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Li F, Sun A, Jiao X, Yu DT, Ren P, Wu BX, He P, Bi L, He JZ, Hu HW. Nitrogenous fertilizer plays a more important role than cultivars in shaping sorghum-associated microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173831. [PMID: 38866152 DOI: 10.1016/j.scitotenv.2024.173831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
The plant microbiome plays a crucial role in facilitating plant growth through enhancing nutrient cycling, acquisition and transport, as well as alleviating stresses induced by nutrient limitations. Despite its significance, the relative importance of common agronomic practices, such as nitrogenous fertilizer, in shaping the plant microbiome across different cultivars remains unclear. This study investigated the dynamics of bacterial and fungal communities in leaf, root, rhizosphere, and bulk soil in response to nitrogenous fertilizer across ten sorghum varieties, using 16S rRNA and ITS gene amplicon sequencing, respectively. Our results revealed that nitrogen addition had a greater impact on sorghum-associated microbial communities compared to cultivar. Nitrogen addition significantly reduced bacterial diversity in all compartments except for the root endophytes. However, N addition significantly increased fungal diversity in both rhizosphere and bulk soils, while significantly reducing fungal diversity in the root endophytes. Furthermore, N addition significantly altered the community composition of bacteria and fungi in all four compartments, while cultivars only affected the community composition of root endosphere bacteria and fungi. Network analysis revealed that fertilization significantly reduced microbial network complexity and increased fungal-related network complexity. Collectively, this study provides empirical evidence that sorghum-associated microbiomes are predominantly shaped by nitrogenous fertilizer rather than by cultivars, suggesting that consistent application of nitrogenous fertilizer will ultimately alter plant-associated microbiomes regardless of cultivar selection.
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Affiliation(s)
- Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaoyan Jiao
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Dan-Ting Yu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China.
| | - Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Bing-Xue Wu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Peng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Li Bi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Przybylska MS, Violle C, Vile D, Scheepens JF, Munoz F, Tenllado Á, Vinyeta M, Le Roux X, Vasseur F. Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana. THE NEW PHYTOLOGIST 2024; 243:620-635. [PMID: 38812269 DOI: 10.1111/nph.19870] [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: 12/26/2023] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.
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Affiliation(s)
- Maria Stefania Przybylska
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
| | - J F Scheepens
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - François Munoz
- LiPhy, Université Grenoble-Alpes, 38041, Grenoble, France
| | - Álvaro Tenllado
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - Mariona Vinyeta
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Xavier Le Roux
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
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Ortúzar M, Riesco R, Criado M, Alonso MDP, Trujillo ME. Unraveling the dynamic interplay of microbial communities associated to Lupinus angustifolius in response to environmental and cultivation conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174277. [PMID: 38944300 DOI: 10.1016/j.scitotenv.2024.174277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.
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Affiliation(s)
- Maite Ortúzar
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Marco Criado
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - María Del Pilar Alonso
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
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Guan Y, Bak F, Hennessy RC, Horn Herms C, Elberg CL, Dresbøll DB, Winding A, Sapkota R, Nicolaisen MH. The potential of Pseudomonas fluorescens SBW25 to produce viscosin enhances wheat root colonization and shapes root-associated microbial communities in a plant genotype-dependent manner in soil systems. mSphere 2024:e0029424. [PMID: 38904362 DOI: 10.1128/msphere.00294-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Microorganisms interact with plant roots through colonization of the root surface, i.e., the rhizoplane or the surrounding soil, i.e., the rhizosphere. Beneficial rhizosphere bacteria such as Pseudomonas spp. can promote plant growth and protect against pathogens by producing a range of bioactive compounds, including specialized metabolites like cyclic lipopeptides (CLPs) known for their biosurfactant and antimicrobial activities. However, the role of CLPs in natural soil systems during bacteria-plant interactions is underexplored. Here, Pseudomonas fluorescens SBW25, producing the CLP viscosin, was used to study the impact of viscosin on bacterial root colonization and microbiome assembly in two cultivars of winter wheat (Heerup and Sheriff). We inoculated germinated wheat seeds with SBW25 wild type or a viscosin-deficient mutant and grew the plants in agricultural soil. After 2 weeks, enhanced root colonization of SBW25 wild type compared to the viscosin-deficient mutant was observed, while no differences were observed between wheat cultivars. In contrast, the impact on root-associated microbial community structure was plant-genotype-specific, and SBW25 wild type specifically reduced the relative abundance of an unclassified oomycete and Phytophthora in Sheriff and Heerup, respectively. This study provides new insights into the natural role of viscosin and specifically highlights the importance of viscosin in wheat root colonization under natural soil conditions and in shaping the root microbial communities associated with different wheat cultivars. Furthermore, it pinpoints the significance of microbial microdiversity, plant genotype, and microbe-microbe interactions when studying colonization of plant roots. IMPORTANCE Understanding parameters governing microbiome assembly on plant roots is critical for successfully exploiting beneficial plant-microbe interactions for improved plant growth under low-input conditions. While it is well-known from in vitro studies that specialized metabolites are important for plant-microbe interactions, e.g., root colonization, studies on the ecological role under natural soil conditions are limited. This might explain the often-low translational power from laboratory testing to field performance of microbial inoculants. Here, we showed that viscosin synthesis potential results in a differential impact on the microbiome assembly dependent on wheat cultivar, unlinked to colonization potential. Overall, our study provides novel insights into factors governing microbial assembly on plant roots, and how this has a derived but differential effect on the bacterial and protist communities.
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Affiliation(s)
- Ying Guan
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Frederik Bak
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Courtney Horn Herms
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Dorte Bodin Dresbøll
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Anne Winding
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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Jin X, Jia H, Ran L, Wu F, Liu J, Schlaeppi K, Dini-Andreote F, Wei Z, Zhou X. Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates. Nat Commun 2024; 15:5125. [PMID: 38879580 PMCID: PMC11180119 DOI: 10.1038/s41467-024-49218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/27/2024] [Indexed: 06/19/2024] Open
Abstract
The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.
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Affiliation(s)
- Xue Jin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Huiting Jia
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Lingyi Ran
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China.
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6
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Wei F, Feng Z, Yang C, Zhao L, Zhang Y, Zhou J, Feng H, Zhu H, Xu X. Genetic control of rhizosphere microbiome of the cotton plants under field conditions. Appl Microbiol Biotechnol 2024; 108:371. [PMID: 38861165 PMCID: PMC11166756 DOI: 10.1007/s00253-024-13143-0] [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: 12/08/2023] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 06/12/2024]
Abstract
Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray-Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. KEY POINTS: • F2 offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses.
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Affiliation(s)
- Feng Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zili Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Chuanzhen Yang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yalin Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Jinglong Zhou
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hongjie Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Heqin Zhu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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7
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Boyle JA, Frederickson ME, Stinchcombe JR. Genetic architecture of heritable leaf microbes. Microbiol Spectr 2024:e0061024. [PMID: 38842309 DOI: 10.1128/spectrum.00610-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown yet fundamental to the community assembly of host-associated microbiomes, with implications for the eco-evolutionary dynamics of microbes and hosts. Using Ipomoea hederacea, ivyleaf morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome and how these two sources of genetic variation contributed to microbe heritability. We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation contribute to microbe heritability and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect Mendelian locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some phyllosphere microbes.IMPORTANCEWe investigated how host genetic variation affects the assembly of Ipomoea hederacea's natural microbiome. We found that the genetic architecture of leaf-associated microbiomes involves both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. The existence of Mendelian and quantitative genetic variation for host-associated microbes means that plant evolution at the leaf shape locus or other quantitative genetic loci has the potential to shape microbial abundance and community composition.
