201
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Adu-Oppong B, Mangan SA, Stein C, Catano CP, Myers JA, Dantas G. Prairie plants harbor distinct and beneficial root-endophytic bacterial communities. PLoS One 2020; 15:e0234537. [PMID: 32574172 PMCID: PMC7310688 DOI: 10.1371/journal.pone.0234537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 05/28/2020] [Indexed: 11/19/2022] Open
Abstract
Plant-soil feedback studies attempt to understand the interplay between composition of plant and soil microbial communities. A growing body of literature suggests that plant species can coexist when they interact with a subset of the soil microbial community that impacts plant performance. Most studies focus on the microbial community in the soil rhizosphere; therefore, the degree to which the bacterial community within plant roots (root-endophytic compartment) influences plant-microbe interactions remains relatively unknown. To determine if there is an interaction between conspecific vs heterospecific soil microbes and plant performance, we sequenced root-endophytic bacterial communities of five tallgrass-prairie plant species, each reciprocally grown with soil microbes from each hosts' soil rhizosphere. We found evidence of plant-soil feedbacks for some pairs of plant hosts; however, the strength and direction of feedbacks varied substantially across plant species pairs-from positive to negative feedbacks. Additionally, each plant species harbored a unique subset of root-endophytic bacteria. Conspecifics that hosted similar bacterial communities were more similar in biomass than individuals that hosted different bacterial communities, suggesting an important functional link between root-endophytic bacterial community composition and plant fitness. Our findings suggest a connection between an understudied component of the root-endophytic microbiome and plant performance, which may have important implications in understanding plant community composition and coexistence.
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Affiliation(s)
- Boahemaa Adu-Oppong
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, Missouri, United States of America
| | - Scott A. Mangan
- Department of Biology and Tyson Research Center, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Claudia Stein
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, Alabama, United States of America
| | - Christopher P. Catano
- Department of Biology and Tyson Research Center, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jonathan A. Myers
- Department of Biology and Tyson Research Center, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, United States of America
- Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
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202
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Liu X, Yang C, Yu X, Yu H, Zhuang W, Gu H, Xu K, Zheng X, Wang C, Xiao F, Wu B, He Z, Yan Q. Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137807. [PMID: 32179356 DOI: 10.1016/j.scitotenv.2020.137807] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.
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Affiliation(s)
- Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Chao Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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203
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Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL. The Plant Microbiome: From Ecology to Reductionism and Beyond. Annu Rev Microbiol 2020; 74:81-100. [PMID: 32530732 DOI: 10.1146/annurev-micro-022620-014327] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Sarah Gilbert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Paulo José Pereira Lima Teixeira
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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204
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Simmons T, Styer AB, Pierroz G, Gonçalves AP, Pasricha R, Hazra AB, Bubner P, Coleman-Derr D. Drought Drives Spatial Variation in the Millet Root Microbiome. FRONTIERS IN PLANT SCIENCE 2020; 11:599. [PMID: 32547572 PMCID: PMC7270290 DOI: 10.3389/fpls.2020.00599] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/20/2020] [Indexed: 05/29/2023]
Abstract
Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize root-associated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA amplicon-based sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.
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Affiliation(s)
- Tuesday Simmons
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Alexander B. Styer
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Grady Pierroz
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Antonio Pedro Gonçalves
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Ramji Pasricha
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Amrita B. Hazra
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Patricia Bubner
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Devin Coleman-Derr
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture–Agriculture Research Service, Albany, CA, United States
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205
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Zolti A, Green SJ, Sela N, Hadar Y, Minz D. The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts. MICROBIOME 2020; 8:71. [PMID: 32438915 PMCID: PMC7243336 DOI: 10.1186/s40168-020-00850-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/28/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants. RESULTS Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies, provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt. CONCLUSIONS We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms. This study is a proof-of-concept for the use of microbial communities as microsensors, with great potential for interrogation of a wide range of host systems. Video Abstract.
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Affiliation(s)
- Avihai Zolti
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization–Volcani Center, 7528809 Rishon Lezion, Israel
| | - Stefan J. Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL USA
| | - Noa Sela
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization–Volcani Center, 7528809 Rishon Lezion, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization–Volcani Center, 7528809 Rishon Lezion, Israel
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206
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de Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science 2020; 368:270-274. [PMID: 32299947 DOI: 10.1126/science.aaz5192] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Root-associated microbes can improve plant growth, and they offer the potential to increase crop resilience to future drought. Although our understanding of the complex feedbacks between plant and microbial responses to drought is advancing, most of our knowledge comes from non-crop plants in controlled experiments. We propose that future research efforts should attempt to quantify relationships between plant and microbial traits, explicitly focus on food crops, and include longer-term experiments under field conditions. Overall, we highlight the need for improved mechanistic understanding of the complex feedbacks between plants and microbes during, and particularly after, drought. This requires integrating ecology with plant, microbiome, and molecular approaches and is central to making crop production more resilient to our future climate.
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Affiliation(s)
- Franciska T de Vries
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK. .,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | | | - Christopher G Knight
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Oceane Nicolitch
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Alex Williams
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
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207
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Zhao X, Jiang Y, Liu Q, Yang H, Wang Z, Zhang M. Effects of Drought-Tolerant Ea-DREB2B Transgenic Sugarcane on Bacterial Communities in Soil. Front Microbiol 2020; 11:704. [PMID: 32431674 PMCID: PMC7214759 DOI: 10.3389/fmicb.2020.00704] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/26/2020] [Indexed: 11/30/2022] Open
Abstract
Drought is a major abiotic stress affecting plant growth and development. Sugarcane, a sugar crop planted in warmer climate, suffers dramatically from drought stress. Bacterial communities colonizing the rhizosphere, where roots sense drought stress initially, have been well studied for their beneficial effects on plant growth and health. The Ea-DREB2B gene cloned from the sugarcane, Saccharum arundinaceum, belongs to the DREB2 subgroup of the DREB gene family, which is involved in drought response regulation. Here, we present a detailed characterization of the rhizoplane, rhizosphere, and bulk soil bacterial communities determined using a high-sequencing approach with the transgenic (TG) sugarcane variety GN18 harboring the drought-tolerant Ea-DREB2B gene and its isogenic wild-type (WT) variety FN95-1702 under the same environmental conditions. In addition, the total carbon (TC), total nitrogen (TN), and total phosphorus (TP) contents in each soil area were compared to explore the relationship between bacterial alteration in the TG and WT plants and environmental factors (TC, TN, TP, C:N, C:P, and N:P). Our results showed that the bacterial communities in the rhizosphere and rhizoplane of TG sugarcane were more similar and perfectly correlated with the environmental factors than those of the WT. This suggested that the bacterial communities of the TG plants were altered in response to the changes in root exudates. The results of our study suggest that the change in soil environment caused by transgenic sugarcane alters soil bacterial communities.
