phase at early ages and a stabilization phase at later ages. Shorter time intervals and a wider range of data sources provided a clearer understanding of the gut microbiota colonization and succession and their associations with pig growth and development. The rapidly changing microbiota of suckling and weaning pigs implies potential time targets for growth and health regulation through gut microbiota manipulation. Since swine gut microbiota development is predictable, swine microbiota age can be calculated and compared between animal treatment groups rather than relying only on static time-matched comparisons.
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Affiliation(s)
- Wenxuan Dong
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Nicole Ricker
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Timothy A. Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
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24
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Pan C, Zhao Y, Chen X, Zhang G, Xie L, Wei Z, Song C. Improved carbon sequestration by utilization of ferrous ions during different organic wastes composting. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119188. [PMID: 37801948 DOI: 10.1016/j.jenvman.2023.119188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
The humic acid (HA) possesses a more recalcitrant structure, making it crucial carbon components that improve carbon sequestration. Moreover, ferrous ions could improve microbial activity and enhance compost humification, and their oxidation into iron oxides could adsorb carbon components for sequestration. Based on the advantages of low cost and easy availability of ferrous sulfate (FeSO4), this study investigated the effect of FeSO4 on carbon sequestration during composting. Chicken manure (CM) and food waste (FW) composting were carried out in four treatments, namely control (CM, FW) and 5% (w/w) FeSO4 treated groups (CM+, FW+). Results indicated that FeSO4 increased HA content, improved organic carbon stability. Carbon loss for CM, CM+, FW and FW + treatments were 48.5%, 46.2%, 45.0%, and 40.3%, respectively. Meanwhile, FeSO4 enhanced the function of bacterial taxa involved in HA synthesis in CM + treatment, and improved the number of core bacteria significantly associated with formation of HA and iron oxide. SEM analysis verified that role of FeSO4 was significant in promoting HA synthesis during CM + composting, while it was remarkably in enhancing HA sequestration during FW + composting. This article provided fundamental theoretical backing for enhancing HA production and improving carbon sequestration during different materials composting.
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Affiliation(s)
- Chaonan Pan
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaomeng Chen
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Guogang Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Lina Xie
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China; Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China.
| | - Caihong Song
- College of Life Science, Liaocheng University, Liaocheng, 252000, China
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25
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Swift JF, Migicovsky Z, Trello GE, Miller AJ. Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California. ENVIRONMENTAL MICROBIOME 2023; 18:84. [PMID: 37996903 PMCID: PMC10668525 DOI: 10.1186/s40793-023-00539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions. RESULTS To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. CONCLUSIONS These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.
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Affiliation(s)
- Joel F Swift
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA.
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
- Department of Biology, Acadia University, Wolfville, NS, B4P 2R6, Canada
| | - Grace E Trello
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
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26
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Centeno-Martinez RE, Klopp RN, Koziol J, Boerman JP, Johnson TA. Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery. Front Vet Sci 2023; 10:1297158. [PMID: 38033643 PMCID: PMC10687565 DOI: 10.3389/fvets.2023.1297158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Bovine respiratory disease (BRD) is a multifactorial disease complex in which bacteria in the upper respiratory tract play an important role in disease development. Previous studies have related the presence of four BRD-pathobionts (Mycoplasma bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) in the upper respiratory tract to BRD incidence and mortalities in the dairy and beef cattle industry, but these studies typically only use one time point to compare the abundance of BRD-pathobionts between apparently healthy and BRD-affected cattle. The objective of this study was to characterize the longitudinal development of the nasopharyngeal (NP) microbiome from apparently healthy calves, and in calves with clinical signs of BRD, the microbiota dynamics from disease diagnosis to recovery. Methods Deep nasopharyngeal swabs were taken from all calves immediately after transport (day 0). If a calf was diagnosed with BRD (n = 10), it was sampled, treated with florfenicol or tulathromycin, and sampled again 1, 5, and 10 days after antibiotic administration. Otherwise, healthy calves (n = 20) were sampled again on days 7 and 14. Bacterial community analysis was performed through 16S rRNA gene amplicon sequencing. Results The NP microbiome of the healthy animals remained consistent throughout the study, regardless of time. The NP microbiota beta diversity and community composition was affected by tulathromycin or florfenicol administration. Even though BRD-pathobionts were identified by 16S rRNA gene sequencing in BRD-affected animals, no difference was observed in their relative abundance between the BRD-affected and apparently healthy animals. The abundance of BRD-pathobionts was not predictive of disease development while the relative abundance of BRD pathobionts was unique to each BRD-affected calf. Interestingly, at the end of the study period, the genera Mycoplasma was the most abundant genus in the healthy group, while Lactobacillus was the most abundant genus in the animals that recovered from BRD. Discussion This study highlights that injected antibiotics seem to improve the NP microbiome composition (higher abundance of Lactobacillus and lower abundance of Mycoplasma), and that the relative abundance of BRD-pathobionts differs between individual calves but is not strongly predictive of BRD clinical signs, indicating that additional factors are likely important in the clinical progression of BRD.