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Affiliation(s)
- Julia A Boyle
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Swedish Collegium for Advanced Study, Uppsala, Sweden
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Xun W, Liu Y, Ma A, Yan H, Miao Y, Shao J, Zhang N, Xu Z, Shen Q, Zhang R. Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture. THE NEW PHYTOLOGIST 2024; 242:2401-2410. [PMID: 38494698 DOI: 10.1111/nph.19697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.
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Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, 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
| | - Aiyuan Ma
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - He Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, 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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9
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Zai X, Cordovez V, Zhu F, Zhao M, Diao X, Zhang F, Raaijmakers JM, Song C. C4 cereal and biofuel crop microbiomes. Trends Microbiol 2024:S0966-842X(24)00093-3. [PMID: 38772810 DOI: 10.1016/j.tim.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.
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Affiliation(s)
- Xiaoyu Zai
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China.
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10
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Ishaq HM, Yasin R, Mohammad IS, Fan Y, Li H, Shahzad M, Xu J. The gut-brain-axis: A positive relationship between gut microbial dysbiosis and glioblastoma brain tumour. Heliyon 2024; 10:e30494. [PMID: 38756585 PMCID: PMC11096965 DOI: 10.1016/j.heliyon.2024.e30494] [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: 12/28/2023] [Revised: 04/28/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
The glioblastoma brain tumour (GBM) stands out as the most aggressive and resistant-to-treatment malignancy. Nevertheless, the gut-brain connection plays a pivotal role in influencing the growth and activation of the central nervous system. In this particular investigation, we aimed to assess and characterize the gut microbial ecosystem in GBM patients, both quantitatively and qualitatively. We collected faecal samples from 15 healthy volunteers and 25 GBM patients. To delve into the microbial content, we employed PCR-DGGE, targeting the V3 region of the 16S rRNA gene, and conducted qPCR to measure the levels of crucial intestinal bacteria. For a more in-depth analysis, high-throughput sequencing was performed on a selection of 20 random faecal samples (10 from healthy individuals and 10 from GBM patients), targeting the V3+V4 region of the 16S rRNA gene. Our findings from examining the richness and diversity of the gut microbiota unveiled that GBM patients exhibited significantly higher microbial diversity compared to healthy individuals. At the phylum level, Proteobacteria saw a significant increase, while Firmicutes experienced a noteworthy decrease in the GBM group. Moving down to the family level, we observed significantly elevated levels of Enterobacteriaceae, Bacteroidaceae, and Lachnospiraceae in GBM patients, while levels of Veillonellaceae, Rikenellaceae, and Prevotellaceae were notably lower. Delving into genera statistics, we noted a substantial increase in the abundance of Parasutterella, Escherichia-Shigella, and Bacteroides, alongside significantly lower levels of Ruminococcus 2, Faecalibacterium, and Prevotella_9 in the GBM group compared to the control group. Furthermore, when examining specific species, we found a significant increase in Bacteroides vulgatus and Escherichia coli in the GBM group. These observations collectively indicate a marked dysbiosis in the gut microbial composition of GBM patients. Additionally, the GBM group exhibited notably higher levels of alpha diversity when compared to the control group. This increase in diversity suggests a significant bacterial overgrowth in the gut of GBM patients in contrast to the controls. As a result, this research opens up potential avenues to gain a better understanding of the underlying mechanisms, pathways, and potential treatments for GBM, stemming from the significant implications of gut microbial dysbiosis in these patients.
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Affiliation(s)
- Hafiz Muhammad Ishaq
- Department of Microbiology and Immunology, Key Laboratory of Environment and Genes Related to Diseases of Chinese Ministry of Education, School of Medicine, Xi'an Jiaotong University, Xi'an, China
- Department of Pathobiology and Biomedical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture Multan, Pakistan
| | - Riffat Yasin
- Department of Zoology University of Education Lahore, D.G. Khan Campus, Pakistan
| | - Imran Shair Mohammad
- Department of Radiology, City of Hope National Medical Center, 1500 East Duarte Rd., Duarte, CA, 91010, USA
| | - Yang Fan
- Department of Microbiology, School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Huan Li
- Xi'an Mental Health Centre, Xi'an, China
| | - Muhammad Shahzad
- Department of Pharmacology, University of Health Sciences, Khyaban-e-Jamia Punjab, Lahore, Pakistan
| | - Jiru Xu
- Department of Microbiology and Immunology, Key Laboratory of Environment and Genes Related to Diseases of Chinese Ministry of Education, School of Medicine, Xi'an Jiaotong University, Xi'an, China
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11
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Huang Q, Zhang Y, Tan Y, Kong H, Cao Y, Wang J, Yin G, Guo A. Bt-Modified Transgenic Rice May Shift the Composition and Diversity of Rhizosphere Microbiota. PLANTS (BASEL, SWITZERLAND) 2024; 13:1300. [PMID: 38794371 PMCID: PMC11125220 DOI: 10.3390/plants13101300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/21/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
Plants significantly shape root-associated microbiota, making rhizosphere microbes useful environmental indicator organisms for safety assessment. Here, we report the pyrosequencing of the bacterial 16S ribosomal RNA in rhizosphere soil samples collected from transgenic cry1Ab/cry1Ac Bt rice Huahui No. 1 (GM crop) and its parental counterpart, Minghui63. We identified a total of 2579 quantifiable bacterial operational taxonomic units (OTUs). Many treatment-enriched microbial OTUs were identified, including 14 NonGM-enriched OTUs and 10 GM-enriched OTUs. OTUs belonging to the phyla Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Nitrospirae, Chlorobi and GN04 were identified as statistically different in abundance between GM and the other two treatments. Compared with the different impacts of different rice varieties on microbiota, the impact of rice planting on microbiota is more obvious. Furthermore, Huahui No. 1 transgenic Bt rice had a greater impact on the rhizosphere bacterial communities than Minghui63. Early developmental stages of the transgenic Bt rice had a significant impact on many Bacillaceae communities. Soil chemical properties were not significantly altered by the presence of transgenic Bt rice. The peak concentration level of Bt protein products was detected during the seedling stage of transgenic Bt rice, which may be an intriguing factor for bacterial diversity variations. Based on these findings, we conclude that transgenic Bt rice has a significant impact on root-associated bacteria. This information may be leveraged in future environmental safety assessments of transgenic Bt rice varieties.
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Affiliation(s)
- Qixing Huang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Yuliang Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Yanhua Tan
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Hua Kong
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Yang Cao
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Jungang Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Guohua Yin
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan 250200, China
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Anping Guo
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
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12
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Hirpara KR, Hinsu AT, Kothari RK. Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India. Sci Rep 2024; 14:10525. [PMID: 38720057 PMCID: PMC11079051 DOI: 10.1038/s41598-024-61343-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/05/2024] [Indexed: 05/12/2024] Open
Abstract
The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.
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Affiliation(s)
- Krunal R Hirpara
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
| | - Ankit T Hinsu
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India
- Royal Veterinary College, London, AL9 7TA, UK
| | - Ramesh K Kothari
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India.
