251
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Tao S, Zhang Y, Tian C, Duplessis S, Zhang N. Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community. J Fungi (Basel) 2022; 8:jof8050523. [PMID: 35628778 PMCID: PMC9148057 DOI: 10.3390/jof8050523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O3 and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O3 and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host–pathogen–environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone ‘107’: Populus euramericana cv. ‘74/76’; clone ‘546’: P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O3 or N addition only; however, the negative impact of elevated O3 could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, rust severity of clone ‘546’ did not differ significantly in the cases of elevated O3 and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O3, as determined by the markedly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | | | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
- Correspondence:
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252
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Jiang X, Li WW, Han M, Chen G, Wu J, Lai S, Fu Z, Zhang S, Deng WW, Gao L, Xia T. Aluminum-tolerant, growth-promoting endophytic bacteria as contributors in promoting tea plant growth and alleviating aluminum stress. TREE PHYSIOLOGY 2022; 42:1043-1058. [PMID: 34850946 PMCID: PMC9092644 DOI: 10.1093/treephys/tpab159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Unlike that of other crops, the growth of tea plants can be promoted by aluminum, but its regulation mechanism remains unclear. Some endophytes can also promote growth of plant hosts. In this paper, tea roots treated with aluminum were used to study the growth-promoting traits and aluminum tolerance of endophytes. Meta-16S rDNA analysis revealed that Burkholderia was enriched in tea roots after aluminum treatment, and it was the dominant strain for hydroponic tea roots and field tea roots. Actinomycetes constituted the dominant strains in hydroponic tea seedlings treated with aluminum. Sixteen endophytic bacteria, including 12 strains of Firmicutes, 2 strains of Proteobacteria and 2 strains of Actinomycetes, were isolated and identified from hydroponic tea roots treated with different aluminum concentrations. Growth-promoting activity analysis showed that the isolated endophytic bacteria all had more than one plant growth-promoting trait. Among them, B4 (Bacillus nealsonii), B8 (Brevibacterium frigoritolerans) and A2 (Nocardia nova) bacteria each had three growth-promoting traits. Aluminum tolerance ability analysis indicated that endophyte A1 (Leifsonia shinshuensis) had the strongest aluminum tolerance ability, up to 200 mg l-1 aluminum. Plant-bacteria interactions showed that endophytes A1, A2 and B4 and their synthetic community all had a growth-promoting effect on the growth of wheat lateral roots. Moreover, endophytes A1 and B4 alleviated aluminum stress in wheat. Endophyte A1 also promoted the growth of tea cuttings, especially lateral roots, with/without aluminum. Taken together, aluminum enhanced the distribution of aluminum-tolerant and growth-promoting bacteria, thereby promoting the growth of tea roots. This study provides a new aspect for research on the mechanism by which aluminum promotes tea plant growth.
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Affiliation(s)
- Xiaolan Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Wei-Wei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Menglin Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Gao Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Jing Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Sanyan Lai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Zhouping Fu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Shuxiang Zhang
- School of Life Science, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, China
| | - Wei-Wei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd, Hefei 230036, Anhui, China
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253
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Li M, Xu M, Su A, Zhang Y, Niu L, Xu Y. Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome. Front Microbiol 2022; 13:888086. [PMID: 35602076 PMCID: PMC9114715 DOI: 10.3389/fmicb.2022.888086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., Herbaspirillum, Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites.
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Affiliation(s)
- Mingyue Li
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
| | - Minmin Xu
- Shandong Academy of Environmental Sciences Co., Ltd., Jinan, China
| | - Aoxue Su
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
| | - Ying Zhang
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
| | - Lili Niu
- Key Laboratory of Pollution Exposure and Health Intervention Technology, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, China
| | - Yan Xu
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao, China
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254
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Wang X, Teng Y, Wang X, Li X, Luo Y. Microbial diversity drives pyrene dissipation in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153082. [PMID: 35038522 DOI: 10.1016/j.scitotenv.2022.153082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Soil microbial diversity is an essential driver of multiple ecosystem functions and services. However, the role and mechanisms of microbial diversity in the dissipation of persistent organic pollutants in soil are largely unexplored. Here, a gradient of soil microbial diversity was constructed artificially by a dilution-to-extinction approach to assess the role of soil microbial diversity in the dissipation of pyrene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), in a 42-day microcosm experiment. The results showed that pyrene dissipation (98.1%) and the abundances of pyrene degradation genes (the pyrene dioxygenase gene nidA and the gram-positive PAH-ring hydroxylating dioxygenase gene PAH-RHDα GP) were highest in soils with high microbial diversity. Random-forest machine learning was combined with linear regression analysis to identify a range of keystone taxa (order level) associated with pyrene dissipation, including Sphingobacteriales, Vampirovibrionales, Blastocatellales, Myxococcales, Micrococcales and Rhodobacterales. The diversity of these keystone taxa was significantly and positively correlated with the abundance of pyrene degradation genes and the removal rate of pyrene. According to (partial) Mantel tests, keystone taxa diversity was the dominant factor determining pyrene dissipation compared with total microbial diversity. Moreover, co-occurrence network analysis revealed that diverse keystone taxa may drive pyrene dissipation via more positive interactions between keystone species and with other species in soil. Taken together, these findings provide new insights on the regulation of keystone taxa diversity to promote the dissipation of PAH in soil.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiufen Li
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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255
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Deng J, Xiao T, Fan W, Ning Z, Xiao E. Relevance of the microbial community to Sb and As biogeochemical cycling in natural wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151826. [PMID: 34822895 DOI: 10.1016/j.scitotenv.2021.151826] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Mining activities lead to elevated levels of antimony (Sb) and arsenic (As) in river systems, having adverse effects on the aquatic environment and human health. Microbes inhabiting river sediment can mediate the transformation of Sb and As, thus changing the toxicity and mobility of Sb and As. Compared to river sediments, natural wetlands could introduce distinct geochemical conditions, leading to the formation of different sedimentary microbial compositions between river sediments and wetland sediments. However, whether such changes in microbial composition could influence the microbially mediated geochemical behavior of Sb or As remains poorly understood. In this study, we collected samples from a river contaminated by Sb tailings and a downstream natural wetland to study the influence of microorganisms on the geochemical behavior of Sb and As after the Sb/As-contaminated river entered the natural wetland. We found that the microbial compositions in the natural wetland soil differed from those in the river sediment. The Sb/As contaminant components (Sb(III), As(III), As(V), Asexe) and nutrients (TC) were important determinants of the difference in the compositions of the microbial communities in the two environments. Taxonomic groups were differentially enriched between the river sediment and wetland soil. For example, the taxonomic groups Xanthomonadales, Clostridiales and Desulfuromonadales were important in the wetland and were likely to involve in Sb/As reduction, sulfate reduction and Fe(III) reduction, whereas Burkholderiales, Desulfobacterales, Hydrogenophilales and Rhodocyclales were important taxonomic groups in the river sediments and were reported to involve in Sb/As oxidation and sulfide oxidation. Our results suggest that microorganisms in both river sediments and natural wetlands can affect the geochemical behavior of Sb/As, but the mechanisms of action are different.