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Affiliation(s)
| | - Rebecca N. Klopp
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
| | - Jennifer Koziol
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
| | - Jacquelyn P. Boerman
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
| | - Timothy A. Johnson
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
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Reis PCJ, Correa-Garcia S, Tremblay J, Beaulieu-Laliberté A, Muench DG, Ahad JME, Yergeau E, Comte J, Martineau C. Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water. FEMS Microbiol Ecol 2023; 99:fiad153. [PMID: 38012121 PMCID: PMC10710301 DOI: 10.1093/femsec/fiad153] [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: 05/31/2023] [Revised: 10/27/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023] Open
Abstract
Naphthenic acids (NAs) are a complex mixture of organic compounds released during bitumen extraction from mined oil sands that are important contaminants of oil sands process-affected water (OSPW). NAs can be toxic to aquatic organisms and, therefore, are a main target compound for OSPW. The ability of microorganisms to degrade NAs can be exploited for bioremediation of OSPW using constructed wetland treatment systems (CWTS), which represent a possible low energy and low-cost option for scalable in situ NA removal. Recent advances in genomics and analytical chemistry have provided insights into a better understanding of the metabolic pathways and genes involved in NA degradation. Here, we discuss the ecology of microbial NA degradation with a focus on CWTS and summarize the current knowledge related to the metabolic pathways and genes used by microorganisms to degrade NAs. Evidence to date suggests that NAs are mostly degraded aerobically through ring cleavage via the beta-oxidation pathway, which can be combined with other steps such as aromatization, alpha-oxidation, omega-oxidation, or activation as coenzyme A (CoA) thioesters. Anaerobic NA degradation has also been reported via the production of benzoyl-CoA as an intermediate and/or through the involvement of methanogens or nitrate, sulfate, and iron reducers. Furthermore, we discuss how genomic, statistical, and modeling tools can assist in the development of improved bioremediation practices.
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Affiliation(s)
- Paula C J Reis
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
| | - Sara Correa-Garcia
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Québec city, QC G1K 9A9, Canada
| | - Julien Tremblay
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Québec city, QC G1K 9A9, Canada
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC H4P 2R2, Canada
| | - Aurélie Beaulieu-Laliberté
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Jason M E Ahad
- Geological Survey of Canada, Natural Resources Canada, Québec city, QC G1K 9A9, Canada
| | - Etienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC H4P 2R2, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Québec city, QC G1V 4C7, Canada
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Francis JS, Mueller TG, Vannette RL. Intraspecific variation in realized dispersal probability and host quality shape nectar microbiomes. THE NEW PHYTOLOGIST 2023; 240:1233-1245. [PMID: 37614102 DOI: 10.1111/nph.19195] [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: 04/25/2023] [Accepted: 07/16/2023] [Indexed: 08/25/2023]
Abstract
Epiphytic microbes frequently affect plant phenotype and fitness, but their effects depend on microbe abundance and community composition. Filtering by plant traits and deterministic dispersal-mediated processes can affect microbiome assembly, yet their relative contribution to predictable variation in microbiome is poorly understood. We compared the effects of host-plant filtering and dispersal on nectar microbiome presence, abundance, and composition. We inoculated representative bacteria and yeast into 30 plants across four phenotypically distinct cultivars of Epilobium canum. We compared the growth of inoculated communities to openly visited flowers from a subset of the same plants. There was clear evidence of host selection when we inoculated flowers with synthetic communities. However, plants with the highest microbial densities when inoculated did not have the highest microbial densities when openly visited. Instead, plants predictably varied in the presence of bacteria, which was correlated with pollen receipt and floral traits, suggesting a role for deterministic dispersal. These findings suggest that host filtering could drive plant microbiome assembly in tissues where species pools are large and dispersal is high. However, deterministic differences in microbial dispersal to hosts may be equally or more important when microbes rely on an animal vector, dispersal is low, or arrival order is important.
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Affiliation(s)
- Jacob S Francis
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Tobias G Mueller
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Rachel L Vannette
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
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Zhang Z, Chai X, Zhang B, Lu Y, Gao Y, Tariq A, Li X, Zeng F. Potential role of root-associated bacterial communities in adjustments of desert plant physiology to osmotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108124. [PMID: 37897889 DOI: 10.1016/j.plaphy.2023.108124] [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: 05/04/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023]
Abstract
Plants possess the ability to adapt to osmotic stress by adjusting their physiology and morphology and by cooperating with their root-associated (rhizosphere and endosphere) microbial communities. However, the coordination of host self-regulation with root-associated microorganisms at the community level, especially for desert plants, remains unclear. This study investigated the morphophysiological responses of seedlings from the desert plant Alhagi sparsifolia Shap to osmotic stress, as well as the relationships between these adaptations and their root-associated bacterial communities. The results indicated that osmotic stress contributed to a reduction in height and increased levels of reactive oxygen species (ROS) and malondialdehyde (MDA). In response, A. sparsifolia exhibited a series of morphophysiological adjustments, including increased ratio of root to shoot biomass (R/S) and the number of root tip, enhanced vitality, high levels of peroxidase (POD), ascorbate peroxidase (APX), and glutathione (GSH), as well as osmolytes (proline, soluble protein, and soluble sugar) and modification in phytohormones (abscisic acid (ABA) and jasmonic acid (JA)). Additionally, osmotic stress resulted in alterations in the compositions and co-occurrence patterns of root-associated bacterial communities, but not α-diversity (Chao1). Specifically, the rhizosphere Actinobacteria phylum was significantly increased by osmotic stress. These shifts in root-associated bacterial communities were significantly correlated with the host's adaptation to osmotic stress. Overall, the findings revealed that osmotic stress, in addition to its impacts on plant physiology, resulted in a restructuring of root-associated microbial communities and suggested that the concomitant adjustment in plant microbiota may potentially contribute to the survival of desert plants under extreme environmental stress.