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Affiliation(s)
- Xiaowen Zhao
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Yuke Jiang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Qi Liu
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Huichun Yang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Ziting Wang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
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208
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Reyes-Hernández SJ, Zamora-Briseño JA, Cerqueda-García D, Castaño E, Rodríguez-Zapata LC. Alterations in the sap-associated microbiota of Carica papaya in response to drought stress. Symbiosis 2020. [DOI: 10.1007/s13199-020-00682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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209
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Azeem M, Sun D, Crowley D, Hayat R, Hussain Q, Ali A, Tahir MI, Jeyasundar PGSA, Rinklebe J, Zhang Z. Crop types have stronger effects on soil microbial communities and functionalities than biochar or fertilizer during two cycles of legume-cereal rotations of dry land. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136958. [PMID: 32032990 DOI: 10.1016/j.scitotenv.2020.136958] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/23/2020] [Accepted: 01/25/2020] [Indexed: 05/22/2023]
Abstract
The addition of biochar to agricultural fields has been widely studied, but most of these studies have emphasized its effects by growing a single type of crop over short- to long-term time spans. Additionally, a limited number of studies have focused on the soil microbial community composition with respect to biochar addition in legume-cereal crop rotation. In this study, we examined soil microbial community structures by adding biochar (0, 5, and 10 t ha-1) and fertilizer (nitrogen-N, phosphorous-P and potassium-K) during 2 cycles of mash bean and wheat rotations. The results showed that the bacterial (16S rRNA) gene abundance was often increased by biochar addition in the presence of mash bean (Vigna mungo L.) but not wheat. When the soil received fertilizer, the bacterial gene abundance was less responsive to biochar addition. Fungal (ITS rRNA) copy numbers were enhanced by biochar and fertilizer in presence of wheat but were decreased in the presence of mash bean. Fertilizer addition also resulted in less change in ITS genes after biochar addition. Microbial functional groups including Gram+, Gram- and Pseudomonas bacteria were stimulated by biochar or fertilizer only in mash bean soils, while mycorrhizae were significantly increased by biochar in wheat soils. Although biochar addition affected soil properties, microbial community assays were not greatly altered by these physicochemical properties. In conclusion, the crop type played a decisive role, rather than biochar or fertilizer addition, in shaping microbial community structures (16S and ITS phyla) during crop rotation.
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Affiliation(s)
- Muhammad Azeem
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, PR China; Department of Environmental Sciences, University of California, Riverside, CA 92507, USA; Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Daquan Sun
- Biology Center, Institute of Soil Biology & SoWa Research Infrastructure, Czech Academy of Science, Na Sadkach 7, Ceske Budejovice, CZ 37005, Czech Republic
| | - David Crowley
- Department of Environmental Sciences, University of California, Riverside, CA 92507, USA
| | - Rifat Hayat
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Qaiser Hussain
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Amjad Ali
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, PR China
| | | | | | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste-Management, Laboratory of Soil and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, PR China.
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210
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Microbial inoculum development for ameliorating crop drought stress: A case study of Variovorax paradoxus 5C-2. N Biotechnol 2020; 56:103-113. [DOI: 10.1016/j.nbt.2019.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 12/24/2019] [Accepted: 12/29/2019] [Indexed: 01/01/2023]
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211
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Beirinckx S, Viaene T, Haegeman A, Debode J, Amery F, Vandenabeele S, Nelissen H, Inzé D, Tito R, Raes J, De Tender C, Goormachtig S. Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions. MICROBIOME 2020; 8:54. [PMID: 32305066 PMCID: PMC7166315 DOI: 10.1186/s40168-020-00833-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/19/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. RESULTS We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. CONCLUSIONS Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions. Video abstract.
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Affiliation(s)
- Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Fien Amery
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Raul Tito
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
- Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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212
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Ju Y, Zhong R, Christensen MJ, Zhang X. Effects of Epichloë gansuensis Endophyte on the Root and Rhizosphere Soil Bacteria of Achnatherum inebrians Under Different Moisture Conditions. Front Microbiol 2020; 11:747. [PMID: 32362891 PMCID: PMC7181407 DOI: 10.3389/fmicb.2020.00747] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/30/2020] [Indexed: 11/25/2022] Open
Abstract
This study was conducted to explore effects of the systemic fungal endophyte Epichloë gansuensis on root and rhizosphere soil bacterial diversity of Achnatherum inebrians host plants growing under different moisture conditions. Soil properties of different treatments were compared using standard techniques. A total of 4371379 16S rRNA gene sequences were obtained and assigned to 5025 operational taxonomic units (OTUs). These OTUs in roots and rhizosphere soil were divided into 13 and 17 phyla, respectively, and the Actinobacteria and Proteobacteria were the most abundant phyla both in roots and rhizosphere soil. Shannon diversity and Chao1 richness index of bacteria in rhizosphere soil was significantly higher than in roots. E. gansuensis decreased the Shannon diversity of the root-associated bacterial community, and increased Shannon diversity and Chao1 richness index of the rhizosphere soil bacterial community of A. inebrians. Meanwhile, Chao1 richness of the rhizosphere soil bacterial community of A. inebrians significantly increased with the increase of the soil moisture level. Structural equation modeling also emphasized that E. gansuensis decreased the diversity of the root-associated bacterial community and increased the diversity of the rhizosphere soil bacterial community through decreasing soil available N. Additionally, soil moisture increased the diversity of the rhizosphere soil bacterial community through increased soil pH, C/N, and NN, and decreased soil AP. The E. gansuensis endophyte and soil moisture effects on root and rhizosphere soil bacterial diversity were likely to be from responses to modifications of the rhizosphere soil properties.
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Affiliation(s)
- Yawen Ju
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Rui Zhong
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | | | - Xingxu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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213
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Arrigoni E, Albanese D, Longa CMO, Angeli D, Donati C, Ioriatti C, Pertot I, Perazzolli M. Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees. Environ Microbiol 2020; 22:2080-2093. [PMID: 32114708 DOI: 10.1111/1462-2920.14963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/09/2023]
Abstract
Plants host microbial communities that can be affected by environmental conditions and agronomic practices. Despite the role of bark as a reservoir of plant pathogens and beneficial microorganisms, no information is available on the effects of disease management on the taxonomic composition of the bark-associated communities of apple trees. We assessed the impact of disease management strategies on fungal and bacterial communities on the bark of a scab-resistant apple cultivar in two orchard locations and for two consecutive seasons. The amplicon sequencing revealed that bark age and orchard location strongly affected fungal and bacterial diversity. Microbiota dissimilarity between orchards evolved during the growing season and showed specific temporal series for fungal and bacterial populations in old and young bark. Disease management did not induce global changes in the microbial populations across locations and seasons, but specifically affected the abundance of some taxa according to bark age, orchard location and sampling time. Therefore, the disease management applied to scab-resistant cultivars, which is based on a limited use of fungicides, partially changed the taxonomic composition of bark-associated fungal and bacterial communities, suggesting the need for a more accurate risk assessment regarding possible pathogen outbreaks.
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Affiliation(s)
- Elena Arrigoni
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Department of Agricultural and Environmental Sciences, University of Udine, 33100, Udine, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | | | - Dario Angeli
- Technology Transfer Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Claudio Ioriatti
- Technology Transfer Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Ilaria Pertot
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige, Italy
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214
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Fu J, Luo Y, Sun P, Gao J, Zhao D, Yang P, Hu T. Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities. BMC PLANT BIOLOGY 2020; 20:92. [PMID: 32122321 PMCID: PMC7053125 DOI: 10.1186/s12870-020-2300-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/21/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. RESULTS OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. CONCLUSION Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.