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13
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Liu Z, Zhang J, Fan C, Sun S, An X, Sun Y, Gao T, Zhang D. Influence of Bacillus subtilis strain Z-14 on microbial ecology of cucumber rhizospheric vermiculite infested with fusarium oxysporum f. sp. cucumerinum. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105875. [PMID: 38685217 DOI: 10.1016/j.pestbp.2024.105875] [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: 02/02/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
Fusarium oxysporum (FO) is a typical soil-borne pathogenic fungus, and the cucumber wilt disease caused by F. oxysporum f. sp. cucumerinum (FOC) seriously affects crop yield and quality. Vermiculite is increasingly being used as a culture substrate; nevertheless, studies exploring the effectiveness and mechanisms of biocontrol bacteria in this substrate are limited. In this study, vermiculite was used as a culture substrate to investigate the control effect of Bacillus subtilis strain Z-14 on cucumber wilt and the rhizospheric microecology, focusing on colonization ability, soil microbial diversity, and rhizosphere metabolome. Pot experiments showed that Z-14 effectively colonized the cucumber roots, achieving a controlled efficacy of 61.32% for wilt disease. It significantly increased the abundance of Bacillus and the expression of NRPS and PKS genes, while reducing the abundance of FO in the rhizosphere. Microbial diversity sequencing showed that Z-14 reduced the richness and diversity of the rhizosphere bacterial community, increased the richness and diversity of the fungal community, and alleviated the effect of FO on the community structure of the cucumber rhizosphere. The metabolomics analysis revealed that Z-14 affected ABC transporters, amino acid synthesis, and the biosynthesis of plant secondary metabolites. Additionally, Z-14 increased the contents of phenylacetic acid, capsidol, and quinolinic acid, all of which were related to the antagonistic activity in the rhizosphere. Z-14 exhibited a significant control effect on cucumber wilt and influenced the microflora and metabolites in rhizospheric vermiculite, providing a theoretical basis for further understanding the control effect and mechanism of cucumber wilt in different culture substrates.
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Affiliation(s)
- Zhaosha Liu
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Jizong Zhang
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Chenxi Fan
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Shangyi Sun
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Xutong An
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Yanheng Sun
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Tongguo Gao
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Dongdong Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China.
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14
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Wen Z, Yang M, Fazal A, Han H, Lin H, Yin T, Zhu Y, Yang S, Niu K, Sun S, Qi J, Lu G, Yang Y. Harnessing the power of microbes: Enhancing soybean growth in an acidic soil through AMF inoculation rather than P-fertilization. HORTICULTURE RESEARCH 2024; 11:uhae067. [PMID: 38725460 PMCID: PMC11079484 DOI: 10.1093/hr/uhae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/23/2024] [Indexed: 05/12/2024]
Abstract
The low phosphorus (P) availability of acidic soils severely limits leguminous plant growth and productivity. Improving the soil P nutritional status can be achieved by increasing the P-content through P-fertilization or stimulating the mineralization of organic P via arbuscular mycorrhizal fungi (AMF) application; however, their corresponding impacts on plant and soil microbiome still remain to be explored. Here, we examined the effects of AMF-inoculation and P-fertilization on the growth of soybean with different P-efficiencies, as well as the composition of rhizo-microbiome in an acidic soil. The growth of recipient soybean NY-1001, which has a lower P-efficiency, was not significantly enhanced by AMF-inoculation or P-fertilization. However, the plant biomass of higher P-efficiency transgenic soybean PT6 was significantly increased by 46.74%-65.22% through AMF-inoculation. Although there was no discernible difference in plant biomass between PT6 and NY-1001 in the absence of AMF-inoculation and P-fertilization, PT6 had approximately 1.9-2.5 times the plant biomass of NY-1001 after AMF-inoculation. Therefore, the growth advantage of higher P-efficiency soybean was achieved through the assistance of AMF rather than P-fertilization in available P-deficient acidic soil. Most nitrogen (N)-fixing bacteria and some functional genes related to N-fixation were abundant in endospheric layer, as were the P-solubilizing Pseudomonas plecoglossicida, and annotated P-metabolism genes. These N-fixing and P-solubilizing bacteria were positive correlated with each other. Lastly, the two most abundant phytopathogenic fungi species accumulated in endospheric layer, they exhibited positive correlations with N-fixing bacteria, but displayed negative interactions with the majority of the other dominant non-pathogenic genera with potential antagonistic activity.
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Affiliation(s)
- Zhongling Wen
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Minkai Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Aliya Fazal
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hongwei Han
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- School of Life Sciences and Chemical Engineering, Jiangsu Second Normal University, Nanjing 210013, China
| | - Hongyan Lin
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuelin Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shouping Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kechang Niu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Shucun Sun
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jinliang Qi
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Guihua Lu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an 223300, China
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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15
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Bamba M, Akyol TY, Azuma Y, Quilbe J, Andersen SU, Sato S. Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus. FEMS Microbiol Ecol 2024; 100:fiae056. [PMID: 38678008 PMCID: PMC11068475 DOI: 10.1093/femsec/fiae056] [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: 10/25/2022] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach, which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.
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Affiliation(s)
- Masaru Bamba
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Yusuke Azuma
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Johan Quilbe
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
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16
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Li X, Zheng X, Yadav N, Saha S, Salama ES, Li X, Wang L, Jeon BH. Rational management of the plant microbiome for the Second Green Revolution. PLANT COMMUNICATIONS 2024; 5:100812. [PMID: 38213028 PMCID: PMC11009158 DOI: 10.1016/j.xplc.2024.100812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/06/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.
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Affiliation(s)
- Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Nikita Yadav
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Hermantown, MN 55811, USA; Department of Biotechnology, Brainware University, Barasat, Kolkata 700125, West Bengal, India
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea.
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17
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Qiang W, Gunina A, Kuzyakov Y, Liu Q, Pang X. Decoupled response of microbial taxa and functions to nutrients: The role of stoichiometry in plantations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120574. [PMID: 38520862 DOI: 10.1016/j.jenvman.2024.120574] [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: 10/26/2023] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
The resource quantity and elemental stoichiometry play pivotal roles in shaping belowground biodiversity. However, a significant knowledge gap remains regarding the influence of different plant communities established through monoculture plantations on soil fungi and bacteria's taxonomic and functional dynamics. This study aimed to elucidate the mechanisms underlying the regulation and adaptation of microbial communities at the taxonomic and functional levels in response to communities formed over 34 years through monoculture plantations of coniferous species (Japanese larch, Armand pine, and Chinese pine), deciduous forest species (Katsura), and natural shrubland species (Asian hazel and Liaotung oak) in the temperate climate. The taxonomic and functional classifications of fungi and bacteria were examined for the mineral topsoil (0-10 cm) using MiSeq-sequencing and annotation tools of microorganisms (FAPROTAX and Funguild). Soil bacterial (6.52 ± 0.15) and fungal (4.46 ± 0.12) OTUs' diversity and richness (5.83*103±100 and 1.12*103±46.4, respectively) were higher in the Katsura plantation compared to Armand pine and Chinese pine. This difference was attributed to low soil DOC/OP (24) and DON/OP (11) ratios in the Katsura, indicating that phosphorus availability increased microbial community diversity. The Chinese pine plantation exhibited low functional diversity (3.34 ± 0.04) and richness (45.2 ± 0.41) in bacterial and fungal communities (diversity 3.16 ± 0.15 and richness 56.8 ± 3.13), which could be attributed to the high C/N ratio (25) of litter. These findings suggested that ecological stoichiometry, such as of enzyme, litter C/N, soil DOC/DOP, and DON/DOP ratios, was a sign of the decoupling of soil microorganisms at the genetic and functional levels to land restoration by plantations. It was found that the stoichiometric ratios of plant biomass served as indicators of microbial functions, whereas the stoichiometric ratios of available nutrients in soil regulated microbial genetic diversity. Therefore, nutrient stoichiometry could serve as a strong predictor of microbial diversity and composition during forest restoration.