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Affiliation(s)
- Jinmei Deng
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu 610059, China
| | - Wenjun Fan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Enzong Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
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256
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Wang L, Rengel Z, Zhang K, Jin K, Lyu Y, Zhang L, Cheng L, Zhang F, Shen J. Ensuring future food security and resource sustainability: insights into the rhizosphere. iScience 2022; 25:104168. [PMID: 35434553 PMCID: PMC9010633 DOI: 10.1016/j.isci.2022.104168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Feeding the world's growing population requires continuously increasing crop yields with less fertilizers and agrochemicals on limited land. Focusing on plant belowground traits, especially root-soil-microbe interactions, holds a great promise for overcoming this challenge. The belowground root-soil-microbe interactions are complex and involve a range of physical, chemical, and biological processes that influence nutrient-use efficiency, plant growth and health. Understanding, predicting, and manipulating these rhizosphere processes will enable us to harness the relevant interactions to improve plant productivity and nutrient-use efficiency. Here, we review the recent progress and challenges in root-soil-microbe interactions. We also highlight how root-soil-microbe interactions could be manipulated to ensure food security and resource sustainability in a changing global climate, with an emphasis on reducing our dependence on fertilizers and agrochemicals.
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Affiliation(s)
- Liyang Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Zed Rengel
- Soil Science & Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Institute for Adriatic Crops and Karst Reclamation, Split 21000, Croatia
| | - Kai Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Kemo Jin
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Yang Lyu
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Lin Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Lingyun Cheng
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Fusuo Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Jianbo Shen
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
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257
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Wang T, Yang K, Ma Q, Jiang X, Zhou Y, Kong D, Wang Z, Parales RE, Li L, Zhao X, Ruan Z. Rhizosphere Microbial Community Diversity and Function Analysis of Cut Chrysanthemum During Continuous Monocropping. Front Microbiol 2022; 13:801546. [PMID: 35369487 PMCID: PMC8967409 DOI: 10.3389/fmicb.2022.801546] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
As an ornamental flower crop, the long-term continuous monocropping of cut chrysanthemum causes frequent occurrence of diseases, seriously affecting the quality of cut chrysanthemum. The rhizosphere microbial community plays an important role in maintaining the healthy growth of plants, whereas the composition and dynamics of rhizosphere microbial community under continuous monocropping of cut chrysanthemum have not been fully revealed. In this study, the Illumina MiSeq high-throughput sequencing platform was used to monitor the dynamic changes of rhizosphere microbial communities in four varieties of cut chrysanthemum during 0–3 years of monocropping, and the soil physicochemical properties were also determined. Results showed that continuous monocropping significantly increased the fungal community richness and altered the profiles of the bacterial and fungal communities, leading to variation of community beta-diversity. With the increase of continuous cropping time, biocontrol bacteria decreased, while some plant pathogenic fungi were enriched in the rhizosphere of cut chrysanthemum. FAPROTAX-based functional prediction showed that the abundance of gene related to nitrogen and sulfur metabolism and chitin lysis was reduced in the rhizosphere of cut chrysanthemum. FUNGuild-based fungal function prediction showed that plant pathogenic fungal taxa were increasing in the rhizosphere of cut chrysanthemum, mainly Acremonium, Plectosphaerellaceae, Fusarium, and Cladosporium. Continuous cropping also reduced the content of ammonium nitrogen and increased soil salinity, resulting in deterioration of soil physical and chemical properties, which, together with the transformation of rhizosphere microbial community, became part of the reasons for the continuous cropping obstacle of cut chrysanthemum.
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Affiliation(s)
- Tan Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Kexin Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingyun Ma
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xu Jiang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiqing Zhou
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Delong Kong
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, United States
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xin Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, China.,College of Life Sciences, Yantai University, Yantai, China
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258
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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259
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Li PD, Zhu ZR, Zhang Y, Xu J, Wang H, Wang Z, Li H. The phyllosphere microbiome shifts toward combating melanose pathogen. MICROBIOME 2022; 10:56. [PMID: 35366955 PMCID: PMC8976405 DOI: 10.1186/s40168-022-01234-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/23/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, the collective community-level change and effect of the phyllosphere microbiome in response to pathogen invasion remains largely elusive. RESULTS Here, we integrated 16S metabarcoding, shotgun metagenomics and culture-dependent methods to systematically investigate the changes in phyllosphere microbiome between infected and uninfected citrus leaves by Diaporthe citri, a fungal pathogen causing melanose disease worldwide. Multiple microbiome features suggested a shift in phyllosphere microbiome upon D. citri infection, highlighted by the marked reduction of community evenness, the emergence of large numbers of new microbes, and the intense microbial network. We also identified the microbiome features from functional perspectives in infected leaves, such as enriched microbial functions for iron competition and potential antifungal traits, and enriched microbes with beneficial genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated with the microbiome shift could positively affect plant performance under D. citri challenge, with reductions in disease index ranging from 65.7 to 88.4%. Among them, Pantoea asv90 and Methylobacterium asv41 identified as "recruited new microbes" in the infected leaves, exhibited antagonistic activities to D. citri both in vitro and in vivo, including inhibition of spore germination and/or mycelium growth. Sphingomonas spp. presented beneficial genomic characteristics and were found to be the main contributor for the functional enrichment of iron complex outer membrane receptor protein in the infected leaves. Moreover, Sphingomonas asv20 showed a stronger suppression ability against D. citri in iron-deficient conditions than iron-sufficient conditions, suggesting a role of iron competition during their antagonistic action. CONCLUSIONS Overall, our study revealed how phyllosphere microbiomes differed between infected and uninfected citrus leaves by melanose pathogen, and identified potential mechanisms for how the observed microbiome shift might have helped plants cope with pathogen pressure. Our findings provide novel insights into understanding the roles of phyllosphere microbiome responses during pathogen challenge. Video abstract.