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Affiliation(s)
- Zhihao Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China.
| | - Xutian Chai
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
| | - Yan Lu
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
| | - Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China
| | - Xiangyi Li
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Hu H, Wei XY, Liu L, Wang YB, Jia HJ, Bu LK, Pei DS. Supervised machine learning improves general applicability of eDNA metabarcoding for reservoir health monitoring. WATER RESEARCH 2023; 246:120686. [PMID: 37812979 DOI: 10.1016/j.watres.2023.120686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Abstract
Effective and standardized monitoring methodologies are vital for successful reservoir restoration and management. Environmental DNA (eDNA) metabarcoding sequencing offers a promising alternative for biomonitoring and can overcome many limitations of traditional morphological bioassessment. Recent attempts have even shown that supervised machine learning (SML) can directly infer biotic indices (BI) from eDNA metabarcoding data, bypassing the cumbersome calculation process of BI regardless of the taxonomic assignment of eDNA sequences. However, questions surrounding the general applicability of this taxonomy-free approach to monitoring reservoir health remain unclear, including model stability, feature selection, algorithm choice, and multi-season biomonitoring. Here, we firstly developed a novel biological integrity index (Me-IBI) that integrates multitrophic interactions and environmental information, based on taxonomy-assigned eDNA metabarcoding data. The Me-IBI can better distinguish the actual health status of the Three Gorges Reservoir (TGR) than physicochemical assessments and have a clear response to human activity. Then, taking this reliable Me-IBI as a supervised label, we compared the impact of selecting different numbers of features and SML algorithms on the stability and predictive performance of the model for predicting ecological conditions in multiple seasons using taxonomy-free eDNA metabarcoding data. We discovered that even with a small number of features, different SML algorithms can establish a stable model and obtain excellent predictive performance. Finally, we proposed a four-step strategy for standardized routine biomonitoring using SML tools. Our study firstly explores the general applicability problem of the taxonomy-free eDNA-SML approach and establishes a solid foundation for the large-scale and standardized biomonitoring application.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing, 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing, 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yuan-Bo Wang
- Chongqing Jiaotong University, Chongqing, 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Huang-Jie Jia
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Ling-Kang Bu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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Gao K, Li W, Gan E, Li J, Jiang L, Liu Y. Impacts of 10 Years of Elevated CO 2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field. MICROBIAL ECOLOGY 2023; 86:2386-2399. [PMID: 37247028 DOI: 10.1007/s00248-023-02248-0] [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: 03/21/2023] [Accepted: 05/20/2023] [Indexed: 05/30/2023]
Abstract
Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.
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Affiliation(s)
- Ke Gao
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Weijie Li
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Enze Gan
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Jiahui Li
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, 830011, People's Republic of China.
| | - Yuan Liu
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei, 235000, Anhui, People's Republic of China.
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Jia F, Chang F, Guan M, Jia Q, Sun Y, Li Z. Effects of rotation and Bacillus on the changes of continuous cropping soil fungal communities in American ginseng. World J Microbiol Biotechnol 2023; 39:354. [PMID: 37874395 PMCID: PMC10598105 DOI: 10.1007/s11274-023-03807-w] [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: 08/03/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023]
Abstract
The continuous cropping obstacle is the main factor in leading to difficulty in American ginseng replanting. The dormant microbiota in the soil may be the cause of American ginseng disease and eventually caused continuous cropping obstacles, but there are few studies on the dynamic changes of soil microenvironment after American ginseng planting. In this study, we tracked short-term variation in physicochemical properties, enzyme activities, and fungal communities over time-series in soils with continuous cropping obstacle under crop rotation and probiotic Bacillus treatments. Furthermore, we examined the relationships between the important fungal compositions and the soil properties. The results showed that sucrase, cellulase, urease and acid phosphatase activities were significantly increased, while catalase and dehydrogenase were decreased with treatments time. Rotation treatment significantly affected the diversity, dissimilarity degree and species distribution of soil fungal community with continuous cropping obstacle over a short-term. Moreover, beneficial fungal biomarkers such as Cladorrhinum, Oidiodendron, and Mariannaea were accumulated at 48 h under rotation treatments. Almost all fungal biomarkers were negatively correlated with hydrolases and positively correlated with oxidoreductases and acid phosphatase under crop rotation treatments. This study suggested that compared to probiotic Bacillus, crop rotation can significantly affect soil fungal community structure, especially the enrichment of specific potentially beneficial fungal species. Our findings provide a scientific basis for understanding the dynamic changes of fungal communities and soil properties with continuous cropping obstacle of American ginseng in initial stage of soil improvement.