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Affiliation(s)
- Wei Qiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany
| | - Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany; Tyumen State University, 625003, Tyumen, Russia; Peoples Friendship University of Russia (RUDN) University, 117198, Moscow, Russia
| | - Yakov Kuzyakov
- Peoples Friendship University of Russia (RUDN) University, 117198, Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049, Kazan, Russia; Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany
| | - Qinghua Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China.
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18
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He X, Wang D, Jiang Y, Li M, Delgado-Baquerizo M, McLaughlin C, Marcon C, Guo L, Baer M, Moya YAT, von Wirén N, Deichmann M, Schaaf G, Piepho HP, Yang Z, Yang J, Yim B, Smalla K, Goormachtig S, de Vries FT, Hüging H, Baer M, Sawers RJH, Reif JC, Hochholdinger F, Chen X, Yu P. Heritable microbiome variation is correlated with source environment in locally adapted maize varieties. NATURE PLANTS 2024; 10:598-617. [PMID: 38514787 DOI: 10.1038/s41477-024-01654-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.
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Affiliation(s)
- Xiaoming He
- College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University (SWU), Chongqing, People's Republic of China
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Danning Wang
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yong Jiang
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Meng Li
- Department of Plant Science, Pennsylvania State University, State College, PA, USA
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Chloee McLaughlin
- Department of Plant Science, Pennsylvania State University, State College, PA, USA
| | - Caroline Marcon
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Li Guo
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Marcel Baer
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yudelsy A T Moya
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nicolaus von Wirén
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Marion Deichmann
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Gabriel Schaaf
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | | | - Zhikai Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Bunlong Yim
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Hubert Hüging
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Mareike Baer
- Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Ruairidh J H Sawers
- Department of Plant Science, Pennsylvania State University, State College, PA, USA.
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
| | - Xinping Chen
- College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University (SWU), Chongqing, People's Republic of China.
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
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19
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Li R, Jiao H, Sun B, Song M, Yan G, Bai Z, Wang J, Zhuang X, Hu Q. Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics. Microorganisms 2024; 12:683. [PMID: 38674627 PMCID: PMC11052110 DOI: 10.3390/microorganisms12040683] [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: 03/03/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.
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Affiliation(s)
- Rui Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou 256606, China;
| | - Haihua Jiao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- Department of Biological Sciences and Technology, Changzhi University, Changzhi 046011, China
| | - Bo Sun
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manjiao Song
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaojun Yan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiancheng Wang
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou 256606, China;
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Hu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (H.J.); (B.S.); (M.S.); (G.Y.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Xiongan Innovation Institute, Xiongan New Area, Baoding 071000, China
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20
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Rojas-Sánchez B, Castelán-Sánchez H, Garfias-Zamora EY, Santoyo G. Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System. PLANTS (BASEL, SWITZERLAND) 2024; 13:954. [PMID: 38611483 PMCID: PMC11013257 DOI: 10.3390/plants13070954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.
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Affiliation(s)
- Blanca Rojas-Sánchez
- Genomic Diversity Lab, Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico; (B.R.-S.); (E.Y.G.-Z.)
| | - Hugo Castelán-Sánchez
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Esmeralda Y. Garfias-Zamora
- Genomic Diversity Lab, Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico; (B.R.-S.); (E.Y.G.-Z.)
| | - Gustavo Santoyo
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
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21
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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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22
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Yang Z, Zhao T, Cheng H, Yang J. Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize. G3 (BETHESDA, MD.) 2024; 14:jkad286. [PMID: 38113533 PMCID: PMC11090461 DOI: 10.1093/g3journal/jkad286] [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: 05/19/2023] [Revised: 05/19/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4-40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.
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Affiliation(s)
- Zhikai Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Tianjing Zhao
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Hao Cheng
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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23
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Guo P, Du H, Zhao W, Xiong B, Wang M, He M, Flemetakis E, Hänsch R, Ma M, Rennenberg H, Wang D. Selenium- and chitosan-modified biochars reduce methylmercury contents in rice seeds with recruiting Bacillus to inhibit methylmercury production. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133236. [PMID: 38141298 DOI: 10.1016/j.jhazmat.2023.133236] [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: 09/28/2023] [Revised: 11/13/2023] [Accepted: 12/10/2023] [Indexed: 12/25/2023]
Abstract
Biochar could reshape microbial communities, thereby altering methylmercury (MeHg) concentrations in rice rhizosphere and seeds. However, it remains unclear whether and how biochar amendment perturbs microbe-mediated MeHg production in mercury (Hg) contaminated paddy soil. Here, we used pinecone-derived biochar and its six modified biochars to reveal the disturbance. Results showed that selenium- and chitosan-modified biochar significantly reduced MeHg concentrations in the rhizosphere by 85.83% and 63.90%, thereby decreasing MeHg contents in seeds by 86.37% and 75.50%. The two modified bicohars increased the abundance of putative Hg-resistant microorganisms Bacillus, the dominant microbe in rhizosphere. These reductions about MeHg could be facilitated by biochar sensitive microbes such as Oxalobacteraceae and Subgroup_7. Pinecone-derived biochar increased MeHg concentration in rhizosphere but unimpacted MeHg content in seeds was observed. This biochar decreased the abundance in Bacillus but enhanced in putative Hg methylator Desulfovibrio. The increasing MeHg concentration in rhizosphere could be improved by biochar sensitive microbes such as Saccharimonadales and Clostridia. Network analysis showed that Saccharimonadales and Clostridia were the most prominent keystone taxa in rhizosphere, and the three biochars manipulated abundances of the microbes related to MeHg production in rhizosphere by those biochar sensitive microbes. Therefore, selenium- and chitosan-modified biochar could reduce soil MeHg production by these microorganisms, and is helpful in controlling MeHg contamination in rice.
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Affiliation(s)
- Pan Guo
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Hongxia Du
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Wancang Zhao
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing 400715, PR China
| | - Bingcai Xiong
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Mingxing Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
| | - Mingyan He
- Chongqing Ecological Environment Monitoring Center, Chongqing 401147, PR China
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Robert Hänsch
- Institute for Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, D-38106, Braunschweig, Germany
| | - Ming Ma
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China.
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Dingyong Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
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24
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Duan J, Kitamura K, Tsukamoto H, Van Phan H, Oba K, Hori T, Fujiwara T, Terada A. Enhanced granulation of activated sludge in an airlift reactor for organic carbon removal and ammonia retention from industrial fermentation wastewater: A comparative study. WATER RESEARCH 2024; 251:121091. [PMID: 38244299 DOI: 10.1016/j.watres.2023.121091] [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: 09/01/2023] [Revised: 12/06/2023] [Accepted: 12/28/2023] [Indexed: 01/22/2024]
Abstract
Ammonia retention and recovery from high-nitrogenous wastewater are new concepts being used for nitrogen management. A microaerophilic activated sludge system was developed to convert organic nitrogen into ammonia and retain it for its recovery; however, the settleability of activated sludge remains a challenge. Therefore, this study proposed an aerobic granular sludge system as a potential solution. Two types of sequencing batch reactors-airlift and upflow reactors-were operated to investigate the feasibility of fast granule formation, the performance of organic carbon removal and ammonia retention, and the dynamics of microbial community composition. The operation fed with industrial fermentation wastewater demonstrated that the airlift reactor ensured a more rapid granule formation than the upflow reactor because of the high shear force, and it maintained a superior ammonia retention stability of approximately 85 %. Throughout the operational period, changes in hydraulic retention time (HRT), settling time, and exchange ratio altered the granular particle sizes and microbial community compositions. Rhodocyclaceae were replaced with Comamonadaceae, Methylophilaceae, Xanthomonadaceae, and Chitinophagaceae as core taxa instrumental in granulation, likely because of their extracellular polymeric substance secretion. As the granulation process progressed, a significant decrease in the relative abundances of nitrifying bacteria-Nitrospiraceae and Nitrosomonadaceae-was observed. The reduction of settling time and HRT enhanced granulation and inhibited the activity of nitrifying bacteria. The success in granulation for ammonia conversion and retention in this study accelerates the paradigm shift from ammonia removal to ammonia recovery from industrial fermentation wastewater.