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Affiliation(s)
- Pu-Dong Li
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zeng-Rong Zhu
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Jianping Xu
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - Hongkai Wang
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zhengyi Wang
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hongye Li
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
- Hainan Institute, Zhejiang University, Sanya, 572000, China.
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260
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Hu H, Chen Q, He J. The end of hunger: fertilizers, microbes and plant productivity. Microb Biotechnol 2022; 15:1050-1054. [PMID: 34767687 PMCID: PMC8966006 DOI: 10.1111/1751-7915.13973] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/05/2022] Open
Abstract
It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant-associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome-based innovations to promote plant productivity and contribute to the end of hunger.
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Affiliation(s)
- Hang‐Wei Hu
- School of Agriculture and FoodFaculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic.3010Australia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVic.3010Australia
| | - Qing‐Lin Chen
- School of Agriculture and FoodFaculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic.3010Australia
| | - Ji‐Zheng He
- School of Agriculture and FoodFaculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic.3010Australia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVic.3010Australia
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261
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Tanvir R, Ping W, Sun J, Cain M, Li X, Li L. AtQQS orphan gene and NtNF-YC4 boost protein accumulation and pest resistance in tobacco (Nicotiana tabacum). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 317:111198. [PMID: 35193747 DOI: 10.1016/j.plantsci.2022.111198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/07/2021] [Accepted: 01/26/2022] [Indexed: 05/19/2023]
Abstract
Qua-Quine Starch (QQS), an orphan gene exclusively found in Arabidopsis thaliana, interacts with Nuclear Factor Y subunit C4 (NF-YC4) and regulates carbon and nitrogen allocation in different plant species. Several studies uncovered its potential in increasing total protein and resistance against pathogens/pests in Arabidopsis and soybean. However, it is still unclear if these attributes QQS offers are universal in all flowering plants. Here we studied AtQQS and Nicotiana tabacum NF-YC4's (NtNF-YC4) influence on starch/protein content and pest resistance in tobacco. Our results showed both AtQQS and NtNF-YC4 had a positive impact on the plant's total protein accumulation. Simultaneously, we have also observed reduced starch biosynthesis and increased resistance against common pests like whiteflies (Bemisia tabaci) and aphids (Myzus persicae) in tobacco plants expressing AtQQS or overexpressing NtNF-YC4. Real-time PCR also revealed increased NF-YC4 expression after aphid infestation in tobacco varieties with higher pest resistance but decreased/unchanged NF-YC4 expression in varieties susceptible to pests. Further analysis revealed that QQS expression and overexpression of NtNF-YC4 strongly repressed expression of genes such as sugar transporter SWEET10 and Flowering Locus T (FT), suggesting involvement of SWEET10 and FT in the QQS and NF-YC4 mediated carbon and nitrogen allocation in tobacco. Our data suggested that the activity of species-specific orphan genes may not be limited to the original species or its close relatives. Sequence alignment revealed the conserved sequence of the NF-YC4s in different plant species that may be responsible for the resulting shift in metabolism, pest resistance. Cis-acting DNA element analysis of NtNF-YC4 promoter region may outline potential mechanisms for these phenotypic changes.
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Affiliation(s)
- Rezwan Tanvir
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Wenli Ping
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pests in Huanghuai Growing Area, Zhengzhou, Henan 450002, China
| | - Jiping Sun
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pests in Huanghuai Growing Area, Zhengzhou, Henan 450002, China
| | - Morgan Cain
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Xuejun Li
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pests in Huanghuai Growing Area, Zhengzhou, Henan 450002, China
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
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262
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Zhang Y, Zhang Y, Xu W, Hu J, Zhang Z. Possible effects of temperature on bacterial communities in the rhizosphere of rice under different climatic regions. Arch Microbiol 2022; 204:212. [PMID: 35296917 DOI: 10.1007/s00203-022-02812-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/21/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
Global warming is an indisputable fact. However, the effect of warming on the rhizosphere bacterial community of crops is not well understood. Therefore, we carried out pot experiments with three rice (Oryza sativa L.) varieties in black soil across three climatic regions of northeast China to simulate temperature change, and analyzed the response of the rhizosphere bacterial community to different temperatures. Results showed that climate had stronger effects on rhizosphere bacterial communities than rice variety. The rhizosphere bacterial diversity differed significantly among the three climatic regions and positively correlated with the mean daily average temperature (MAveT), mean daily maximum temperature (MMaxT), and mean daily minimum temperature (MMinT), and negatively correlated with the daily temperature range (DTR). Principal co-ordinate analysis revealed that bulk soil bacterial communities maintained a high similarity across the three climatic regions, while rhizosphere bacterial communities notably varied. This change was significantly correlated with MAveT, MMaxT, MMinT, and DTR. Compared with bulk soil, Proteobacteria and Bacteroidetes were enriched in the rhizosphere, while Actinobacteria was depleted. Moreover, these changes were strengthened by increasing the temperature and decreasing DTR. Additionally, correlation analysis revealed that changes in rhizosphere bacterial communities were closely related to the formation of rice yields. Our study revealed that the increasing temperature indirectly reshapes the rhizosphere bacterial community that may promote rice production in areas with lower temperatures.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Yujie Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Wenjie Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, People's Republic of China.