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Affiliation(s)
- Fengan Jia
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Fan Chang
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Min Guan
- Shaanxi Agricultural Machinery Research Institute, Xianyang, 712000, China
| | - Qingan Jia
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yan Sun
- College of Life Science, Shaanxi Normal University, Xi'an, 710062, China
| | - Zhi Li
- College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
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Fang J, Shi G, Wei S, Ma J, Zhang X, Wang J, Chen L, Liu Y, Zhao X, Lu Z. Drought Sensitivity of Spring Wheat Cultivars Shapes Rhizosphere Microbial Community Patterns in Response to Drought. PLANTS (BASEL, SWITZERLAND) 2023; 12:3650. [PMID: 37896113 PMCID: PMC10609721 DOI: 10.3390/plants12203650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023]
Abstract
Drought is the most important natural disaster affecting crop growth and development. Crop rhizosphere microorganisms can affect crop growth and development, enhance the effective utilization of nutrients, and resist adversity and hazards. In this paper, six spring wheat varieties were used as research material in the dry farming area of the western foot of the Greater Khingan Mountains, and two kinds of water control treatments were carried out: dry shed rain prevention (DT) and regulated water replenishment (CK). Phenotypic traits, including physiological and biochemical indices, drought resistance gene expression, soil enzyme activity, soil nutrient content, and the responses of potential functional bacteria and fungi under drought stress, were systematically analyzed. The results showed that compared with the control (CK), the leaf wilting, drooping, and yellowing of six spring wheat varieties were enhanced under drought (DT) treatment. The plant height, fresh weight (FW), dry weight (DW), net photosynthetic rate (Pn) and stomatal conductance (Gs), soil total nitrogen (TN), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), microbial biomass phosphorus (MBP), organic carbon (SOC), and soil alkaline phosphatase (S-ALP) contents were significantly decreased, among which, FW, Gs and MBC decreased by more than 7.84%, 17.43% and 11.31%, respectively. By contrast, the soil total phosphorus (TP), total potassium (TK), and soil catalase (S-CAT) contents were significantly increased (p < 0.05). TaWdreb2 and TaBADHb genes were highly expressed in T.D40, T.L36, and T.L33 and were expressed at low levels in T.N2, T.B12, and T.F5. Among them, the relative expression of the TaWdreb2 gene in T.L36 was significantly increased by 2.683 times compared with CK. Soil TN and TP are the most sensitive to drought stress and can be used as the characteristic values of drought stress. Based on this, a drought-tolerant variety (T.L36) and a drought-sensitive variety (T.B12) were selected to further analyze the changes in rhizosphere microorganisms. Drought treatment and cultivar differences significantly affected the composition of the rhizosphere microbial community. Drought caused a decrease in the complexity of the rhizosphere microbial network, and the structure of bacteria was more complex than that of fungi. The Shannon index and network modular number of bacteria in these varieties (T.L36) increased, with rich small-world network properties. Actinobacteria, Chloroflexi, Firmicutes, Basidiomycota, and Ascomycota were the dominant bacteria under drought treatment. The beneficial bacteria Bacillus, Penicillium, and Blastococcus were enriched in the rhizosphere of T.L36. Brevibacillus and Glycomyce were enriched in the rhizosphere of T.B12. In general, drought can inhibit the growth and development of spring wheat, and spring wheat can resist drought hazards by regulating the expression of drought-related genes, regulating physiological metabolites, and enriching beneficial microorganisms.
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Affiliation(s)
- Jing Fang
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Gongfu Shi
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
| | - Shuli Wei
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Jianguo Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Liyu Chen
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Ying Liu
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
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Zecchin S, Wang J, Martin M, Romani M, Planer-Friedrich B, Cavalca L. Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speciation. FEMS Microbiol Ecol 2023; 99:fiad121. [PMID: 37804167 PMCID: PMC10630088 DOI: 10.1093/femsec/fiad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023] Open
Abstract
Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.
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Affiliation(s)
- Sarah Zecchin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milano-20133, Italy
| | - Jiajia Wang
- Environmental Geochemistry Group, Bayreuth Center for Ecology and Environmental Research (BAYCEER), Bayreuth University, 95440, Germany
| | - Maria Martin
- Department of Agriculture, Forest and Food Science, University of Turin, Turin-10095, Italy
| | - Marco Romani
- Rice Research Centre, Ente Nazionale Risi, Castello d'Agogna, Pavia-27030, Italy
| | - Britta Planer-Friedrich
- Environmental Geochemistry Group, Bayreuth Center for Ecology and Environmental Research (BAYCEER), Bayreuth University, 95440, Germany
| | - Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milano-20133, Italy
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Sun Z, Zhang W, Liu Y, Ding C, Zhu W. The Changes of Phyllosphere Fungal Communities among Three Different Populus spp. Microorganisms 2023; 11:2479. [PMID: 37894137 PMCID: PMC10609125 DOI: 10.3390/microorganisms11102479] [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: 08/28/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
As an ecological index for plants, the diversity and structure of phyllosphere microbial communities play a crucial role in maintaining ecosystem stability and balance; they can affect plant biogeography and ecosystem function by influencing host fitness and function. The phyllosphere microbial communities reflect the immigration, survival, and growth of microbial colonists, which are influenced by various environmental factors and leaves' physical and chemical properties. This study investigated the structure and diversity of phyllosphere fungal communities in three different Populus spp., namely-P. × euramaricana (BF3), P. nigra (N46), and P. alba × P. glandulosa (84K). Leaves' chemical properties were also analyzed to identify the dominant factors affecting the phyllosphere fungal communities. N46 exhibited the highest contents of total nitrogen (Nt), total phosphorus (Pt), soluble sugar, and starch. Additionally, there were significant variations in the abundance, diversity, and composition of phyllosphere fungal communities among the three species: N46 had the highest Chao1 index and observed_species, while 84K had the highest Pielou_e index and Simpson index. Ascomycota and Basidiomycota are the dominant fungal communities at the phylum level. Results from typical correlation analyses indicate that the chemical properties of leaves, especially total phosphorus (Pt), total nitrogen (Nt), and starch content, significantly impact the structure and diversity of the phyllosphere microbial community. However, it is worth noting that even under the same stand conditions, plants from different species have distinct leaf characteristics, proving that the identity of the host species is the critical factor affecting the structure of the phyllosphere fungal community.
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Affiliation(s)
- Zhuo Sun
- College of Forestry, Shenyang Agriculture University, Shenyang 110000, China; (Z.S.); (Y.L.)
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China;
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China;
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang 110000, China; (Z.S.); (Y.L.)
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling 110161, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China;
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang 110000, China; (Z.S.); (Y.L.)
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling 110161, China
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Feng H, Fu R, Luo J, Hou X, Gao K, Su L, Xu Y, Miao Y, Liu Y, Xu Z, Zhang N, Shen Q, Xun W, Zhang R. Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria. THE NEW PHYTOLOGIST 2023; 239:2307-2319. [PMID: 37357338 DOI: 10.1111/nph.19086] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 05/31/2023] [Indexed: 06/27/2023]
Abstract
Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.