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Affiliation(s)
- Jingyu Duan
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Kotaro Kitamura
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Hiroki Tsukamoto
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Hop Van Phan
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Kohei Oba
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Taku Fujiwara
- Department of Global Ecology, Graduate School of Global Environmental Studies, Kyoto University, Kyoto 615-8540, Japan
| | - Akihiko Terada
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan; Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan.
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25
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Santos LRC, Barros PSDR, Monteiro DA, Tabosa JN, de Melo AF, de Lyra MDCCP, Oliveira JRDS, Fernandes Júnior PI, de Freitas ADS, Rachid CTCDC. Influences of plant organ, genotype, and cultivation site on the endophytic bacteriome of maize (Zea mays L.) in the semi-arid region of Pernambuco, Brazil. Braz J Microbiol 2024; 55:789-797. [PMID: 38146049 PMCID: PMC10920498 DOI: 10.1007/s42770-023-01221-w] [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: 08/16/2023] [Accepted: 12/16/2023] [Indexed: 12/27/2023] Open
Abstract
Endophytic bacteria play a crucial role in plant development and adaptation, and the knowledge of how endophytic bacteria assemblage is influenced by cultivation site and plant genotype is an important step to achieve microbiome manipulation. This work aimed to study the roots and stems of endophytic bacteriome of four maize genotypes cultivated in two regions of the semi-arid region of Pernambuco - Brazil. Our hypothesis is that the endophytic community assemblage will be influenced by plant genotypes and cultivation region. Metabarcoding sequencing data revealed significant differences in alfa diversity in function of both factors, genotypes, and maize organs. Beta diversity analysis showed that the bacterial communities differ mainly in function of the plant organ. The most abundant genera found in the samples were Leifsonia, Bacillus, Klebsiella, Streptomyces, and Bradyrhizobium. To understand ecological interactions within each compartment, we constructed co-occurrence network for each organ. This analysis revealed important differences in network structure and complexity and suggested that Leifsonia (the main genera found) had distinct ecological roles depending on the plant organ. Our data showed that root endophytic maize bacteria would be influenced by cultivation site, but not by genotype. We believe that, collectively, our data not only characterize the bacteriome associated with this plant and how different factors shape it, but also increase the knowledge to select potential bacteria for bioinoculant production.
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Affiliation(s)
- Leandro Reis Costa Santos
- Departamento de Agronomia, UFRPE - Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52061060, Brazil
| | - Pedro Sodré do Rêgo Barros
- Laboratory of Biotechnology and Microbial Ecology (LABEM), Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Av. Carlos Chagas Filho, Rio de Janeiro, 373, Brazil
| | - Douglas Alfradique Monteiro
- Laboratory of Biotechnology and Microbial Ecology (LABEM), Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Av. Carlos Chagas Filho, Rio de Janeiro, 373, Brazil
| | - José Nildo Tabosa
- Laboratory of Genomic, Instituto Agronômico de Pernambuco (IPA), Av. Gen. San Martin 1371, bl D, Pernambuco Agronomic Institute, Recife, Pernambuco, Brazil
| | - Aline Fernandes de Melo
- Departamento de Agronomia, UFRPE - Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52061060, Brazil
| | - Maria do Carmo Catanho Pereira de Lyra
- Laboratory of Genomic, Instituto Agronômico de Pernambuco (IPA), Av. Gen. San Martin 1371, bl D, Pernambuco Agronomic Institute, Recife, Pernambuco, Brazil
| | - Jéssica Rafaella de Sousa Oliveira
- Departamento de Agronomia, UFRPE - Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52061060, Brazil
| | | | - Ana Dolores Santiago de Freitas
- Departamento de Agronomia, UFRPE - Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52061060, Brazil
| | - Caio Tavora Coelho da Costa Rachid
- Laboratory of Biotechnology and Microbial Ecology (LABEM), Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Av. Carlos Chagas Filho, Rio de Janeiro, 373, Brazil.
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Wan X, Zhou R, Yuan Y, Xing W, Liu S. Microbiota associated with urban forests. PeerJ 2024; 12:e16987. [PMID: 38444615 PMCID: PMC10913776 DOI: 10.7717/peerj.16987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
Urban forests are essential for maintaining urban ecological stability. As decomposers, soil microorganisms play an indispensable role in the stability of urban forest ecosystems, promoting the material cycle of the ecosystems. This study used high-throughput sequencing technology to explore the bacteria in six forest stands, including Phyllostachys edulis (ZL), Metasequoia glyptostroboides (SSL), Cornus officinalis (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Meanwhile, the differences in fungal communities were investigated. The results show that ZL has the highest alpha diversity of bacterial communities, while its fungal community is the lowest; Proteobacteria is the most abundant bacterial phylum in the six forest stands; ZKQ has the highest fungal diversity. In addition, soil microbial communities are affected by environmental factors. Soil pH, organic matter (SOM), and available phosphorus (AP) significantly influence the compositions of urban forest soil microbial communities. This study revealed the differences in bulk soil (BS) microbial community structures among six forest stands and the relationship between environmental factors and soil microbial communities, which has important guiding significance for creating healthy and stable urban forests with profound ecological benefits.
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Affiliation(s)
- Xin Wan
- Jiangsu Academy of Forestry, Nanjing, China
| | | | | | - Wei Xing
- Jiangsu Academy of Forestry, Nanjing, China
| | - Sian Liu
- Yangzhou University, Yangzhou, China
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [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: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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Bak GR, Lee KK, Clark IM, Mauchline TH, Kavamura VN, Lund G, Jee S, Lee JT, Kim H, Lee YH. The potato rhizosphere microbiota correlated to the yield of three different regions in Korea. Sci Rep 2024; 14:4536. [PMID: 38402369 PMCID: PMC10894198 DOI: 10.1038/s41598-024-55263-7] [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: 12/19/2023] [Accepted: 02/21/2024] [Indexed: 02/26/2024] Open
Abstract
We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield. Both bacterial and fungal microbiota showed distinct patterns according to the regions. ASVs positively correlated with yield were predominantly found in the Pyeongchang region which also produced the highest yields, while ASVs negatively correlated with yield were associated with Gangneung where the lowest yields were observed. The greatest bacterial and fungal diversity was detected in Pyeongchang consisting of Propionibacteriales, Burkholderiales, and Vicinamibacteriales. Gangneung, on the other hand primarily belong to Sordariales, Mortierellales, Cystofilobasidiales, and Tremellales. The putative yield-negative ASVs detected in Gangneung may have been influenced by drought stress. This work has highlighted key bacterial and fungal taxa as well as core taxa that may potentially be associated with high and low yields of potato in relation to metadata which includes soil chemical and physical parameters as well as weather data. Taken together we suggest that this information can be used to assess site suitability for potato production.