| | - Zujian Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture/Key Laboratory of Crop Genetic and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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263
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Galindo-Castañeda T, Lynch JP, Six J, Hartmann M. Improving Soil Resource Uptake by Plants Through Capitalizing on Synergies Between Root Architecture and Anatomy and Root-Associated Microorganisms. FRONTIERS IN PLANT SCIENCE 2022; 13:827369. [PMID: 35356114 PMCID: PMC8959776 DOI: 10.3389/fpls.2022.827369] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/15/2022] [Indexed: 05/14/2023]
Abstract
Root architectural and anatomical phenotypes are highly diverse. Specific root phenotypes can be associated with better plant growth under low nutrient and water availability. Therefore, root ideotypes have been proposed as breeding targets for more stress-resilient and resource-efficient crops. For example, root phenotypes that correspond to the Topsoil Foraging ideotype are associated with better plant growth under suboptimal phosphorus availability, and root phenotypes that correspond to the Steep, Cheap and Deep ideotype are linked to better performance under suboptimal availability of nitrogen and water. We propose that natural variation in root phenotypes translates into a diversity of different niches for microbial associations in the rhizosphere, rhizoplane and root cortex, and that microbial traits could have synergistic effects with the beneficial effect of specific root phenotypes. Oxygen and water content, carbon rhizodeposition, nutrient availability, and root surface area are all factors that are modified by root anatomy and architecture and determine the structure and function of the associated microbial communities. Recent research results indicate that root characteristics that may modify microbial communities associated with maize include aerenchyma, rooting angle, root hairs, and lateral root branching density. Therefore, the selection of root phenotypes linked to better plant growth under specific edaphic conditions should be accompanied by investigating and selecting microbial partners better adapted to each set of conditions created by the corresponding root phenotype. Microbial traits such as nitrogen transformation, phosphorus solubilization, and water retention could have synergistic effects when correctly matched with promising plant root ideotypes for improved nutrient and water capture. We propose that elucidation of the interactive effects of root phenotypes and microbial functions on plant nutrient and water uptake offers new opportunities to increase crop yields and agroecosystem sustainability.
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Affiliation(s)
- Tania Galindo-Castañeda
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Jonathan P. Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Johan Six
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
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264
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Li H, Shi H, Xu P, Yu D. Metabolomics and microbiome reveal potential root microbiota affecting the alkaloidal metabolome in Aconitum vilmorinianum Kom. BMC Microbiol 2022; 22:70. [PMID: 35264111 PMCID: PMC8905797 DOI: 10.1186/s12866-022-02486-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/03/2022] [Indexed: 12/23/2022] Open
Abstract
Background The plant microbiome is vital for plant health, fitness, and productivity. Interestingly, plant metabolites and the plant microbiome can influence each other. The combination of metabolomics and microbiome may reveal the critical links between the plant and its microbiome. It is of great significance to agricultural production and human health, especially for Chinese medicine research. Aconitum vilmorinianum Kom. is a herb with alkaloid activities, and its roots are the raw material for some Chinese medicines. Former studies have investigated alkaloidal metabolites and antibacterial activities of endophytes in A. vilmorinianum roots. However, there are limited reports on the root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum. Results This research used ultra performance liquid chromatography-tandem mass spectrometry technology and high-throughput sequencing to examine the alkaloidal metabolome, bacterial microbiota, and fungal microbiota in A. vilmorinianum roots at two different sites in China. The results revealed that the samples from the two sites were rich in distinct alkaloidal metabolites and recruited significantly different root microbiota. Based on bioinformatics analysis, we found the potential bacterial and fungal microbiota impacting the alkaloidal metabolome in A. vilmorinianum. Conclusion Our findings reveal the composition of the alkaloidal metabolome, bacterial root microbiota, and fungal root microbiota in A. vilmorinianum roots at two different sites. Potential root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum are indicated. This study provides a strategy for the cultivation and research of A. vilmorinianum and other Chinese herbs. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02486-1.
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Affiliation(s)
- Hongrui Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongdi Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
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265
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Xu F, Liao H, Zhang Y, Yao M, Liu J, Sun L, Zhang X, Yang J, Wang K, Wang X, Ding Y, Liu C, Rensing C, Zhang J, Yeh K, Xu W. Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying. THE ISME JOURNAL 2022; 16:801-811. [PMID: 34621017 PMCID: PMC8857228 DOI: 10.1038/s41396-021-01133-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/10/2022]
Abstract
Moderate soil drying (MSD) is a promising agricultural technique that can reduce water consumption and enhance rhizosheath formation promoting drought resistance in plants. The endophytic fungus Piriformospora indica (P. indica) with high auxin production may be beneficial for rhizosheath formation. However, the integrated role of P. indica with native soil microbiome in rhizosheath formation is unclear. Here, we investigated the roles of P. indica and native bacteria on rice rhizosheath formation under MSD using high-throughput sequencing and rice mutants. Under MSD, rice rhizosheath formation was significantly increased by around 30% with P. indica inoculation. Auxins in rice roots and P. indica were responsible for the rhizosheath formation under MSD. Next, the abundance of the genus Bacillus, known as plant growth-promoting rhizobacteria, was enriched in the rice rhizosheath and root endosphere with P. indica inoculation under MSD. Moreover, the abundance of Bacillus cereus (B. cereus) with high auxin production was further increased by P. indica inoculation. After inoculation with both P. indica and B. cereus, rhizosheath formation in wild-type or auxin efflux carrier OsPIN2 complemented line rice was higher than that of the ospin2 mutant. Together, our results suggest that the interaction of the endophytic fungus P. indica with the native soil bacterium B. cereus favors rice rhizosheath formation by auxins modulation in rice and microbes under MSD. This finding reveals a cooperative contribution of P. indica and native microbiota in rice rhizosheath formation under moderate soil drying, which is important for improving water use in agriculture.
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Affiliation(s)
- Feiyun Xu
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Hanpeng Liao
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yingjiao Zhang
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Minjie Yao
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianping Liu
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Leyun Sun
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Xue Zhang
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jinyong Yang
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Ke Wang
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Xiaoyun Wang
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Yexin Ding
- grid.256111.00000 0004 1760 2876Center 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, Fuzhou, 350002 China
| | - Chen Liu
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Christopher Rensing
- grid.256111.00000 0004 1760 2876Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianhua Zhang
- grid.221309.b0000 0004 1764 5980Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Kaiwun Yeh
- grid.19188.390000 0004 0546 0241Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - 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, Fuzhou, 350002, China.
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266
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Wang Z, Song Y. Toward understanding the genetic bases underlying plant-mediated "cry for help" to the microbiota. IMETA 2022; 1:e8. [PMID: 38867725 PMCID: PMC10989820 DOI: 10.1002/imt2.8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2024]
Abstract
Canonical plant stress biology research has focused mainly on the dynamic regulation of internal genetic pathways in stress responses. Increasingly more studies suggest that plant-mediated timely reshaping of the microbiota could also confer benefits in responding to certain biotic and abiotic stresses. This has led to the "cry for help" hypothesis, which is supported by the identification of plant genetic regulators integrating biotic/abiotic stress signaling and microbiota sculpting. Although diverse genetic mutants have been reported to affect microbiota composition, it has been challenging to confirm the causal link between specific microbiota changes and plant phenotypic outputs (e.g., fitness benefits) due to the complexity of microbial community composition. This limits the understanding of the relevance of plant-mediated microbiota changes. We reviewed the genetic bases of host-mediated reshaping of beneficial microbiota in response to biotic and abiotic stresses, and summarized the practical approaches linking microbiota changes and "functional outputs" in plants. Further understanding of the key regulators and pathways governing the assembly of stress-alleviating microbiota would benefit the design of crops that could dynamically enlist beneficial microbiota under conditions of stress.