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Affiliation(s)
- Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- College of Agriculture, Henan University, Zhengzhou, 450046, China
| | - Ruixin Fu
- School of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Jiayu Luo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueqin Hou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kun Gao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lv Su
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Xu
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Yuhua District, Shijiazhuang, 050021, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Wang Z, Liu J, Xu H, Liu J, Zhao Z, Gong X. Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China. Microorganisms 2023; 11:2144. [PMID: 37763988 PMCID: PMC10537389 DOI: 10.3390/microorganisms11092144] [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: 07/14/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.
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Affiliation(s)
- Zhaochun Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
| | - Haiyan Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhiwei Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China;
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (J.L.)
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Liu H, Li Y, Liang J, Nong D, Li Y, Huang Z. Evaluation of Gut Microbiota Stability and Flexibility as a Response to Seasonal Variation in the Wild François' Langurs (Trachypithecus francoisi) in Limestone Forest. Microbiol Spectr 2023; 11:e0509122. [PMID: 37404157 PMCID: PMC10433995 DOI: 10.1128/spectrum.05091-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/10/2023] [Indexed: 07/06/2023] Open
Abstract
The coevolution between gut microbiota and the host markedly influences the digestive strategies of animals to cope with changes in food sources. We have explored the compositional structure and seasonal variation in the gut microbiota of François' langur in a limestone forest in Guangxi, southwest China, using 16S rRNA sequencing. Our results demonstrated that Firmicutes and Bacteroidetes were the dominant phyla in langurs, followed by Oscillospiraceae, Christensenellaceae, and Lachnospiraceae at the family level. The top five dominant phyla did not show significant seasonal variations, and only 21 bacterial taxa differed at the family level, indicating stability in gut the microbiota possibly with respect to foraging for several dominant plants and high-leaf feeding by the langurs. Moreover, rainfall and minimum humidity are important factors affecting the gut microbiota of the langurs, but they explain few changes in bacterial taxa. The activity budget and thyroid hormone levels of the langurs did not differ significantly between seasons, indicating that these langurs did not respond to seasonal changes in food by regulating behavior or reducing metabolism. The present study indicates that the gut microbiota's structure is related to digestion and energy absorption of these langurs, providing new perspectives on their adaptation to limestone forests. IMPORTANCE François' langur is a primate that particularly lives in karst regions. The adaptation of wild animals to karst habitats has been a hot topic in behavioral ecology and conservation biology. In this study, gut microbiota, behavior, and thyroid hormone data were integrated to understand the interaction of the langurs and limestone forests from the physiological response, providing basic data for assessing the adaptation of the langurs to the habitats. The responses of the langurs to environmental changes were explored from the seasonal variations in gut microbiota, which would help to further understand the adaptive strategies of species to environmental changes.
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Affiliation(s)
- Hongying Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Jipeng Liang
- Administration Center of Guangxi Chongzuo White-Headed Langur National Nature Reserve, Chongzuo, China
| | - Dengpan Nong
- Administration Center of Guangxi Chongzuo White-Headed Langur National Nature Reserve, Chongzuo, China
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
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Liu C, Wu F, Jiang X, Hu Y, Shao K, Tang X, Qin B, Gao G. Climate Change Causes Salinity To Become Determinant in Shaping the Microeukaryotic Spatial Distribution among the Lakes of the Inner Mongolia-Xinjiang Plateau. Microbiol Spectr 2023; 11:e0317822. [PMID: 37306569 PMCID: PMC10434070 DOI: 10.1128/spectrum.03178-22] [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: 08/12/2022] [Accepted: 05/06/2023] [Indexed: 06/13/2023] Open
Abstract
Climate change greatly affects lake microorganisms in arid and semiarid zones, which alters ecosystem functions and the ecological security of lakes. However, the responses of lake microorganisms, especially microeukaryotes, to climate change are poorly understood. Here, using 18S ribosomal RNA (rRNA) high-throughput sequencing, we investigated the distribution patterns of microeukaryotic communities and whether and how climate change directly or indirectly affected the microeukaryotic communities on the Inner Mongolia-Xinjiang Plateau. Our results showed that climate change, as the main driving force of lake change, drives salinity to become a determinant of the microeukaryotic community among the lakes of the Inner Mongolia-Xinjiang Plateau. Salinity shapes the diversity and trophic level of the microeukaryotic community and further affects lake carbon cycling. Co-occurrence network analysis further revealed that increasing salinity reduced the complexity but improved the stability of microeukaryotic communities and changed ecological relationships. Meanwhile, increasing salinity enhanced the importance of deterministic processes in microeukaryotic community assembly, and the dominance of stochastic processes in freshwater lakes transformed into deterministic processes in salt lakes. Furthermore, we established lake biomonitoring and climate sentinel models by integrating microeukaryotic information, which would provide substantial improvements to our predictive ability of lake responses to climate change. IMPORTANCE Our findings have important implications for understanding the distribution patterns and the driving mechanisms of microeukaryotic communities among the lakes of the Inner Mongolia-Xinjiang Plateau and whether and how climate change directly or indirectly affects microeukaryotic communities. Our study also establishes the groundwork to use the lake microbiome for the assessment of aquatic ecological health and climate change, which is critical for ecosystem management and for projecting the ecological consequences of future climate warming.