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Affiliation(s)
- Juanjuan Fu
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yilan Luo
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Pengyue Sun
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jinzhu Gao
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Donghao Zhao
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Peizhi Yang
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Tianming Hu
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
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215
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Man Y, Wang J, Tam NFY, Wan X, Huang W, Zheng Y, Tang J, Tao R, Yang Y. Responses of rhizosphere and bulk substrate microbiome to wastewater-borne sulfonamides in constructed wetlands with different plant species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135955. [PMID: 31855648 DOI: 10.1016/j.scitotenv.2019.135955] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/01/2019] [Accepted: 12/04/2019] [Indexed: 05/20/2023]
Abstract
Constructed wetlands (CWs) have been used to remove organic pollutants including antibiotics based on the roles of plants and microbial communities, but how rhizosphere and bulk substrate-associated microbiomes respond to antibiotics during biodegradation have seldom been researched. The effects of sulfonamides (SAs) on the microbiome composition in different compartments, namely rhizosphere, near rhizosphere and bulk substrate, in CWs planted with either Cyperus alternifolius, Cyperus papyrus or Juncus effuses were evaluated using specially designed rhizoboxes and 16S rRNA gene high-throughput sequencing. Results revealed that wastewater-borne SAs significantly reduced the microbial biodiversity in CWs, and inhibited the functional bacterial groups related to sulphur and nitrogen cycles. On the contrary, SAs significantly enriched methylotrophs with potential to initially biodegrade SAs, such as Methylosinus, Methylotenera, Methylocaldum and Methylomonas, and such enrichment was more significant in rhizosphere than in bulk substrate. The network analysis indicated that a more complex network in bulk substrate was more fragile to SA stress. The presence of wetland plants significantly influenced the bacterial community structure in CWs, but in the same compartment, the difference among the three plants species was not obvious. Wetland plants ensured the stability of rhizosphere microorganisms and increased their ability to tolerate SA stress. The present study enhances our understanding of the importance of plant-bacteria interactions in CWs and responses of substrate microbiome to antibiotics.
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Affiliation(s)
- Ying Man
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Jiaxi Wang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Nora Fung-Yee Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region
| | - Xiang Wan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China
| | - Wenda Huang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Yu Zheng
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Jinpeng Tang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Ran Tao
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China.
| | - Yang Yang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China.
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216
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Firrincieli A, Khorasani M, Frank AC, Doty SL. Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar. FRONTIERS IN PLANT SCIENCE 2020; 11:203. [PMID: 32184800 PMCID: PMC7058686 DOI: 10.3389/fpls.2020.00203] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/11/2020] [Indexed: 05/02/2023]
Abstract
Plant-associated microbial communities play a central role in the plant response to biotic and abiotic stimuli, improving plant fitness under challenging growing conditions. Many studies have focused on the characterization of changes in abundance and composition of root-associated microbial communities as a consequence of the plant response to abiotic factors such as altered soil nutrients and drought. However, changes in composition in response to abiotic factors are still poorly understood concerning the endophytic community associated to the phyllosphere, the above-ground plant tissues. In the present study, we applied high-throughput 16S rDNA gene sequencing of the phyllosphere endophytic bacterial communities colonizing wild Populus trichocarpa (black cottonwood) plants growing in native, nutrient-limited environments characterized by hot-dry (xeric) riparian zones (Yakima River, WA), riparian zones with mid hot-dry (Tieton and Teanaway Rivers, WA) and moist (mesic) climates (Snoqualmie, Skykomish and Skagit Rivers, WA). From sequencing data, 587 Amplicon Sequence Variants (ASV) were identified. Surprisingly, our data show that a core microbiome could be found in phyllosphere-associated endophytic communities in trees growing on opposite sides of the Cascades Mountain Range. Considering only taxa appearing in at least 90% of all samples within each climatic zone, the core microbiome was dominated only by two ASVs affiliated Pseudomonadaceae and two ASVs of the Enterobacteriaceae family. Alpha-diversity measures indicated that plants colonizing hot-dry environments showed a lower diversity than those from mid hot-dry and moist climates. Beta-diversity measures showed that bacterial composition was significantly different across sampling sites. Accordingly, we found that specific ASV affiliated to Pseudomonadaceae and Enterobacteriaceae were significantly more abundant in the phyllosphere endophytic community colonizing plants adapted to the xeric environment. In summary, this study highlights that sampling site is the major driver of variation and that only a few ASV showed a distribution that significantly correlated to climate variables.
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Affiliation(s)
- Andrea Firrincieli
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
| | - Mahsa Khorasani
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
| | - A. Carolin Frank
- Life & Environmental Sciences School of Natural Sciences, University of California, Merced, Merced, CA, United States
- Sierra Nevada Research Institute, School of Natural Sciences, University of California, Merced, Merced, CA, United States
| | - Sharon Lafferty Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
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217
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Acosta K, Xu J, Gilbert S, Denison E, Brinkman T, Lebeis S, Lam E. Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome. PLoS One 2020; 15:e0228560. [PMID: 32027711 PMCID: PMC7004381 DOI: 10.1371/journal.pone.0228560] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/19/2020] [Indexed: 12/20/2022] Open
Abstract
Culture-independent characterization of microbial communities associated with popular plant model systems have increased our understanding of the plant microbiome. However, the integration of other model systems, such as duckweed, could facilitate our understanding of plant microbiota assembly and evolution. Duckweeds are floating aquatic plants with many characteristics, including small size and reduced plant architecture, that suggest their use as a facile model system for plant microbiome studies. Here, we investigated the structure and assembly of the duckweed bacterial microbiome. First, a culture-independent survey of the duckweed bacterial microbiome from different locations in New Jersey revealed similar phylogenetic profiles. These studies showed that Proteobacteria is a dominant phylum in the duckweed bacterial microbiome. To observe the assembly dynamics of the duckweed bacterial community, we inoculated quasi-gnotobiotic duckweed with wastewater effluent from a municipal wastewater treatment plant. Our results revealed that duckweed strongly shapes its bacterial microbiome and forms distinct associations with bacterial community members from the initial inoculum. Additionally, these inoculation studies showed the bacterial communities of different duckweed species were similar in taxa composition and abundance. Analysis across the different duckweed bacterial communities collected in this study identified a set of "core" bacterial taxa consistently present on duckweed irrespective of the locale and context. Furthermore, comparison of the duckweed bacterial community to that of rice and Arabidopsis revealed a conserved taxonomic structure between the duckweed microbiome and the terrestrial leaf microbiome. Our results suggest that duckweeds utilize similar bacterial community assembly principles as those found in terrestrial plants and indicate a highly conserved structuring effect of leaf tissue on the plant microbiome.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Jenny Xu
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Elizabeth Denison
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas Brinkman
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
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218
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Xu Y, Zhang G, Ding H, Ci D, Dai L, Zhang Z. Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.). Int Microbiol 2020; 23:453-465. [PMID: 31933013 DOI: 10.1007/s10123-020-00118-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/29/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022]
Abstract
Soil salinity is regarded as severe environmental stress that can change the composition of rhizosphere soil bacterial community and import a plethora of harms to crop plants. However, relatively little is known about the relationship between salt stress and root microbial communities in groundnuts. The goal of this study was to assess the effect of salt stress on groundnut growth performance and rhizosphere microbial community structure. Statistical analysis exhibited that salt stress indeed affected groundnut growth and pod yield. Further taxonomic analysis showed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Saccharibacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of Cyanobacteria and Acidobacteria mainly increased, while that of Actinobacteria and Chloroflexi decreased after salt treatment via taxonomic and qPCR analysis. Moreover, Sphingomonas and Microcoleus as the predominant genera in salt-treated rhizosphere soils might enhance salt tolerance as plant growth-promoting rhizobacteria. Metagenomic profiling showed that series of sequences related to signaling transduction, posttranslational modification, and chaperones were enriched in the salt-treated soils, which may have implications for plant survival and salt tolerance. These data will help us better understand the symbiotic relationship between the dominant microbial community and groundnuts and form the foundation for further improvement of salt tolerance of groundnuts via modification of soil microbial community.