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Affiliation(s)
- Zhenghong Wang
- Institute of Plant and Food Science, Department of BiologyUniversity of Science and TechnologyShenzhenChina
| | - Yi Song
- Institute of Plant and Food Science, Department of BiologyUniversity of Science and TechnologyShenzhenChina
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267
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Liu M, Ke X, Liu X, Fan X, Xu Y, Li L, Solaiman ZM, Pan G. The effects of biochar soil amendment on rice growth may vary greatly with rice genotypes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152223. [PMID: 34896147 DOI: 10.1016/j.scitotenv.2021.152223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
While plant growth promotion with increased nutrient uptake had been well addressed for biochar soil amendment in agriculture, there was limited knowledge on the variation of such effects with crop genotypes. In a rice field experiment without and with biochar soil amendment at 20 t ha-1, 19 mutants of a rice cultivar Wuyunjing 7 (Oryza sativa L.) were tested for plant growth in split plots respectively. At harvest, the biomass of grain, stem and leaves were measured and soil and plant samples were collected for measuring N, P and K nutrients. Across the 19 mutants, relative change with biochar soil amendment varied in a range of -41.6% to +35.6% for biomass production and agronomic traits, and -87.0% to +117% for nutrient accumulation. For the nutrients content, the relative change for N was seen in a narrow range of -29.4% to +16.6%, being similar among grain, leaf and shoot samples while that for P in a wide range of -109% to +105%. With factor analysis, variation of biomass and nutrient uptake was least explained with biochar effect (up to 7.0%) but largely by genotype effect (mostly by 40-70%). However, the genotype × biochar interaction effect could also explain 10-40% of the total variations though the interaction explained 40-70% of leaf P variation. Therefore, mutant and mutant × biochar interactions dominated the agronomic variation of rice production of the Wuyunjing 7 cultivar. Furthermore, across the traits analyzed, genotype effects were shown very significantly but negatively correlated to biochar effects. In other words, biochar soil amendment provided little growth or nutrient enhancement for those mutants bred for high efficiency. Hence, genotype selection should be considered in optimizing prioritizing biochar application in crop production. Of course, variation of biochar effect with crop genotypes deserved further plant physio-ecological studies.
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Affiliation(s)
- Minglong Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Xianlin Ke
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Fan
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Youzun Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zakaria M Solaiman
- UWA School of Agriculture and Environment, and the UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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268
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Xu T, Tao Y, Song L, Wang H, Ren B. A unique microbiome in a highly polluted and alkalic lake in a seasonally frozen area. ENVIRONMENTAL RESEARCH 2022; 204:112056. [PMID: 34534523 DOI: 10.1016/j.envres.2021.112056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Highly polluted waters profoundly promoted microbial activities and vice versa. Although microbial community structures and bioprocesses in polluted environments have been fully investigated, they are rarely uncovered in abandoned and highly polluted aquatic environment, especially in a seasonally frozen area. East Lake had been polluted by surrounding paper mills and dairy plants from the 1960s to the early 2000s. Under low biodegradability (BOD5/COD ratio<0.2) and alkalic (pH > 9) conditions, a unique microbiome was discovered in East lake. Proteobacteria was the largest taxonomic group in the microbial community, covering almost half of the top-100 genera. Among them, seven genera are sulfate-reducing bacteria, including Desulfuromusa, Desulfuromonas, Desulfobulbus, Desulfocapsa, Desulfurivibrio, Desulfatiglans, and Desulfomicrobium. Functional analysis revealed abundant predicted functional genes for the respiration of sulfur compounds and sulfate respiration. Great vertical variations were found to both microbial community structures and predicted functions. This work provides unique evidence for future microbiome studies of nutrient-rich, alkalic, and seasonally frozen water habitats.
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Affiliation(s)
- Tiefu Xu
- School of Civil Engineering, Heilongjiang University, Harbin, 150080, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yu Tao
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
| | - Lan Song
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Haoyu Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Binqiao Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150028, China.
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269
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Tayyab M, Fallah N, Zhang C, Pang Z, Islam W, Lin S, Lin W, Zhang H. Sugarcane cultivar-dependent changes in assemblage of soil rhizosphere fungal communities in subtropical ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:20795-20807. [PMID: 34741271 DOI: 10.1007/s11356-021-17229-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Sugarcane cultivars (Saccharum officinarum L.) are widely cultivated for both sugar and renewable energy in China. The response of rhizosphere fungal composition and diversity to different emerging sugarcane cultivars is limited. Therefore, utilizing high-throughput sequencing, we explored fungal communities' structure in soils adhering to six sugarcane cultivars' roots (Guitang 08-120, Regan14-62, Guitang 08-1180, Haizhe 22, Liucheng 05-136, Taitang 22) in Guangxi Province, China. Our results suggested that sugarcane varieties significantly altered rhizosphere soil attributes, with Haizhe 22 having substantially lower soil pH, organic matter (OM), available phosphorus (AP), and soil water contents (SWC) than others cultivars. Different sugarcane varieties did not substantially affected the Shannon fungal diversity index, but the apparent effect on fungal richness was significant. Beta diversity analysis revealed that "Haizhe 22" distinguished the fungal community from the other five cultivars. Soil pH, OM, cultivars, and soil moisture were crucial determinants in shaping soil fungal composition. The Haizhe 22 rhizosphere significantly enriched the operational taxonomic units (OTUs) assigned to two fungal genera (Cephalotheca and Sagenomella), while rhizosphere of other verities significantly enriched the OTUs assigned to four fungal genera (Chaetomium, Chaetosphaeria, Mortierella, and Talaromyces), suggesting their essential role in plant development, disease tolerance, and bioremediation. These findings may help in selecting or breeding innovative genotypes capable of supporting abundant rhizosphere fungi beneficial to plants that would likely improve crops' agronomic potential and maintain soil ecosystem sustainability.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Caifang Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Waqar Islam
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Wenxiong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Li T, Li Y, Zhang X, Yuan J, Guo J, Wang P, Wei G, Chen C. Distinct response patterns of bacterial communities in Ag- and ZnO-rGO nanocomposite-amended silt loam soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151270. [PMID: 34756902 DOI: 10.1016/j.scitotenv.2021.151270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/26/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