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Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingyu Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Boqiang Qin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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Sun S, Li K, Du H, Luo J, Jiang Y, Wang J, Liu M, Liu G, Han S, Che H. Integrating Widely Targeted Lipidomics and Transcriptomics Unravels Aberrant Lipid Metabolism and Identifies Potential Biomarkers of Food Allergies in Rats. Mol Nutr Food Res 2023; 67:e2200365. [PMID: 37057506 DOI: 10.1002/mnfr.202200365] [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: 06/05/2022] [Revised: 01/17/2023] [Indexed: 04/15/2023]
Abstract
SCOPE Oral food challenges (OFCs) are currently the gold standard for determining the clinical reactivity of food allergy (FA) but are time-consuming, expensive, and risky. To screen novel peripheral biomarkers of FA and characterize the aberrant lipid metabolism in serum, 24 rats are divided into four groups: peanut, milk, and shrimp allergy (PA, MA, and SA, respectively) and control groups, with six rats in each group, and used for widely targeted lipidomics and transcriptomics analysis. METHODS AND RESULTS Widely targeted lipidomics reveal 144, 162, and 206 differentially accumulated lipids in PA, MA, and SA groups, respectively. The study integrates widely targeted lipidomics and transcriptomics and identifies abnormal lipid metabolism correlated with widespread differential accumulation of diverse lipids (including triacylglycerol, diacylglycerol, sphingolipid, and glycerophospholipid) in PA, MA, and SA. Simplified random forest classifier is constructed through five repetitions of 10-fold cross-validation to distinguish allergy from control. A subset of 15 lipids as potential biomarkers allows for more reliable and more accurate prediction of FA. Independent replication validates the reproducibility of potential biomarkers. CONCLUSION The results reveal the major abnormalities in lipid metabolism and suggest the potential role of lipids as novel molecular signatures for FA.
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Affiliation(s)
- Shanfeng Sun
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kexin Li
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hang Du
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jiangzuo Luo
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yuchi Jiang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Junjuan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Manman Liu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guirong Liu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Shiwen Han
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Huilian Che
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, The 2115 Talent Development Program of China Agricultural University College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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Dong H, Sun H, Chen C, Zhang M, Ma D. Compositional Shifts and Assembly in Rhizosphere-Associated Fungal Microbiota Throughout the Life Cycle of Japonica Rice Under Increased Nitrogen Fertilization. RICE (NEW YORK, N.Y.) 2023; 16:34. [PMID: 37526797 PMCID: PMC10393908 DOI: 10.1186/s12284-023-00651-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Soil fungal microbiomes facilitate a range of beneficial functions for their host plants, and rhizosphere fungal community composition, richness, and diversity affect plant growth and development, and crop yield. Therefore, exploring the community structure and assembly of the rhizosphere fungal microbiome and its relationship with soil biochemical properties are fundamental to elucidating how rice plants benefit from their fungal symbionts. In this study, soil samples were collected at seedling, tillering, heading, and ripening stages of rice subjected to three levels of nitrogen fertilization. Plant growth demonstrates a substantial influence on fungal community composition and diversity. From the tillering to the ripening stage, the fungal communities were governed by homogenizing dispersal and dispersal limitation. The prevalence of Glomeromycota, the beneficial fungi, was considerably higher during the heading stage compared to the three other growth stages. This increase in abundance was strongly associated with increased levels of soil nutrients and enhanced activity of nitrogen acquisition enzymes. This may be a strategy developed by rice grown in flooded soil to recruit beneficial fungi in the rhizosphere to meet high nitrogen demands. Our study findings contribute to elucidating the influence of plant development and nitrogen fertilization on the structure and composition of the fungal community as well as its relationship with soil key soil nutrient content and nitrogen-related enzyme activities. They also illustrate how a shift in the fungal community mediates and reflects the effects of nitrogen fertilization input in rice agroecosystems. These findings provide new insights into the effects of changes in nitrogen application in rice rhizosphere at different growth stages on fungal communities and soil biochemical characteristics.
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Affiliation(s)
- Hangyu Dong
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Haoyuan Sun
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Conglin Chen
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Mingyu Zhang
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Agronomy College, Liaodong University, Dandong, China.
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Hu S, He R, He X, Zeng J, Zhao D. Niche-Specific Restructuring of Bacterial Communities Associated with Submerged Macrophyte under Ammonium Stress. Appl Environ Microbiol 2023; 89:e0071723. [PMID: 37404156 PMCID: PMC10370296 DOI: 10.1128/aem.00717-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023] Open
Abstract
Submerged macrophytes and their epiphytic microbes form a "holobiont" that plays crucial roles in regulating the biogeochemical cycles of aquatic ecosystems but is sensitive to environmental disturbances such as ammonium loadings. Increasingly more studies suggest that plants may actively seek help from surrounding microbial communities whereby conferring benefits in responding to particular abiotic stresses. However, empirical evidence is scarce regarding how aquatic plants reconstruct their microbiomes as a "cry-for-help" against acute ammonium stress. Here, we investigated the temporal dynamics of the phyllosphere and rhizosphere bacterial communities of Vallisneria natans following ammonium stress and recovery periods. The bacterial community diversity of different plant niches exhibited opposite patterns with ammonium stress, that is, decreasing in the phyllosphere while increasing in the rhizosphere. Furthermore, both phyllosphere and rhizosphere bacterial communities underwent large compositional changes at the end of ammonium stress, significantly enriching of several nitrifiers and denitrifiers. Meanwhile, bacterial legacies wrought by ammonium stress were detected for weeks; some plant growth-promoting and stress-relieving bacteria remained enriched even after stress disappeared. Structural equation model analysis showed that the reshaped bacterial communities in plant niches collectively had a positive effect on maintaining plant biomass. Additionally, we applied an age-prediction model to predict the bacterial community's successional trajectory, and the results revealed a persistent change in bacterial community development under ammonium treatment. Our findings highlight the importance of plant-microbe interactions in mitigating plant stress and fostering a better understanding of the assembly of plant-beneficial microbes under ammonium stress in aquatic ecosystems. IMPORTANCE Increasing anthropogenic input of ammonium is accelerating the decline of submerged macrophytes in aquatic ecosystems. Finding efficient ways to release submerged macrophytes from ammonium stress is crucial to maintain their ecological benefits. Microbial symbioses can alleviate abiotic stress in plants, but harnessing these beneficial interactions requires a detailed understanding of plant microbiome responses to ammonium stress, especially over a continuous time course. Here, we tracked the temporal changes in bacterial communities associated with the phyllosphere and rhizosphere of Vallisneria natans during ammonium stress and recovery periods. Our results showed that severe ammonium stress triggers a plant-driven timely reshaping of the associated bacterial community in a niche-specific strategy. The reassembled bacterial communities could potentially benefit the plant by positively contributing to nitrogen transformation and plant growth promotion. These findings provide empirical evidence regarding the adaptive strategy of aquatic plants whereby they recruit beneficial microbes against ammonium stress.