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Affiliation(s)
- Yang Xu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Guanchu Zhang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Hong Ding
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Dunwei Ci
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Liangxiang Dai
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, 266100, China.
| | - Zhimeng Zhang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, 266100, China.
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219
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Guo X, Zhang X, Qin Y, Liu YX, Zhang J, Zhang N, Wu K, Qu B, He Z, Wang X, Zhang X, Hacquard S, Fu X, Bai Y. Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome. PLANT COMMUNICATIONS 2020; 1:100003. [PMID: 33404537 PMCID: PMC7747982 DOI: 10.1016/j.xplc.2019.100003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/09/2019] [Accepted: 07/29/2019] [Indexed: 05/08/2023]
Abstract
Plant-associated microbes are critical for plant growth and survival under natural environmental conditions. To date, most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa. However, this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues. Here, we report the development of a host-associated quantitative abundance profiling (HA-QAP) method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome. We validate the HA-QAP method using mock experiments, perturbation experiments, and metagenomic sequencing. The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance, and reveals the load of root microbiome to host plants. Using the HA-QAP method, we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat. Furthermore, using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease, which significantly influences patterns of differential taxa and species interaction networks. Given its accuracy and technical feasibility, HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.
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Affiliation(s)
- Xiaoxuan Guo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xiaoning Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuan Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Na Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Kun Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoyuan Qu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Zishan He
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xinjian Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
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220
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de Souza RSC, Armanhi JSL, Arruda P. From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency. FRONTIERS IN PLANT SCIENCE 2020; 11:1179. [PMID: 32983187 PMCID: PMC7484511 DOI: 10.3389/fpls.2020.01179] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/21/2020] [Indexed: 05/19/2023]
Abstract
Plants teem with microorganisms, whose tremendous diversity and role in plant-microbe interactions are being increasingly explored. Microbial communities create a functional bond with their hosts and express beneficial traits capable of enhancing plant performance. Therefore, a significant task of microbiome research has been identifying novel beneficial microbial traits that can contribute to crop productivity, particularly under adverse environmental conditions. However, although knowledge has exponentially accumulated in recent years, few novel methods regarding the process of designing inoculants for agriculture have been presented. A recently introduced approach is the use of synthetic microbial communities (SynComs), which involves applying concepts from both microbial ecology and genetics to design inoculants. Here, we discuss how to translate this rationale for delivering stable and effective inoculants for agriculture by tailoring SynComs with microorganisms possessing traits for robust colonization, prevalence throughout plant development and specific beneficial functions for plants. Computational methods, including machine learning and artificial intelligence, will leverage the approaches of screening and identifying beneficial microbes while improving the process of determining the best combination of microbes for a desired plant phenotype. We focus on recent advances that deepen our knowledge of plant-microbe interactions and critically discuss the prospect of using microbes to create SynComs capable of enhancing crop resiliency against stressful conditions.
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Affiliation(s)
- Rafael Soares Correa de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Jaderson Silveira Leite Armanhi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Paulo Arruda,
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221
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Emmett BD, Buckley DH, Drinkwater LE. Plant growth rate and nitrogen uptake shape rhizosphere bacterial community composition and activity in an agricultural field. THE NEW PHYTOLOGIST 2020; 225:960-973. [PMID: 31487394 DOI: 10.1111/nph.16171] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Plant-microbial interactions in the rhizosphere are an essential link in soil nitrogen (N) cycling and plant N supply. Plant phenotype and genotype interact with the soil environment to determine rhizosphere community structure and activity. However, the relative contributions of plant identity, phenology and soil resource availability in shaping rhizosphere effects are not well understood. Four summer annuals and a collection of maize hybrids were grown in a common garden experiment conducted at two levels of organic nutrient availability. Plant biomass, N accumulation, rhizosphere bacterial community composition, and rhizosphere potential extracellular enzyme activity were assessed at vegetative, flowering and grain-filling stages of maize. Plant N uptake was strongly coupled with protease activity in the rhizosphere. Temporal trends in rhizosphere community composition varied between plant species. Changes in rhizosphere community composition could be explained by variation in plant growth dynamics. These findings indicate that species-level variation in plant growth dynamics and resource acquisition drive variation in rhizosphere bacterial community composition and activity linked to plant N uptake.
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Affiliation(s)
- Bryan D Emmett
- Horticulture Section, School of Integrative Plant Science, Cornell University, 134A Plant Science Building, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, 232 Emerson Hall, Ithaca, NY, 14853, USA
| | - Laurie E Drinkwater
- Horticulture Section, School of Integrative Plant Science, Cornell University, 134A Plant Science Building, Ithaca, NY, 14853, USA
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222
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Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities. Microorganisms 2019; 8:microorganisms8010009. [PMID: 31861554 PMCID: PMC7022406 DOI: 10.3390/microorganisms8010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 11/17/2022] Open
Abstract
We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.
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223
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Hannula SE, Ma HK, Pérez-Jaramillo JE, Pineda A, Bezemer TM. Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen. Environ Microbiol 2019; 22:660-676. [PMID: 31788934 PMCID: PMC7027455 DOI: 10.1111/1462-2920.14882] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/22/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022]
Abstract
Interactions between plants and soil microbes are important for plant growth and resistance. Through plant–soil‐feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant–soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant‐induced changes in soil microbiomes on the growth of the commercially important cut‐flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next‐generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species‐specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.
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Affiliation(s)
- S Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Hai-Kun Ma
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Ana Pineda
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - T Martijn Bezemer
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
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224
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Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proc Natl Acad Sci U S A 2019; 117:1148-1159. [PMID: 31806755 DOI: 10.1073/pnas.1908600116] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health.
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225
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Liu H, Macdonald CA, Cook J, Anderson IC, Singh BK. An Ecological Loop: Host Microbiomes across Multitrophic Interactions. Trends Ecol Evol 2019; 34:1118-1130. [DOI: 10.1016/j.tree.2019.07.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/12/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022]
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226
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Deng S, Wipf HML, Pierroz G, Raab TK, Khanna R, Coleman-Derr D. A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome. Sci Rep 2019; 9:17677. [PMID: 31776356 PMCID: PMC6881409 DOI: 10.1038/s41598-019-53623-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/01/2019] [Indexed: 12/22/2022] Open
Abstract
Despite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.
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Affiliation(s)
- Siwen Deng
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Heidi M-L Wipf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Ted K Raab
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
| | - Rajnish Khanna
- i-Cultiver, Inc., 404 Clipper Cove Way, San Francisco, CA, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA.