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Affiliation(s)
- Gye-Ryeong Bak
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
- Interdisciplinary Programs in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA
| | - Ian M Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | | | - George Lund
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Samnyu Jee
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jeong-Tae Lee
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yong-Hwan Lee
- Interdisciplinary Programs in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Center for Plant Microbiome Research, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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Zhang M, Xiong Y, Sun H, Xiao T, Xiao E, Sun X, Li B, Sun W. Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132948. [PMID: 37984136 DOI: 10.1016/j.jhazmat.2023.132948] [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: 09/03/2023] [Revised: 10/27/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.
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Affiliation(s)
- Miaomiao Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiqun Xiong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Huicai Sun
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Tangfu Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Enzong Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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30
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Ren Q, Khan A, Zhang J, Bao Y, Khan MT, Wang J, Xu S, Zhang M. Fungal community dynamics associated with the outbreaks of sugarcane root rot disease. Microbiol Spectr 2024; 12:e0309023. [PMID: 38189328 PMCID: PMC10845956 DOI: 10.1128/spectrum.03090-23] [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: 08/12/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Sugarcane is a critical sugar and bioenergy crop in China. However, numerous factors, including root rot disease, hamper its yield. Root rot disease is a severe agricultural issue, reducing yield and threatening sustainable crop production. The current study aimed to explore the fungal community structure, identify and characterize the primary pathogen for sugarcane root rot in Guangzhou, China. Eighty-nine samples of sugarcane root, stalk, rhizosphere soil, and irrigation water were collected from five sites in Guangzhou, China. Subsequently, 276 fungal strains were isolated to identify the primary pathogens. The five most common genera identified were Penicillium, Fusarium, Gongronella, Trichoderma, and Cladosporium. Fusarium was more prevalent in the infected soil samples than in healthy ones. Pathogenic assays of the strains revealed that the strain GX4-46 caused 80% of the disease. The strain was confirmed as Fusarium commune through phylogenetic and genome sequence analysis. Rhizosphere soil samples from different regional crops were collected to better understand the fungal community structure and the primary pathogen. We observed a significant presence of Fusarium in irrigation water, indicating that the root rot disease could originate from the irrigation water and then spread as a soil-borne disease. This research is pioneering and one of the most comprehensive investigations on the occurrence and prevalence of sugarcane root rot disease. This study will serve as a reference for expanding the sugarcane industry and a foundation for further exploration and control of root rot.IMPORTANCESugarcane, a significant economic crop, faces challenges due to root rot pathogens that accumulate each year in plants and soil through ratoon planting. This disrupts soil microbial balance and greatly impedes sugarcane industry growth. Symptoms range from wilting and yellowing leaves to stunted growth and reduced seedling tillers. The rhizosphere microbiota plays an important role in plant development and soil health. Little is known about root rot fungal community structure, especially in sugarcane. Here, we focused on exploring the main causative pathogen of root rot in the area alongside a detailed survey of the rhizosphere soil of different severity sugarcane cultivars and rotation crops of the region. To validate the findings, we also investigated the irrigation water of the area. Our study revealed Fusarium commune as the causative pathogen of root rot in the area, primarily originating from water and later as soil-borne. Using Trichoderma can control the disease effectively.
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Affiliation(s)
- Qingxiao Ren
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Abdullah Khan
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jinxu Zhang
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Yixue Bao
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Muhammad Tahir Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Jihua Wang
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shiqiang Xu
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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31
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Chen L, Liu Y. The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria. BIOLOGY 2024; 13:95. [PMID: 38392313 PMCID: PMC10886372 DOI: 10.3390/biology13020095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.
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Affiliation(s)
- Lin Chen
- National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain, Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing 102300, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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32
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Nazir MJ, Hussain MM, Albasher G, Iqbal B, Khan KA, Rahim R, Li G, Du D. Glucose input profit soil organic carbon mineralization and nitrogen dynamics in relation to nitrogen amended soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119715. [PMID: 38064981 DOI: 10.1016/j.jenvman.2023.119715] [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: 09/02/2023] [Revised: 11/10/2023] [Accepted: 11/23/2023] [Indexed: 01/14/2024]
Abstract
Exogenous carbon (C) inputs stimulate soil organic carbon (SOC) decomposition, strongly influencing atmospheric concentrations and climate dynamics. The direction and magnitude of C decomposition depend on the C and nitrogen (N) addition, types and pattern. Despite the importance of decomposition, it remains unclear whether organic C input affects the SOC decomposition under different N-types (Ammonium Nitrate; AN, Urea; U and Ammonium Sulfate; AS). Therefore, we conducted an incubation experiment to assess glucose impact on N-treated soils at various levels (High N; HN: 50 mg/m2, Low N; LN: 05 mg/m2). The glucose input increased SOC mineralization by 38% and 35% under HN and LN, respectively. Moreover, it suppressed the concentration of NO3--N by 35% and NH4+-N by 15% in response to HN and LN soils, respectively. Results indicated higher respiration in Urea-treated soils and elevated net total nitrogen content (TN) in AS-treated soils. AN-amended soil exhibited no notable rise in C mineralization and TN content compared to other N-type soils. Microbial biomass carbon (MBC) was higher in glucose treated soils under LN conditions than control. This could result that high N suppressed microbial N mining and enhancing SOM stability by directing microbes towards accessible C sources. Our results suggest that glucose accelerated SOC mineralization in urea-added soils and TN contents in AS-amended soils, while HN levels suppressed C release and increased TN contents in all soil types except glucose-treated soils. Thus, different N-types and levels play a key role in modulating the stability of SOC over C input.
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Affiliation(s)
- Muhammad Junaid Nazir
- School of Emergency Management, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Muhammad Mahroz Hussain
- School of Emergency Management, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Gadah Albasher
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Babar Iqbal
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Khalid Ali Khan
- Applied College and Unit of Bee Research and Honey Production, Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Riffat Rahim
- Forschungszentrum Jülich GmbH, Agrosphere Institute (IBG-3), Wilhelm Johnen Strasse, Jülich, 52428, Germany
| | - Guanlin Li
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Daolin Du
- School of Emergency Management, School of Environment and Safety Engineering, Jiangsu Province Engineering Research Center of Green Technology and Contingency Management for Emerging Pollutants, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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O'Brien AM, Laurich JR, Frederickson ME. Evolutionary consequences of microbiomes for hosts: impacts on host fitness, traits, and heritability. Evolution 2024; 78:237-252. [PMID: 37828761 DOI: 10.1093/evolut/qpad183] [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: 02/22/2022] [Revised: 08/30/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
An organism's phenotypes and fitness often depend on the interactive effects of its genome (Ghost), microbiome (Gmicrobe), and environment (E). These G × G, G × E, and G × G × E effects fundamentally shape host-microbiome (co)evolution and may be widespread, but are rarely compared within a single experiment. We collected and cultured Lemnaminor (duckweed) and its associated microbiome from 10 sites across an urban-to-rural ecotone. We factorially manipulated host genotype and microbiome in two environments (low and high zinc, an urban aquatic stressor) in an experiment with 200 treatments: 10 host genotypes × 10 microbiomes × 2 environments. Host genotype explained the most variation in L.minor fitness and traits, while microbiome effects often depended on host genotype (G × G). Microbiome composition predicted G × G effects: when compared in more similar microbiomes, duckweed genotypes had more similar effects on traits. Further, host fitness increased and microbes grew faster when applied microbiomes more closely matched the host's field microbiome, suggesting some local adaptation between hosts and microbiota. Finally, selection on and heritability of host traits shifted across microbiomes and zinc exposure. Thus, we found that microbiomes impact host fitness, trait expression, and heritability, with implications for host-microbiome evolution and microbiome breeding.