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Affiliation(s)
- Siwen Hu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaowei He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
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Sun P, Wang M, Liu YX, Li L, Chai X, Zheng W, Chen S, Zhu X, Zhao S. High-fat diet-disturbed gut microbiota-colonocyte interactions contribute to dysregulating peripheral tryptophan-kynurenine metabolism. MICROBIOME 2023; 11:154. [PMID: 37468922 PMCID: PMC10355067 DOI: 10.1186/s40168-023-01606-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Aberrant tryptophan (Trp)-kynurenine (Kyn) metabolism has been implicated in the pathogenesis of human disease. In particular, populations with long-term western-style diets are characterized by an excess of Kyn in the plasma. Host-gut microbiota interactions are dominated by diet and are essential for maintaining host metabolic homeostasis. However, the role of western diet-disturbed gut microbiota-colonocyte interactions in Trp metabolism remains to be elucidated. RESULTS Here, 4-week-old mice were fed with a high-fat diet (HFD), representing a typical western diet, for 4 weeks, and multi-omics approaches were adopted to determine the mechanism by which HFD disrupted gut microbiota-colonocyte interplay causing serum Trp-Kyn metabolism dysfunction. Our results showed that colonocyte-microbiota interactions dominated the peripheral Kyn pathway in HFD mice. Mechanistically, persistent HFD-impaired mitochondrial bioenergetics increased colonic epithelial oxygenation and caused metabolic reprogramming in colonites to support the expansion of Proteobacteria in the colon lumen. Phylum Proteobacteria-derived lipopolysaccharide (LPS) stimulated colonic immune responses to upregulate the indoleamine 2,3-dioxygenase 1 (IDO1)-mediated Kyn pathway, leading to Trp depletion and Kyn accumulation in the circulation, which was further confirmed by transplantation of Escherichia coli (E.coli) indicator strains and colonic IDO1 depletion. Butyrate supplementation promoted mitochondrial functions in colonocytes to remodel the gut microbiota in HFD mice, consequently ameliorating serum Kyn accumulation. CONCLUSIONS Our results highlighted that HFD disrupted the peripheral Kyn pathway in a gut microbiota-dependent manner and that the continuous homeostasis of gut bacteria-colonocytes interplay played a central role in the regulation of host peripheral Trp metabolism. Meanwhile, this study provided new insights into therapies against western diet-related metabolic disorders. Video Abstract.
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Affiliation(s)
- Penghao Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mengli Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yong-Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
| | - Luqi Li
- Life Science Research Core Services, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xuejun Chai
- College of Basic Medicine, Xi'an Medical University, Xi'an, 710000, Shaanxi, China.
| | - Wei Zheng
- College of Resources and Environment Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shulin Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoyan Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Shanting Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Dong M, Shi L, Xie Z, Lian L, Zhang J, Jiang Z, Wu C. Shifts in the diversity of root endophytic microorganisms across the life cycle of the ratooning rice Jiafuzhan. Front Microbiol 2023; 14:1161263. [PMID: 37455730 PMCID: PMC10348713 DOI: 10.3389/fmicb.2023.1161263] [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: 02/08/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The diversity of root endophytic microorganisms, which is closely related to plant life activities, is known to vary with the plant growth stage. This study on the ratooning rice Jiafuzhan explored the diversity of the root endophytic bacteria and fungi and their dynamics during the plant life cycle. By sequencing the 16S ribosomal ribonucleic acid (16S rRNA) and internal transcribed spacer (ITS) genes, 12,154 operational taxonomic units (OTUs) and 497 amplicon sequence variants (ASVs) were obtained, respectively. The root endophytic microorganisms of rice in the seedling, tillering, jointing, heading, and mature stages of the first crop and at 13, 25, and 60 days after regeneration (at the heading, full heading, and mature stages of the second crop, respectively) were analyzed using diversity and correlation analyses. There were significant differences in the α-diversity and β-diversity of root endophytic bacteria and fungi in the growth stage. Additionally, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed biomarker bacteria for each growth stage, but biomarker fungi did not exist in every stage. Moreover, the correlation analysis showed that the bacterial and fungal biomarkers interacted with each other. Furthermore, the nitrogen-fixing genus Bradyrhizobium existed in all growth stages. These findings indicate the pattern of root endophytic microorganisms of ratooning rice at different growth stages, and they provide new insights into the high yield of the second crop of ratooning rice (in light of the abundance of various bacteria and fungi).