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227
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Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9120779] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Endophytic microbiota plays a role not only in supplying plants with the basic nutrients indispensable for their growth, but also helps them in the mechanisms of adaptation to various environmental stresses (i.e., salinity, drought), which is important in the aspect of crop yields. From the agricultural and biotechnological points of view, the knowledge of endophytes and their roles in increasing crop yields, plant resistance to diseases, and helping to survive environmental stress is extremely desirable. This paper reviews some of the beneficial plant–microbe interactions that might be potentially used in both agriculture (plant growth stimulation effect, adaptation of host organisms in salinity and drought conditions, and support of defense mechanisms in plants), and in biotechnology (bioactive metabolites, application of endophytes for bioremediation and biotransformation processes, and production of biofertilizers and biopreparations). Importantly, relatively recent reports on endophytes from the last 10 years are summarized in this paper.
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228
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Escudero-Martinez C, Bulgarelli D. Tracing the evolutionary routes of plant-microbiota interactions. Curr Opin Microbiol 2019; 49:34-40. [PMID: 31698159 DOI: 10.1016/j.mib.2019.09.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 11/26/2022]
Abstract
The microbiota thriving at the root-soil interface plays a crucial role in supporting plant growth, development and health. The interactions between plant and soil microbes can be traced back to the initial plant's colonisation of dry lands. Understanding the evolutionary drivers of these interactions will be key to re-wire them for the benefit of mankind. Here we critically assess recent insights into the evolutionary history of plant-microbiota interactions in natural and agricultural ecosystems. We identify distinctive features, as well as commonalities, of these two distinct scenarios and areas requiring further research efforts. Finally, we propose strategies that combining advances in molecular microbiology and crop genomics will be key towards a predictable manipulation of plant-microbiota interactions for sustainable crop production.
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Affiliation(s)
| | - Davide Bulgarelli
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, United Kingdom.
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229
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Nilsson LKJ, de Oliveira MR, Marinotti O, Rocha EM, Håkansson S, Tadei WP, de Souza AQL, Terenius O. Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area. MICROBIAL ECOLOGY 2019; 78:781-791. [PMID: 30989355 PMCID: PMC6842340 DOI: 10.1007/s00248-019-01369-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 03/19/2019] [Indexed: 05/19/2023]
Abstract
The microbiota in mosquito breeding waters can affect ovipositing mosquitoes, have effects on larval development, and can modify adult mosquito-gut bacterial composition. This, in turn, can affect transmission of human pathogens such as malaria parasites. Here, we explore the microbiota of four breeding sites for Anopheles darlingi, the most important malaria vector in Latin America. The sites are located in Manaus in the Amazon basin in Brazil, an area of active malaria transmission. Using 16S rRNA gene sequencing by MiSeq, we found that all sites were dominated by Proteobacteria and Firmicutes and that 94% of the total number of reads belonged to 36 operational taxonomic units (OTUs) identified in all sites. Of these, the most common OTUs belonged to Escherichia/Shigella, Staphylococcus, and Pseudomonas. Of the remaining 6% of the reads, the OTUs found to differentiate between the four sites belonged to the orders Burkholderiales, Actinomycetales, and Clostridiales. We conclude that An. darlingi can develop in breeding waters with different surface-water bacteria, but that the common microbiota found in all breeding sites might indicate or contribute to a suitable habitat for this important malaria vector.
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Affiliation(s)
- Louise K J Nilsson
- Department of Cell and Molecular Biology, Microbiology, Uppsala University, P.O. Box 596, 751 24, Uppsala, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7044, 750 07, Uppsala, Sweden
| | - Marta Rodrigues de Oliveira
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, AM, 69065-001, Brazil
| | - Osvaldo Marinotti
- Department of Molecular Biology and Biochemistry, University of California, 3205 Mc-Gaugh Hall, Irvine, CA, 92697, USA
| | - Elerson Matos Rocha
- Programa de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas, Manaus, AM, Brazil
- Laboratório de Malária e Dengue, Instituto Nacional de Pesquisas da Amazonia, Manaus, AM, 69011-970, Brazil
| | - Sebastian Håkansson
- Uppsala BioCenter. Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), P.O. Box 7025, 750 07, Uppsala, Sweden
| | - Wanderli P Tadei
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, AM, 69065-001, Brazil
- Laboratório de Malária e Dengue, Instituto Nacional de Pesquisas da Amazonia, Manaus, AM, 69011-970, Brazil
| | - Antonia Queiroz Lima de Souza
- Programa de Pós-graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, AM, 69065-001, Brazil
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas (FCA/UFAM), Manaus, AM, 69080-900, Brazil
| | - Olle Terenius
- Department of Cell and Molecular Biology, Microbiology, Uppsala University, P.O. Box 596, 751 24, Uppsala, Sweden.
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7044, 750 07, Uppsala, Sweden.
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230
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Finkel OM, Salas-González I, Castrillo G, Spaepen S, Law TF, Teixeira PJPL, Jones CD, Dangl JL. The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLoS Biol 2019; 17:e3000534. [PMID: 31721759 PMCID: PMC6876890 DOI: 10.1371/journal.pbio.3000534] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/25/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms-the plant microbiota-are exposed to direct influence by the soil's phosphorus (P) content itself as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient and compared the composition of their shoot and root microbiota to wild-type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota than soil P concentrations in both roots and shoots. To dissect plant-microbe interactions under variable P conditions, we conducted a microbiota reconstitution experiment. Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift was accompanied by changes in microbiota composition: the genus Burkholderia was specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrated that in the absence of Burkholderia from the SynCom, plant shoots accumulated higher ortophosphate (Pi) levels than shoots colonized with the full SynCom but only under Pi starvation conditions. Therefore, Pi-stressed plants are susceptible to colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant's Pi starvation.
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Affiliation(s)
- Omri M. Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stijn Spaepen
- Department Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Theresa F. Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paulo José Pereira Lima Teixeira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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231
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Brisson VL, Schmidt JE, Northen TR, Vogel JP, Gaudin ACM. Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil. Sci Rep 2019; 9:15611. [PMID: 31666614 PMCID: PMC6821752 DOI: 10.1038/s41598-019-52148-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/13/2019] [Indexed: 11/09/2022] Open
Abstract
Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.
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Affiliation(s)
- Vanessa L Brisson
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,The DOE Joint Genome Institute, Walnut Creek, CA, USA. .,Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jennifer E Schmidt
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,The DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - John P Vogel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,The DOE Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Amélie C M Gaudin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant Sciences, University of California at Davis, Davis, CA, USA
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232
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Hartman K, Tringe SG. Interactions between plants and soil shaping the root microbiome under abiotic stress. Biochem J 2019; 476:2705-2724. [PMID: 31654057 PMCID: PMC6792034 DOI: 10.1042/bcj20180615] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/24/2019] [Accepted: 09/12/2019] [Indexed: 01/06/2023]
Abstract
Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes - collectively termed the root microbiome - are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.