The widespread application of metal-based nanoparticle (MNPs)/reduced graphene oxide (rGO) composites inevitably leads to their release into soils. However, we lack a detailed understanding of the bacterial community response to MNPs-rGO exposure in farmland soils. Here, we conducted a soil microcosm experiment to analyze the potential impact of MNPs-rGO on bacterial communities in two field soils via high-throughput sequencing. The change in alpha diversity of bacterial communities was more susceptible to Ag-rGO and ZnO-rGO treatments than CuO-rGO. In both soils, MNPs-rGO significantly changed the bacterial community structure even at a low dose (1 mg kg-1). The bacterial community structure was most strongly affected by Ag-rGO at 30 days, but the greatest changes occurred in ZnO-rGO at 60 days. The differences in soil properties could shape bacterial communities to MNPs-rGO exposure. Distance-based redundancy analysis and functional annotation of prokaryotic taxa showed that some bacterial species associated with nitrogen cycling were greatly influenced by Ag-rGO and ZnO-rGO exposure. In sum, Ag-rGO and ZnO-rGO may potentially affect bacterial communities and nitrogen turnover under long-term realistic field exposure. These findings present a perspective on the response of bacterial communities to MNPs-rGO and provide a fundamental basis for estimating the ecological behavior of MNPs-rGO.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Yuhua Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Xike Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Jiawei Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Junkang Guo
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an 710021, Shaanxi, PR China
| | - Pan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Chun Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
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271
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Liu Y, Chen T, Li D, Fu J, Liu S. iMeta: Integrated meta-omics for biology and environments. IMETA 2022; 1:e15. [PMID: 38867730 PMCID: PMC10989748 DOI: 10.1002/imt2.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 06/14/2024]
Abstract
The cover of iMeta's inaugural issue. The galaxy represents the complexity and value of bioinformatics and metagenomics. DNA, which represents genetic components that guide biological diversity, is at the center of the galaxy. The spiral arms are the microbiome welcoming scientists from all over the world to make novel discoveries. Let us usher in the metaverse era of the microbiome.
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Affiliation(s)
- Yong‐Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Tong Chen
- State Key Laboratory Breeding Base of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Danyi Li
- Beijing Rexinchang Biotechnology Research Institute Co., Ltd.BeijingChina
| | - Jingyuan Fu
- Department of GeneticsUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Shuang‐Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
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272
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Yu T, Cheng L, Liu Q, Wang S, Zhou Y, Zhong H, Tang M, Nian H, Lian T. Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence. Microbiol Spectr 2022; 10:e0201121. [PMID: 35171049 PMCID: PMC8849089 DOI: 10.1128/spectrum.02011-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/16/2022] [Indexed: 12/26/2022] Open
Abstract
Waterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples. IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.
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Affiliation(s)
- Taobing Yu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Shasha Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Yuan Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
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273
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Gong S, Feng B, Jian SP, Wang GS, Ge ZW, Yang ZL. Elevation Matters More than Season in Shaping the Heterogeneity of Soil and Root Associated Ectomycorrhizal Fungal Community. Microbiol Spectr 2022; 10:e0195021. [PMID: 35019700 PMCID: PMC8754124 DOI: 10.1128/spectrum.01950-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/13/2021] [Indexed: 01/29/2023] Open
Abstract
Ectomycorrhizal (EcM) fungi play important roles in forest ecosystems, and their richness and composition can change along with elevation and season changes. However, no study has estimated the relative importance of altitudinal and seasonal heterogeneity in predicting the distribution of EcM fungal communities by simultaneously considering different sample types (root versus soil). In this study, we collected root and soil samples along a > 1,500-m elevation gradient during wet and dry seasons from Baima Snow Mountain, located in "the Mountains of Southwest China," one of the 34 biodiversity hot spots, and we analyzed them using next-generation sequencing. Regardless of the sample type, similar EcM fungal richness pattern with increasing elevation (decline in the forest zone, and an increase at the alpine meadow zone) and strong community turnovers among different elevational zones and between two seasons were detected, and changes of EcM fungal community similarity on 400-m altitude gradient were equivalent to the community turnover between dry and wet seasons. Elevation and edaphic factors were shown to have the largest effects on EcM fungal community. The heterogeneity of richness and community composition was stronger among different elevational zones than across different seasons, mainly because the elevation variations in the EcM fungal community were shaped by the combined effects of different environmental factors, while seasonal changes were mainly controlled by temperature and fast-changing soil nutrients. IMPORTANCE Altitude and season represent two important environmental gradients that shape the structure of biome, including the heterogeneity of EcM fungi. Previous studies have separately considered the influences of altitude and season on EcM fungal communities, but the relative importance of altitude and season is still unknown. The present study revealed that elevation influences the heterogeneity of EcM fungal community more than season; this may be because the variability of environmental factors is higher across different elevations than that across seasons.
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Affiliation(s)
- Sai Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bang Feng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Si-Peng Jian
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Geng Shen Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zai-Wei Ge
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhu Liang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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274
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Zhu AM, Wu Q, Liu HL, Sun HL, Han GD. Isolation of rhizosheath and analysis of microbial community structure around roots of Stipa grandis. Sci Rep 2022; 12:2707. [PMID: 35177730 PMCID: PMC8854629 DOI: 10.1038/s41598-022-06708-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/28/2022] [Indexed: 11/09/2022] Open
Abstract
Root zone microbial structure is particularly complex in plants with rhizosheaths, and greater understanding of the rhizosheath may play an important role in the future development of sustainable agricultural practices. However, one important reason to focus study on rhizosheath microbial structure is that there is no definite method for rhizosheath separation. The aim of this study was to explore rhizosheath isolation methods and the diversity characteristics of microorganisms around the rhizosphere. In this study, we isolated the rhizosheath of Stipa grandis, a dominant species in desert steppe, and the microorganisms in the roots, root epidermis, rhizosheath and rhizosphere soil were extracted and sequenced by 16S rRNA and ITS. The alpha diversity index of bacteria in Stipa grandis rhizosphere soil was the greatest, followed by rhizosheath, and the alpha diversity index of endophytic bacteria in root system was the smallest. The alpha diversity index of fungi in the rhizosheath and rhizosphere soil were significantly higher than that in the root epidermis and root system. There were significant differences in bacterial community structure between the root epidermis, endophytic bacteria, rhizosheath and rhizosphere soil. Unlike bacterial community structure, the community structure of fungi in the root epidermis was similar that of endophytic fungi, but significantly different from those in rhizosheath and rhizosphere soil. This study demonstrated a feasible method for separating plant rhizosheath and root epidermis. We suggest that the root epidermis can act as the interface between the host plant root and the external soil environment. We will have to re-examine the biological and ecological significance of rhizosheath and microorganisms in rhizosheath, as well as the mechanism explaining the close relationship of the rhizosheath and the plant root epidermis. This study provides theoretical and technical guidance for the isolation of the plant rhizosheath and the study of microorganisms in plant rhizosheath.