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Affiliation(s)
- Anna M O'Brien
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason R Laurich
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Chai YN, Qi Y, Goren E, Chiniquy D, Sheflin AM, Tringe SG, Prenni JE, Liu P, Schachtman DP. Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum. mSystems 2024; 9:e0119023. [PMID: 38132569 PMCID: PMC10804983 DOI: 10.1128/msystems.01190-23] [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: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.IMPORTANCEThe development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.
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Affiliation(s)
- Yen Ning Chai
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yunhui Qi
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Emily Goren
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Dawn Chiniquy
- Environmental Genomics and System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amy M. Sheflin
- Department of Horticulture and Landscape Architecture, Colorado State University, Colorado State University, Fort Collins, Colorado, USA
| | - Susannah G. Tringe
- Environmental Genomics and System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jessica E. Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Colorado State University, Fort Collins, Colorado, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Lanzavecchia G, Frascarelli G, Rocchetti L, Bellucci E, Bitocchi E, Di Vittori V, Sillo F, Ferraris I, Carta G, Delledonne M, Nanni L, Papa R. Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System. Int J Mol Sci 2024; 25:1288. [PMID: 38279288 PMCID: PMC10815965 DOI: 10.3390/ijms25021288] [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: 10/30/2023] [Revised: 12/23/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
In an intercropping system, the interplay between cereals and legumes, which is strongly driven by the complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and bean (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Through amplicon sequencing of bacterial 16S rRNA genes from rhizosphere samples, our results unveil that the intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhances community complexity. Nevertheless, combinations of maize and bean genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.
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Affiliation(s)
- Giovanna Lanzavecchia
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Lorenzo Rocchetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Fabiano Sillo
- National Research Council of Italy, Institute for Sustainable Plant, Strada delle Cacce 73, 10135 Torino, Italy;
| | - Irene Ferraris
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Giada Carta
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Massimo Delledonne
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
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Tran DT, Mitchum MG, Zhang S, Wallace JG, Li Z. Soybean microbiome composition and the impact of host plant resistance. FRONTIERS IN PLANT SCIENCE 2024; 14:1326882. [PMID: 38288404 PMCID: PMC10822979 DOI: 10.3389/fpls.2023.1326882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Microbial communities play an important role in the growth and development of plants, including plant immunity and the decomposition of complex substances into absorbable nutrients. Hence, utilizing beneficial microbes becomes a promising strategy for the optimization of plant growth. The objective of this research was to explore the root bacterial profile across different soybean genotypes and the change in the microbial community under soybean cyst nematode (SCN) infection in greenhouse conditions using 16S rRNA sequencing. Soybean genotypes with soybean cyst nematode (SCN) susceptible and resistant phenotypes were grown under field and greenhouse conditions. Bulked soil, rhizosphere, and root samples were collected from each replicate. Sequencing of the bacterial 16S gene indicated that the bacterial profile of soybean root and soil samples partially overlapped but also contained different communities. The bacterial phyla Proteobacteria, Actinobacteria, and Bacteroidetes dominate the soybean root-enriched microbiota. The structure of bacteria was significantly affected by sample year (field) or time point (greenhouse). In addition, the host genotype had a small but significant effect on the diversity of the root microbiome under SCN pressure in the greenhouse test. These differences may potentially represent beneficial bacteria or secondary effects related to SCN resistance.
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Affiliation(s)
- Dung T. Tran
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Melissa G. Mitchum
- Department of Plant Pathology, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Shuzhen Zhang
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Soybean Research Institute, Northeast Agricultural University, Harbin, China
| | - Jason G. Wallace
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Zenglu Li
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Yan K, Lu DS, Ding CJ, Wang Y, Tian YR, Su XH, Dong YF, Wang YP. Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168216. [PMID: 37923276 DOI: 10.1016/j.scitotenv.2023.168216] [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: 05/24/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.
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Affiliation(s)
- Kun Yan
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - De Shan Lu
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Chang Jun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yan Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Yong Ren Tian
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Hua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | | | - Yan Ping Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
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Wang Q, Zhou D, Chu C, Zhao Z, Ma M, Wu S. The choice of rice rotation system affects the composition of the soil fungal community and functional traits. Heliyon 2024; 10:e24027. [PMID: 38268583 PMCID: PMC10805912 DOI: 10.1016/j.heliyon.2024.e24027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
Plant rotation is a common practice in upland rice production. However, the effects of plant rotation on the interactions between rice plants, soil and underground ecosystems need to be studied further. Here, quantitative PCR and high-throughput pyrosequencing of the ITS region was applied to investigate the fungal abundance, diversity, and composition of fungal functional guilds in rice field soils and after different rotation practices ((rice-fallow (RF), rice-Chinese milk vetch (RV) and rice-wheat (RW)) and their relationship with rice yields. The results showed that the six-year RV and RW rotations increased fungal abundance by 42.7 %-69.2 % relative to RF, but decreased the soil bacterial-to-fungi ratio and fungal diversity. For the functional guilds, RV rotation significantly increased the relative abundance of soil saprotrophs and pathotrophs by 73.30 % and 32.94 %, respectively, while that of symbiotrophs was decreased by 35.96 %, compared to RF. RW rotation was found to significantly decrease all three fungal functional guilds, but increased the symbiotroph-saprotroph ratio. A structure equal model analysis indicated that the diversity of saprotrophs was significantly and negatively correlated with rice yield. Altogether, this work provides a detailed description of how the soil fungal community, including saprotrophic, symbiotrophic and pathotrophic functional guilds, responded to different upland rice rotation practices after eight years of application.
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Affiliation(s)
- Qingfeng Wang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Deping Zhou
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Changbin Chu
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Zheng Zhao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuhang Wu
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
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Iqbal A, Maqsood Ur Rehman M, Sajjad W, Degen AA, Rafiq M, Jiahuan N, Khan S, Shang Z. Patterns of bacterial communities in the rhizosphere and rhizoplane of alpine wet meadows. ENVIRONMENTAL RESEARCH 2024; 241:117672. [PMID: 37980986 DOI: 10.1016/j.envres.2023.117672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
Wet meadows, a type of wetland, are vulnerable to climate change and human activity, impacting soil properties and microorganisms that are crucial to the ecosystem processes of wet meadows. To decipher the ecological mechanisms and processes involved in wet meadows, it is necessary to examine the bacterial communities associated with plant roots. To gain valuable insight into the microbial dynamics of alpine wet meadows, we used Illumina MiSeq sequencing to investigate how environmental factors shape the bacterial communities thriving in the rhizosphere and rhizoplane of three plant species: Cremanthodium ellisii, Caltha scaposa, and Cremanthodium lineare. The most abundant bacterial phyla in rhizosphere and rhizoplane were Proteobacteria > Firmicutes > Actinobacteria, while Macrococcus, Lactococcus, and Exiguobacterium were the most abundant bacterial genera between rhizosphere and rhizoplane. The mantel test, network, and structure equation models revealed that bacterial communities of rhizosphere were shaped by total nitrogen (TN), soil water content (SWC), soil organic carbon (SOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), pH, however, rhizoplane bacterial communities exhibited varying results. The bacterial communities exhibited significant heterogeneity, with stochastic process predominating in both the rhizosphere and rhizoplane. PICRUSt2 and FAPROTAX analysis revealed substantial differences in key biogeochemical cycles and metabolic functional predictions. It was concluded that root compartments significantly influenced the bacterial communities, although plant species and elevation asserted varying effects. This study portrays how physicochemical properties, plant species, and elevations can shift the overall structure and functional repertoire of bacterial communities in alpine wet meadows.