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Affiliation(s)
- Kyle Hartman
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, U.S.A
| | - Susannah G. Tringe
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, U.S.A
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
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Zhang Y, Wang X, Xu F, Song T, Du H, Gui Y, Xu M, Cao Y, Dang X, Rensing C, Zhang J, Xu W. Combining Irrigation Scheme and Phosphorous Application Levels for Grain Yield and Their Impacts on Rhizosphere Microbial Communities of Two Rice Varieties in a Field Trial. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10577-10586. [PMID: 31490682 DOI: 10.1021/acs.jafc.9b03124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Root and rhizosphere is important for phosphorus (P) uptake in rice plants. However, little is known about the detailed regulation of irrigation regimes, especially frequently alternate wetting and drying (FAWD), on P usage of rice plants. Here, we found that compared with normal water and P dose, FAWD with a reduced P dose maintained the grain yield in two rice varieties. Compared to rice variety Gaoshan1, rice variety WufengyouT025 displayed a higher grain yield, shoot P content, rhizosphere acid phosphatase activity, abundance of bacteria, and bacterial acid phosphatase gene of rhizosphere. Moreover, the FAWD regime may increase the abundance of bacteria with acid phosphatase activity to release available phosphorus in the rhizosphere, which is associated with rice varieties. Our results suggest that an optimized management of irrigation and phosphorous application can enhance both water and phosphorus use efficiency without sacrificing the yield, which may contribute significantly to sustainable agriculture production.
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Affiliation(s)
- Yingjiao Zhang
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Xiaoyun Wang
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Feiyun Xu
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Tao Song
- School of Life Sciences and State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong 999077 , China
| | - Huan Du
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Yao Gui
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Min Xu
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Yiying Cao
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Xiaolin Dang
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Christopher Rensing
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong 999077 , China
| | - Weifeng Xu
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop , Fujian Agriculture and Forestry University , Jinshan, Fuzhou 350002 , China
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235
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Imchen M, Kumavath R, Vaz ABM, Góes-Neto A, Barh D, Ghosh P, Kozyrovska N, Podolich O, Azevedo V. 16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages. Front Microbiol 2019; 10:2103. [PMID: 31616390 PMCID: PMC6764247 DOI: 10.3389/fmicb.2019.02103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/26/2019] [Indexed: 11/21/2022] Open
Abstract
Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Aline B M Vaz
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Natalia Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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236
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Carrell AA, Kolton M, Glass JB, Pelletier DA, Warren MJ, Kostka JE, Iversen CM, Hanson PJ, Weston DJ. Experimental warming alters the community composition, diversity, and N 2 fixation activity of peat moss (Sphagnum fallax) microbiomes. GLOBAL CHANGE BIOLOGY 2019; 25:2993-3004. [PMID: 31148286 PMCID: PMC6852288 DOI: 10.1111/gcb.14715] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 05/19/2023]
Abstract
Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole-ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next-generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over 2 years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (p < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.
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Affiliation(s)
- Alyssa A. Carrell
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Max Kolton
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | | | - Melissa J. Warren
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
- Present address:
CH2MAtlantaGeorgia30328USA
| | - Joel E. Kostka
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | - Colleen M. Iversen
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - David J. Weston
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
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237
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Kang MS, Hur M, Park SJ. Rhizocompartments and environmental factors affect microbial composition and variation in native plants. J Microbiol 2019; 57:550-561. [DOI: 10.1007/s12275-019-8646-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 11/27/2022]
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238
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Wang P, Marsh EL, Kruger G, Lorenz A, Schachtman DP. Belowground microbial communities respond to water deficit and are shaped by decades of maize hybrid breeding. Environ Microbiol 2019; 22:889-904. [DOI: 10.1111/1462-2920.14701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Peng Wang
- Department of Agronomy and Horticulture University of Nebraska Lincoln Lincoln NE 68588 USA
| | - Ellen L. Marsh
- Department of Agronomy and Horticulture University of Nebraska Lincoln Lincoln NE 68588 USA
| | - Greg Kruger
- Department of Agronomy and Horticulture University of Nebraska Lincoln Lincoln NE 68588 USA
| | - Aaron Lorenz
- Department of Agronomy and Plant Genetics University of Minnesota St. Paul MN 55108
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture University of Nebraska Lincoln Lincoln NE 68588 USA
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239
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Wen ZL, Yang MK, Du MH, Zhong ZZ, Lu YT, Wang GH, Hua XM, Fazal A, Mu CH, Yan SF, Zhen Y, Yang RW, Qi JL, Hong Z, Lu GH, Yang YH. Enrichments/Derichments of Root-Associated Bacteria Related to Plant Growth and Nutrition Caused by the Growth of an EPSPS-Transgenic Maize Line in the Field. Front Microbiol 2019; 10:1335. [PMID: 31275269 PMCID: PMC6591461 DOI: 10.3389/fmicb.2019.01335] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/29/2019] [Indexed: 11/13/2022] Open
Abstract
During the past decades, the effects of the transgenic crops on soil microbial communities have aroused widespread interest of scientists, which was mainly related to the health and growth of plants. In this study, the maize root-associated bacterial communities of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) transgenic glyphosate-tolerant (GT) maize line CC-2 (CC2) and its recipient variety Zhengdan958 (Z958) were compared at the tasseling and flowering stages by high-throughput sequencing of V3-V4 hypervariable regions of 16S rRNA gene (16S rDNA) amplicons via Illumina MiSeq. In addition, real-time quantitative PCR (qPCR) was also performed to analyze the nifH gene abundance between CC2 and Z958. Our results showed no significant difference in alpha/beta diversity of root-associated bacterial communities at the tasseling or flowering stage between CC2 and Z958 under field growth conditions. The relative abundances of the genera Bradyrhizobium and Bacillus including species B. cereus and B. muralis were significantly lower in the roots of CC2 than that of Z985 under field conditions. Both these species are regarded as plant growth promoting bacteria (PGPB), as they belong to both nitrogen-fixing and phosphate-solubilizing bacterial genera. The comparison of the relative abundance of nitrogen-fixing/phosphate-solubilizing bacteria at the class, order or family levels indicated that only one class Bacilli, one order Bacillales and one family Bacillaceae were found to be significantly lower in the roots of CC2 than that of Z985. These bacteria were also enriched in the roots and rhizospheric soil than in the surrounding soil at both two stages. Furthermore, the class Betaproteobacteria, the order Burkholderiales, the family Comamonadaceae, and the genus Acidovorax were significantly higher in the roots of CC2 than that of Z985 at the tasseling stage, meanwhile the order Burkholderiales and the family Comamonadaceae were also enriched in the roots than in the rhizospheric soil at both stages. Additionally, the nifH gene abundance at the tasseling stage in the rhizosphere soil also showed significant difference. The relative abundance of nifH gene was higher in the root samples and lower in the surrounding soil, which implicated that the roots of maize tend to be enriched in nitrogen-fixing bacteria.
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Affiliation(s)
- Zhong-Ling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Min-Kai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Mei-Hang Du
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhao-Zhao Zhong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Yun-Ting Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Gu-Hao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Xiao-Mei Hua
- Research Center for Soil Pollution Prevention and Control, Nanjing Institute of Environmental Sciences, MEE, Nanjing, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Chun-Hua Mu
- Shandong Academy of Agriculture Sciences, Jinan, China
| | - Shu-Feng Yan
- Henan Academy of Agriculture Sciences, Zhengzhou, China
| | - Yan Zhen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Rong-Wu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Jin-Liang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Gui-Hua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yong-Hua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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240
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Abstract
Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community's metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies.IMPORTANCE Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. In this study, we found that soil drying had a significant impact on the structure and function of soil microbial communities, including shifts in expression of specific metabolic pathways, such as those leading toward production of osmoprotectant compounds. This study demonstrates the application of an untargeted multi-omics approach to decipher details of the soil microbial community's metaphenotypic response to environmental perturbations and should be applicable to studies of other complex microbial systems as well.