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Affiliation(s)
- Ai-Min Zhu
- College of Grassland, Resources and Environment, Key Laboratory of Grassland Resources of the Ministry of Education of China, Key Laboratory of Forage Cultivation, Processing and Higher Efficient Utilization of the Ministry of Agriculture and Rural Affairs of China, Inner Mongolia Key Laboratory of Grassland Management and Utilization, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Qian Wu
- College of Grassland, Resources and Environment, Key Laboratory of Grassland Resources of the Ministry of Education of China, Key Laboratory of Forage Cultivation, Processing and Higher Efficient Utilization of the Ministry of Agriculture and Rural Affairs of China, Inner Mongolia Key Laboratory of Grassland Management and Utilization, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Hai-Li Liu
- College of Grassland, Resources and Environment, Key Laboratory of Grassland Resources of the Ministry of Education of China, Key Laboratory of Forage Cultivation, Processing and Higher Efficient Utilization of the Ministry of Agriculture and Rural Affairs of China, Inner Mongolia Key Laboratory of Grassland Management and Utilization, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Hai-Lian Sun
- Research Base of the Academy of Agriculture and Animal Husbandry of Inner Mongolia, Hohhot, 010031, China
| | - Guo-Dong Han
- College of Grassland, Resources and Environment, Key Laboratory of Grassland Resources of the Ministry of Education of China, Key Laboratory of Forage Cultivation, Processing and Higher Efficient Utilization of the Ministry of Agriculture and Rural Affairs of China, Inner Mongolia Key Laboratory of Grassland Management and Utilization, Inner Mongolia Agricultural University, Hohhot, 010019, China.
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275
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Jiang G, Zhang Y, Gan G, Li W, Wan W, Jiang Y, Yang T, Zhang Y, Xu Y, Wang Y, Shen Q, Wei Z, Dini-Andreote F. Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation. ISME COMMUNICATIONS 2022; 2:10. [PMID: 37938685 PMCID: PMC9723603 DOI: 10.1038/s43705-022-00094-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 04/20/2023]
Abstract
The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.
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Affiliation(s)
- Gaofei Jiang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yuling Zhang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wen Wan
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Tianjie Yang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yong Zhang
- College of Resources and Environment, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Yangchun Xu
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China.
| | - Qirong Shen
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Zhong Wei
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China.
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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276
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Jin X, Chen Z, Shi Y, Gui J, Zhao Z. Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus. Microb Biotechnol 2022; 15:683-702. [PMID: 33393737 PMCID: PMC8867974 DOI: 10.1111/1751-7915.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023] Open
Abstract
Environmental bacteria have a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to the disturbance from environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon the hindgut microbiota of cultured fugu. Consequently, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, implying a reduced stability upon bacterial disturbance from feed. Moreover, quantitative ecological analyses indicated that homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts in the context of lower degree of disturbance. While the disturbance peaked, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Our findings emphasized the intricate linkage between feed and gut microbiota and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.
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Affiliation(s)
- Xingkun Jin
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Ziwei Chen
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Yan Shi
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Jian‐Fang Gui
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
- State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of HydrobiologyThe Innovation Academy of Seed DesignChinese Academy of SciencesWuhan430072China
| | - Zhe Zhao
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
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277
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Custódio V, Gonin M, Stabl G, Bakhoum N, Oliveira MM, Gutjahr C, Castrillo G. Sculpting the soil microbiota. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:508-522. [PMID: 34743401 DOI: 10.1111/tpj.15568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Soil is a living ecosystem, the health of which depends on fine interactions among its abiotic and biotic components. These form a delicate equilibrium maintained through a multilayer network that absorbs certain perturbations and guarantees soil functioning. Deciphering the principles governing the interactions within soils is of critical importance for their management and conservation. Here, we focus on soil microbiota and discuss the complexity of interactions that impact the composition and function of soil microbiota and their interaction with plants. We discuss how physical aspects of soils influence microbiota composition and how microbiota-plant interactions support plant growth and responses to nutrient deficiencies. We predict that understanding the principles determining the configuration and functioning of soil microbiota will contribute to the design of microbiota-based strategies to preserve natural resources and develop more environmentally friendly agricultural practices.
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Affiliation(s)
- Valéria Custódio
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Mathieu Gonin
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Georg Stabl
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Niokhor Bakhoum
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Gabriel Castrillo
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
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278
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Xie K, Ren Y, Chen A, Yang C, Zheng Q, Chen J, Wang D, Li Y, Hu S, Xu G. Plant nitrogen nutrition: The roles of arbuscular mycorrhizal fungi. JOURNAL OF PLANT PHYSIOLOGY 2022; 269:153591. [PMID: 34936969 DOI: 10.1016/j.jplph.2021.153591] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Nitrogen (N) is the most abundant mineral nutrient required by plants, and crop productivity depends heavily on N fertilization in many soils. Production and application of N fertilizers consume huge amounts of energy and substantially increase the costs of agricultural production. Excess N compounds released from agricultural systems are also detrimental to the environment. Thus, increasing plant N uptake efficiency is essential for the development of sustainable agriculture. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most terrestrial plants that facilitate plant nutrient uptake and increase host resistance to diverse environmental stresses. AM association is an endosymbiotic process that relies on the differentiation of both host plant roots and AM fungi to create novel contact interfaces within the cells of plant roots. AM plants have two pathways for nutrient uptake: either direct uptake via the root hairs and root epidermis, or indirectly through AM fungal hyphae into root cortical cells. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake processes, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungi-root interface have been identified. Here, we mainly summarize the recent advances in N uptake, assimilation, and translocation in AM symbiosis, and also discuss how N interplays with C and P in modulating AM development, as well as the synergies between AM fungi and soil microbial communities in N uptake.