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Wang X, Zhang G, Ding A, Zheng L, Xie E, Yuan D, Tan Q, Xing Y, Wu H. Nitrite-resistance mechanisms on wastewater treatment in denitrifying phosphorus removal process revealed by machine learning, co-occurrence, and metagenomics analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121549. [PMID: 37019260 DOI: 10.1016/j.envpol.2023.121549] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/02/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Nitrite is a key intermediate in nitrogen metabolism that determines microbial transformations of N and P, greenhouse gas (N2O) emissions, and system nutrient removal efficiency. However, nitrite also exerts toxic effects on microorganisms. A lack of understanding of high nitrite-resistance mechanisms at community- and genome-scale resolutions hinders the optimization for robustness of wastewater treatment systems. Here, we established nitrite-dependent denitrifying and phosphorus removal (DPR) systems under a gradient concentration of nitrite (0, 5, 10, 15, 20, and 25 mg N/L), relying on 16S rRNA gene amplicon and metagenomics to explore high nitrite-resistance mechanism. The results demonstrated that specific taxa were adopted to change the metabolic relationship of the community through phenotypic evolution to resist toxic nitrite contributing to the enhancement of denitrification and inhibition of nitrification and phosphorus removal. The key specific species, Thauera enhanced denitrification, whereas Candidatus Nitrotoga decreased in abundance to maintain partial nitrification. The extinction of Candidatus Nitrotoga induced a simpler restructuring-community, forcing high nitrite-stimulating microbiome to establish a more focused denitrification rather than nitrification or P metabolism in response to nitrite toxicity. Our work provides insights for understanding microbiome adaptation to toxic nitrite and giving theoretical support for operation strategy of nitrite-based wastewater treatment technology.
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Affiliation(s)
- Xue Wang
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guoyu Zhang
- Department of Environmental Engineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083, China
| | - Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Qiuyang Tan
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yuzi Xing
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Haoming Wu
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
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Hereira-Pacheco SE, Estrada-Torres A, Dendooven L, Navarro-Noya YE. Shifts in root-associated fungal communities under drought conditions in Ricinus communis. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Li Y, Kong F, Li S, Wang J, Hu J, Chen S, Chen Q, Li Y, Ha X, Sun W. Insights into the driving factors of vertical distribution of antibiotic resistance genes in long-term fertilized soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131706. [PMID: 37247491 DOI: 10.1016/j.jhazmat.2023.131706] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs) in soils has aroused wide attention. However, the influence of long-term fertilization on the distribution of ARGs in different soil layers and its dominant drivers remain largely unknown. In this study, a total of 203 ARGs were analyzed in greenhouse vegetable soils (0-100 cm from a 13-year field experiment applied with different fertilizers (control, chemical fertilizer, organic manure, and mixed fertilizer). Compared with unfertilized and chemically fertilized soils, manure application significantly increased the abundance and alpha diversity of soil ARGs, where the assembly of ARG communities was strongly driven by stochastic processes. The distribution of ARGs was significantly driven by manure application within 60 cm, while it was insignificantly changed in soil below 60 cm under different fertilization regimes. The inter-correlations of ARGs with mobile genetic elements (MGEs) and microbiota were strengthened in manured soil, indicating manure application posed a higher risk for ARGs diffusion in subsurface soil. Bacteria abundance and MGEs directly influenced ARG abundance and composition, whereas soil depth and manure application indirectly influenced ARG abundance and composition by affecting antibiotics. These results strengthen our understanding of the long-term anthropogenic influence on the vertical distribution of soil ARGs and highlight the ecological risk of ARGs in subsurface soil induced by long-term manure application.
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Affiliation(s)
- Ying Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Fanguang Kong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Si Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Yantai Institute of China Agricultural University, Yantai 264670, China.
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jingrun Hu
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Shuo Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yanming Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xuejiao Ha
- Planting Technology Promotion Station of Daxing District, Beijing 102600, China
| | - Weiling Sun
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
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Dondjou DT, Diedhiou AG, Mbodj D, Mofini MT, Pignoly S, Ndiaye C, Diedhiou I, Assigbetse K, Manneh B, Laplaze L, Kane A. Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem. ENVIRONMENTAL MICROBIOME 2023; 18:42. [PMID: 37198640 PMCID: PMC10193678 DOI: 10.1186/s40793-023-00500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta. RESULTS We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages. CONCLUSIONS Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.
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Affiliation(s)
- Donald Tchouomo Dondjou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Abdala Gamby Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Daouda Mbodj
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Marie-Thérèse Mofini
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Sarah Pignoly
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Issa Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Komi Assigbetse
- Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L’Ouest (IESOL), Dakar, Sénégal
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Baboucarr Manneh
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Laurent Laplaze
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Aboubacry Kane
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain « Environnement, Sociétés » (CEA-AGIR), UCAD, Santé, Dakar, Sénégal
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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Zhao L, Walkowiak S, Fernando WGD. Artificial Intelligence: A Promising Tool in Exploring the Phytomicrobiome in Managing Disease and Promoting Plant Health. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091852. [PMID: 37176910 PMCID: PMC10180744 DOI: 10.3390/plants12091852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
There is increasing interest in harnessing the microbiome to improve cropping systems. With the availability of high-throughput and low-cost sequencing technologies, gathering microbiome data is becoming more routine. However, the analysis of microbiome data is challenged by the size and complexity of the data, and the incomplete nature of many microbiome databases. Further, to bring microbiome data value, it often needs to be analyzed in conjunction with other complex data that impact on crop health and disease management, such as plant genotype and environmental factors. Artificial intelligence (AI), boosted through deep learning (DL), has achieved significant breakthroughs and is a powerful tool for managing large complex datasets such as the interplay between the microbiome, crop plants, and their environment. In this review, we aim to provide readers with a brief introduction to AI techniques, and we introduce how AI has been applied to areas of microbiome sequencing taxonomy, the functional annotation for microbiome sequences, associating the microbiome community with host traits, designing synthetic communities, genomic selection, field phenotyping, and disease forecasting. At the end of this review, we proposed further efforts that are required to fully exploit the power of AI in studying phytomicrobiomes.
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Affiliation(s)
- Liang Zhao
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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