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241
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Xu L, Coleman-Derr D. Causes and consequences of a conserved bacterial root microbiome response to drought stress. Curr Opin Microbiol 2019; 49:1-6. [DOI: 10.1016/j.mib.2019.07.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
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242
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Dai L, Zhang G, Yu Z, Ding H, Xu Y, Zhang Z. Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil. Int J Mol Sci 2019; 20:ijms20092265. [PMID: 31071918 PMCID: PMC6540327 DOI: 10.3390/ijms20092265] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/13/2023] Open
Abstract
Background: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts. Method: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts. Results: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance. Conclusion: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.
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Affiliation(s)
- Liangxiang Dai
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266100, China.
| | - Guanchu Zhang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266100, China.
| | - Zipeng Yu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China.
| | - Hong Ding
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266100, China.
| | - Yang Xu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266100, China.
| | - Zhimeng Zhang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266100, China.
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243
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Liu H, Khan MY, Carvalhais LC, Delgado-Baquerizo M, Yan L, Crawford M, Dennis PG, Singh B, Schenk PM. Soil amendments with ethylene precursor alleviate negative impacts of salinity on soil microbial properties and productivity. Sci Rep 2019; 9:6892. [PMID: 31053834 PMCID: PMC6499801 DOI: 10.1038/s41598-019-43305-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/12/2019] [Indexed: 12/04/2022] Open
Abstract
Some microbes enhance stress tolerance in plants by minimizing plant ethylene levels via degradation of its immediate precursor, 1-aminocyclopropane-1-carboxylate (ACC), in the rhizosphere. In return, ACC is used by these microbes as a source of nitrogen. This mutualistic relationship between plants and microbes may be used to promote soil properties in stressful environments. In this study, we tested the hypothesis that amendments of ACC in soils reshape the structure of soil microbiome and alleviate the negative impacts of salinity on soil properties. We treated non-saline and artificially-developed saline soils with ACC in different concentrations for 14 days. The structure of soil microbiome, soil microbial properties and productivity were examined. Our results revealed that microbial composition of bacteria, archaea and fungi in saline soils was affected by ACC amendments; whereas community composition in non-saline soils was not affected. The amendments of ACC could not fully counteract the negative effects of salinity on soil microbial activities and productivity, but increased the abundance of ACC deaminase-encoding gene (acdS), enhanced soil microbial respiration, enzymatic activity, nitrogen and carbon cycling potentials and Arabidopsis biomass in saline soils. Collectively, our study indicates that ACC amendments in soils could efficiently ameliorate salinity impacts on soil properties and plant biomass production.
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Affiliation(s)
- Hongwei Liu
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia. .,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.
| | - Muhammad Yahya Khan
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.,Institute of Soil and Environmental Science, The University of Agriculture, Faisalabad, 38000, Pakistan.,The University of Agriculture Faisalabad, Sub-Campus Burewala, Vehari, 61100, Pakistan
| | - Lilia C Carvalhais
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.,Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, Queensland, 4102, Australia
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA
| | - Lijuan Yan
- Institute of Biodiversity, Friedrich Schiller University, Jena, 07749, Germany
| | - Mark Crawford
- Department of Natural Resources and Mines, Toowoomba, QLD, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Peer M Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
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244
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The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China. Appl Microbiol Biotechnol 2019; 103:3899-3913. [PMID: 30903216 DOI: 10.1007/s00253-019-09747-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/28/2019] [Accepted: 03/11/2019] [Indexed: 12/26/2022]
Abstract
Few studies have investigated the effect of environment on the root-associated microbiome, especially for woody plants in their native environment. The roots and rhizosphere soils of a native woody species (Broussonetia papyrifera) sampled across four different climate types in China were used to elucidate the influence of environment on the root-associated microbiome. Our results showed that the B. papyrifera root-associated microbiome contained abundant Proteobacteria and Basidiomycota, especially Pseudomonas and Rhizobium. The root-associated microbiomes were found to be significantly different under different climate types except for the bacterial community in the rhizosphere, and the proportion of bacterial operational taxonomic units (OTUs) shared among different climate types was lower than that of fungi. More than 50% of the total variance between microbiomes could be explained by 15 environmental factors, six of which, especially soil concentration phosphate and nitrate, had a significant effect. This study provided a comprehensive understanding of the root-associated microbiome of B. papyrifera and further confirmed the effect of environment on the root-associated microbiome of B. papyrifera under different climate types, with some exceptions in the rhizobacterial community and fungal OTUs. Our findings advanced knowledge of the effect of environment through an exploration of environmental factors and found that the nitrogen and phosphorus content represented the key factors.
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Zhang Q, Acuña JJ, Inostroza NG, Mora ML, Radic S, Sadowsky MJ, Jorquera MA. Endophytic Bacterial Communities Associated with Roots and Leaves of Plants Growing in Chilean Extreme Environments. Sci Rep 2019; 9:4950. [PMID: 30894597 PMCID: PMC6426880 DOI: 10.1038/s41598-019-41160-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
Several studies have demonstrated the relevance of endophytic bacteria on the growth and fitness of agriculturally-relevant plants. To our knowledge, however, little information is available on the composition, diversity, and interaction of endophytic bacterial communities in plants struggling for existence in the extreme environments of Chile, such as the Atacama Desert (AD) and Patagonia (PAT). The main objective of the present study was to analyze and compare the composition of endophytic bacterial communities associated with roots and leaves of representative plants growing in Chilean extreme environments. The plants sampled were: Distichlis spicate and Pluchea absinthioides from the AD, and Gaultheria mucronata and Hieracium pilosella from PAT. The abundance and composition of their endophytic bacterial communities was determined by quantitative PCR and high–throughput sequencing of 16S rRNA, respectively. Results indicated that there was a greater abundance of 16S rRNA genes in plants from PAT (1013 to 1014 copies g−1 DNA), compared with those from AD (1010 to 1012 copies g−1 DNA). In the AD, a greater bacterial diversity, as estimated by Shannon index, was found in P. absinthioides, compared with D. spicata. In both ecosystems, the greater relative abundances of endophytes were mainly attributed to members of the phyla Proteobacteria (14% to 68%), Firmicutes (26% to 41%), Actinobacteria (6 to 23%) and Bacteroidetes (1% to 21%). Our observations revealed that most of operational taxonomic units (OTUs) were not shared between tissue samples of different plant species in both locations, suggesting the effect of the plant genotype (species) on the bacterial endophyte communities in Chilean extreme environments, where Bacillaceae and Enterobacteriacea could serve as keystone taxa as revealed our linear discriminant analysis.