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Affiliation(s)
- Awais Iqbal
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Muhammad Maqsood Ur Rehman
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Abraham Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, 8410500, Israel
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Baluchistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Niu Jiahuan
- Department of Health and Environmental Sciences, Xian Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Salman Khan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhanhuan Shang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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Zhang Y, Zhan J, Ma C, Liu W, Huang H, Yu H, Christie P, Li T, Wu L. Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115739. [PMID: 38016191 DOI: 10.1016/j.ecoenv.2023.115739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.
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Affiliation(s)
- Yunhong Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China
| | - Juan Zhan
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chuang Ma
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huagang Huang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China
| | - Haiying Yu
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China
| | - Peter Christie
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Tingxuan Li
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu 611130, China.
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Zhang X, Zhou R, Teng L, Chen H, Li M, Wang L, Zhran M, Cao F. Genotypic variation in grain cadmium concentration in wheat: Insights into soil pollution, agronomic characteristics, and rhizosphere microbial communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122792. [PMID: 37879552 DOI: 10.1016/j.envpol.2023.122792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Soil cadmium (Cd) pollution poses a serious threat to both the productivity and quality of wheat. This study aimed to investigate the genotypic variation in grain Cd concentration in wheat through field and pot experiments. Among 273 wheat genotypes, a significant genotypic difference was found in grain Cd concentration, ranging from 0.01 to 0.14 mg kg-1. Two contrasting genotypes, X321 (a low grain Cd accumulator) and X128 (a high grain Cd accumulator), were selected for pot experiments. X321 exhibited a 17.9% greater reduction in yield and a 10.2% lower shoot-to-grain Cd translocation rate than X128 under Cd treatment. Grain Cd content showed a positive correlation with soil available Cd content and a negative correlation with Cu content. Soil catalase activity significantly decreased in X128 under Cd stress, whereas no difference was found in X321. The grains of X321 exhibited a more compact spatial distribution of starch grains and protein matrix than those of X128. Moreover, the size of A-type starch in X128 was larger than in X321. Meanwhile, X128 contained much B-type starch, with some surface pits observed on A-type granules under Cd stress. Cd treatment increased the abundance of rhizosphere microorganism communities, with Ellin6067 and Ramlibacter being enriched in X128 under Cd treatment, which might facilitate Cd uptake. The accumulation of Cd in grains demonstrated a strong positive correlation with the rhizosphere bacterial diversity (correlation coefficient = 0.78). These findings provide new insights into the basis of grain Cd accumulation in wheat and have potential implications for developing new verities with low Cd accumulation to ensure food safety and minimize human exposure.
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Affiliation(s)
- Xueqing Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China.
| | - Runxin Zhou
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China.
| | - Lidong Teng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China.
| | - Huabin Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China.
| | - Meng Li
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China.
| | - Li Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China.
| | - Mostafa Zhran
- Soil and Water Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, 11787, Cairo, Egypt.
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China.
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Tamang A, Swarnkar M, Kumar P, Kumar D, Pandey SS, Hallan V. Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb. Microbiol Spectr 2023; 11:e0227923. [PMID: 37811959 PMCID: PMC10715050 DOI: 10.1128/spectrum.02279-23] [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: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.
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Affiliation(s)
- Anish Tamang
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Mohit Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Pawan Kumar
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dinesh Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Shiv Shanker Pandey
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
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Yadav P, Quattrone A, Yang Y, Owens J, Kiat R, Kuppusamy T, Russo SE, Weber KA. Zea mays genotype influences microbial and viral rhizobiome community structure. ISME COMMUNICATIONS 2023; 3:129. [PMID: 38057501 DOI: 10.1038/s43705-023-00335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.
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Affiliation(s)
- Pooja Yadav
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amanda Quattrone
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, USA
- Texas A&M University, College Station, TX, USA
| | - Yuguo Yang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jacob Owens
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- University of Nebraska-Medical Center, Omaha, NE, USA
| | - Rebecca Kiat
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Sabrina E Russo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Karrie A Weber
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Daugherty Water for Food Global Institute, University of Nebraska, Lincoln, NE, USA.
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44
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Kural-Rendon C, Ford NE, Wagner MR. Interactions with fungi vary among Tripsacum dactyloides genotypes from across a precipitation gradient. AOB PLANTS 2023; 15:plad072. [PMID: 38028745 PMCID: PMC10667659 DOI: 10.1093/aobpla/plad072] [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: 04/18/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
Plant-associated microbes, specifically fungal endophytes, augment the ability of many grasses to adapt to extreme environmental conditions. Tripsacum dactyloides (Eastern gamagrass) is a perennial, drought-tolerant grass native to the tallgrass prairies of the central USA. The extent to which the microbiome of T. dactyloides contributes to its drought tolerance is unknown. Ninety-seven genotypes of T. dactyloides were collected from native populations across an east-west precipitation gradient in Kansas, Oklahoma and Texas, and then grown together in a common garden for over 20 years. Root and leaf samples were visually examined for fungal density. Because fungal endophytes confer drought-tolerant capabilities to their host plants, we expected to find higher densities of fungal endophytes in plants from western, drier regions, compared to plants from eastern, wetter regions. Results confirmed a negative correlation between endophyte densities in roots and precipitation at the genotype's original location (r = -0.21 P = 0.04). Our analyses reveal that the host genotype's origin along the precipitation gradient predicts the absolute abundance of symbionts in the root, but not the relative abundances of particular organisms or the overall community composition. Overall, these results demonstrate that genetic variation for plant-microbe interactions can reflect historical environment, and reinforce the importance of considering plant genotype in conservation and restoration work in tallgrass prairie ecosystems.
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Affiliation(s)
- Ceyda Kural-Rendon
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Natalie E Ford
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS 66045, USA
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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King WL, Yates CF, Cao L, O'Rourke-Ibach S, Fleishman SM, Richards SC, Centinari M, Hafner BD, Goebel M, Bauerle T, Kim YM, Nicora CD, Anderton CR, Eissenstat DM, Bell TH. Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites. PLANT, CELL & ENVIRONMENT 2023; 46:3919-3932. [PMID: 37675977 DOI: 10.1111/pce.14705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/12/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Caylon F Yates
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Lily Cao
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sean O'Rourke-Ibach
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Suzanne M Fleishman
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michela Centinari
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Benjamin D Hafner
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Marc Goebel
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Taryn Bauerle
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - David M Eissenstat
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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46
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Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165801. [PMID: 37499809 DOI: 10.1016/j.scitotenv.2023.165801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/26/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongtao Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
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47
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Fu X, Huang Y, Fu Q, Qiu Y, Zhao J, Li J, Wu X, Yang Y, Liu H, Yang X, Chen H. Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects. FRONTIERS IN PLANT SCIENCE 2023; 14:1252821. [PMID: 38023904 PMCID: PMC10676204 DOI: 10.3389/fpls.2023.1252821] [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: 07/04/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xian Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, Guangdong, China
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48
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [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: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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49
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Ujvári G, Capo L, Grassi A, Cristani C, Pagliarani I, Turrini A, Blandino M, Giovannetti M, Agnolucci M. Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity. FRONTIERS IN PLANT SCIENCE 2023; 14:1240310. [PMID: 38023909 PMCID: PMC10651756 DOI: 10.3389/fpls.2023.1240310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.
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Affiliation(s)
- Gergely Ujvári
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Luca Capo
- Department of Agriculture, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Arianna Grassi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Caterina Cristani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Irene Pagliarani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Massimo Blandino
- Department of Agriculture, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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50
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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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