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Affiliation(s)
- Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - María Luz Mora
- Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Sergio Radic
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad de Magallanes, Ave. Bulnes 01855, Punta Arenas, Chile
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA.,Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. .,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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246
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Brisson V, Schmidt J, Northen TR, Vogel JP, Gaudin A. A New Method to Correct for Habitat Filtering in Microbial Correlation Networks. Front Microbiol 2019; 10:585. [PMID: 30949160 PMCID: PMC6435493 DOI: 10.3389/fmicb.2019.00585] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/07/2019] [Indexed: 11/21/2022] Open
Abstract
Amplicon sequencing of 16S, ITS, and 18S regions of microbial genomes is a commonly used first step toward understanding microbial communities of interest for human health, agriculture, and the environment. Correlation network analysis is an emerging tool for investigating the interactions within these microbial communities. However, when data from different habitats (e.g., sampling sites, host genotype, etc.) are combined into one analysis, habitat filtering (co-occurrence of microbes due to habitat sampled rather than biological interactions) can induce apparent correlations, resulting in a network dominated by habitat effects and masking correlations of biological interest. We developed an algorithm to correct for habitat filtering effects in microbial correlation network analysis in order to reveal the true underlying microbial correlations. This algorithm was tested on simulated data that was constructed to exhibit habitat filtering. Our algorithm significantly improved correlation detection accuracy for these data compared to Spearman and Pearson correlations. We then used our algorithm to analyze a two real data sets of 16S variable region amplicon sequences that were expected to exhibit habitat filtering. Our algorithm was found to effectively reduce habitat effects, enabling the construction of consensus correlation networks from data sets combining multiple related sample habitats.
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Affiliation(s)
- Vanessa Brisson
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- The DOE Joint Genome Institute, Walnut Creek, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Jennifer Schmidt
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- The DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - John P. Vogel
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- The DOE Joint Genome Institute, Walnut Creek, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Amélie Gaudin
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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247
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Hara S, Morikawa T, Wasai S, Kasahara Y, Koshiba T, Yamazaki K, Fujiwara T, Tokunaga T, Minamisawa K. Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses. Front Microbiol 2019; 10:407. [PMID: 30915047 PMCID: PMC6422874 DOI: 10.3389/fmicb.2019.00407] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/15/2019] [Indexed: 02/04/2023] Open
Abstract
Sorghum (Sorghum bicolor) is cultivated worldwide for food, bioethanol, and fodder production. Although nitrogen fixation in sorghum has been studied since the 1970s, N2-fixing bacteria have not been widely examined in field-grown sorghum plants because the identification of functional diazotrophs depends on the culture method used. The aim of this study was to identify functional N2-fixing bacteria associated with field-grown sorghum by using “omics” approaches. Four lines of sorghum (KM1, KM2, KM4, and KM5) were grown in a field in Fukushima, Japan. The nitrogen-fixing activities of the roots, leaves, and stems were evaluated by acetylene reduction and 15N2-feeding assays. The highest nitrogen-fixing activities were detected in the roots of lines KM1 and KM2 at the late growth stage. Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. Most sequences were assigned to nifHDK of Bradyrhizobium species, including non-nodulating Bradyrhizobium sp. S23321 and photosynthetic B. oligotrophicum S58T. Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9–3.6%) of Bradyrhizobium in the roots. Proteome analysis indicated that three NifHDK proteins of Bradyrhizobium species were consistently detected across sample replicates. By using oligotrophic media, we purified eight bradyrhizobial isolates. Among them, two bradyrhizobial isolates possessed 16S rRNA and nif genes similar to those in S23321 and S58T which were predicted as functional diazotrophs by omics approaches. Both free-living cells of the isolates expressed N2-fixing activity in a semi-solid medium according to an acetylene reduction assay. These results suggest that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhizobium sp. S23321. Based on our findings, we discuss the N2-fixing activity level of sorghum plants, phylogenetic and genomic comparison with diazotrophic bacteria in other crops, and Bradyrhizobium diversity in N2 fixation and nodulation.
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Affiliation(s)
- Shintaro Hara
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takashi Morikawa
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sawa Wasai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | | | - Kiyoshi Yamazaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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248
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Fitzpatrick CR, Mustafa Z, Viliunas J. Soil microbes alter plant fitness under competition and drought. J Evol Biol 2019; 32:438-450. [PMID: 30739360 DOI: 10.1111/jeb.13426] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 02/02/2019] [Accepted: 02/05/2019] [Indexed: 01/02/2023]
Abstract
Plants exist across varying biotic and abiotic environments, including variation in the composition of soil microbial communities. The ecological effects of soil microbes on plant communities are well known, whereas less is known about their importance for plant evolutionary processes. In particular, the net effects of soil microbes on plant fitness may vary across environmental contexts and among plant genotypes, setting the stage for microbially mediated plant evolution. Here, we assess the effects of soil microbes on plant fitness and natural selection on flowering time in different environments. We performed two experiments in which we grew Arabidopsis thaliana genotypes replicated in either live or sterilized soil microbial treatments, and across varying levels of either competition (isolation, intraspecific competition or interspecific competition) or watering (well-watered or drought). We found large effects of competition and watering on plant fitness as well as the expression and natural selection of flowering time. Soil microbes increased average plant fitness under interspecific competition and drought and shaped the response of individual plant genotypes to drought. Finally, plant tolerance to either competition or drought was uncorrelated between soil microbial treatments suggesting that the plant traits favoured under environmental stress may depend on the presence of soil microbes. In summary, our experiments demonstrate that soil microbes can have large effects on plant fitness, which depend on both the environment and individual plant genotype. Future work in natural systems is needed for a complete understanding of the evolutionary importance of interactions between plants and soil microorganisms.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Zainab Mustafa
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Joani Viliunas
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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249
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Koyama A, Steinweg JM, Haddix ML, Dukes JS, Wallenstein MD. Soil bacterial community responses to altered precipitation and temperature regimes in an old field grassland are mediated by plants. FEMS Microbiol Ecol 2019; 94:4628037. [PMID: 29145592 DOI: 10.1093/femsec/fix156] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/13/2017] [Indexed: 01/10/2023] Open
Abstract
The structure and function of soil microbiomes often change in response to experimental climate manipulations, suggesting an important role in ecosystem feedbacks. However, it is difficult to know if microbes are responding directly to environmental changes or are more strongly impacted by plant responses. We investigated soil microbial responses to precipitation and temperature manipulations at the Boston-Area Climate Experiment in Massachusetts, USA, in both vegetated and bare plots to parse direct vs. plant-mediated responses to multi-factor climate change. We assessed the bacterial community in vegetated soils in 2009, two years after the experiment was initiated, and bacterial and fungal community in vegetated and bare soils in 2011. The bacterial community structure was significantly changed by the treatments in vegetated soils. However, such changes in the bacterial community across the treatments were absent in the 2011 bare soils. These results suggest that the bacterial communities in vegetated soils were structured via plant community shifts in response to the abiotic manipulations. Co-variation between bacterial community structure and temperature sensitivities and stoichiometry of potential enzyme activities in the 2011 vegetated soils suggested a link between bacterial community structure and ecosystem function. This study emphasizes the importance of plant-soil-microbial interactions in mediating responses to future climate change.
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Affiliation(s)
- Akihiro Koyama
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Biology, Algoma University, Queen Street East, Sault Ste. Marie, Ontario P6A 2G4, Canada
| | - J Megan Steinweg
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Biology, Roanoke College, Salem, Virginia 24153, USA
| | - Michelle L Haddix
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Jeffrey S Dukes
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana 47907, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Matthew D Wallenstein
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA.,Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, Colorado 80523, USA
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250
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Ullah A, Akbar A, Luo Q, Khan AH, Manghwar H, Shaban M, Yang X. Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions. MICROBIAL ECOLOGY 2019; 77:429-439. [PMID: 30196314 DOI: 10.1007/s00248-018-1260-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/02/2018] [Indexed: 05/18/2023]
Abstract
Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.
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Affiliation(s)
- Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Adnan Akbar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Qingqing Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
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