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Affiliation(s)
- Kun Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuhan Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Aiqun Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Congfan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qingsong Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Chen
- College of Horticulture Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Dongsheng Wang
- Department of Ecological Environment and Soil Science, Nanjing Institute of Vegetable Science, Nanjing, Jiangsu, China
| | - Yiting Li
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Shuijin Hu
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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279
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Li M, Liu R, Li Y, Wang C, Ma W, Zheng L, Zhang K, Fu X, Li X, Su Y, Huang G, Zhong Y, Liao H. Functional Investigation of Plant Growth Promoting Rhizobacterial Communities in Sugarcane. Front Microbiol 2022; 12:783925. [PMID: 35058904 PMCID: PMC8763851 DOI: 10.3389/fmicb.2021.783925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Plant microbiota are of great importance for host nutrition and health. As a C4 plant species with a high carbon fixation capacity, sugarcane also associates with beneficial microbes, though mechanisms underlying sugarcane root-associated community development remain unclear. Here, we identify microbes that are specifically enriched around sugarcane roots and report results of functional testing of potentially beneficial microbes propagating with sugarcane plants. First, we analyzed recruitment of microbes through analysis of 16S rDNA enrichment in greenhouse cultured sugarcane seedlings growing in field soil. Then, plant-associated microbes were isolated and assayed for beneficial activity, first in greenhouse experiments, followed by field trials for selected microbial strains. The promising beneficial microbe SRB-109, which quickly colonized both roots and shoots of sugarcane plants, significantly promoted sugarcane growth in field trials, nitrogen and potassium acquisition increasing by 35.68 and 28.35%, respectively. Taken together, this report demonstrates successful identification and utilization of beneficial plant-associated microbes in sugarcane production. Further development might facilitate incorporation of such growth-promoting microbial applications in large-scale sugarcane production, which may not only increase yields but also reduce fertilizer costs and runoff.
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Affiliation(s)
- Mingjia Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ran Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanjun Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cunhu Wang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjing Ma
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lei Zheng
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kefei Zhang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing Fu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yachun Su
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guoqiang Huang
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
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280
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Wu Y, Santos SS, Vestergård M, Martín González AM, Ma L, Feng Y, Yang X. A field study reveals links between hyperaccumulating Sedum plants-associated bacterial communities and Cd/Zn uptake and translocation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150400. [PMID: 34818769 DOI: 10.1016/j.scitotenv.2021.150400] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Hyperaccumulating ecotypes of Sedum plants are promising Cd/Zn phytoextractors, with potential for leveraging its rhizospheric or endophytic microbiomes to improve phytoremediation efficiency. However, research of bacteria associated with Sedum at field scale is still lacking. Here, we presented a detailed investigation of the bacterial microbiome of hyperaccumulating Sedum ecotypes (S. alfredii and S. plumbizincicola) and a non-hyperaccumulating S. alfredii ecotype, which grow at different soil environments. Moreover, we evaluated the heavy metal uptake and translocation potential of Sedum plants at different locations. The results showed that both HE ecotypes, contrary to the NHE, were efficient for phytoremediation in mine areas and farmlands. For NHE plants, rhizosphere co-occurrence networks were more complex than the networks of other compartments, while networks of HE plants were more complex in bulk soil and roots. The proportion of positive correlations within co-occurrence networks was higher for the HE plants, suggesting a greater potential for mutualistic interactions. Plant compartment and location predominantly shaped the microbiome assembly, and Proteobacteria, Actinobacteria and Acidobacteria dominated the bacterial communities of Sedum plants. Keystone taxa related to Zn hyperaccumulation are similar to those related to Cd hyperaccumulation, and nine bacterial genera had significantly positive correlation with Cd/Zn hyperaccumulation. Taxa, linked to phytoremediation in both mine and farmland (i.e. Actinospica and Streptomyces from Actinobacteria), could be targets for further investigation of their ability to promote metal phytoremediation of Sedum species.
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Affiliation(s)
- Yingjie Wu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, Denmark; College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Susana S Santos
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, Denmark
| | - Mette Vestergård
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, Denmark.
| | | | - Luyao Ma
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
| | - Xiaoe Yang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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281
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Durán P, Flores-Uribe J, Wippel K, Zhang P, Guan R, Melkonian B, Melkonian M, Garrido-Oter R. Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota. Nat Commun 2022; 13:406. [PMID: 35058457 PMCID: PMC8776852 DOI: 10.1038/s41467-022-28055-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Microscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Using synthetic communities derived from C. reinhardtii and Arabidopsis thaliana, we show that phycosphere and root bacteria assemble into taxonomically similar communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggest the existence of shared ecological principles driving the assembly of the A. thaliana root and C. reinhardtii phycosphere microbiota, despite the vast evolutionary distance between these two photosynthetic organisms.
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Affiliation(s)
- Paloma Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences, 40225, Düsseldorf, Germany
| | - José Flores-Uribe
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Kathrin Wippel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Rui Guan
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Barbara Melkonian
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Michael Melkonian
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, 40225, Düsseldorf, Germany.
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282
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Study of Rhizosphere Microbial Community Structures of Asian Wild and Cultivated Rice Showed That Cultivated Rice Had Decreased and Enriched Some Functional Microorganisms in the Process of Domestication. DIVERSITY 2022. [DOI: 10.3390/d14020067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice.
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283
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Wu R, Liu Z, Wang J, Guo C, Zhou Y, Bawa G, Rochaix JD, Sun X. COE2 Is Required for the Root Foraging Response to Nitrogen Limitation. Int J Mol Sci 2022; 23:ijms23020861. [PMID: 35055047 PMCID: PMC8778332 DOI: 10.3390/ijms23020861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 01/10/2023] Open
Abstract
There are numerous exchanges of signals and materials between leaves and roots, including nitrogen, which is one of the essential nutrients for plant growth and development. In this study we identified and characterized the Chlorophyll A/B-Binding Protein (CAB) (named coe2 for CAB overexpression 2) mutant, which is defective in the development of chloroplasts and roots under normal growth conditions. The phenotype of coe2 is caused by a mutation in the Nitric Oxide Associated (NOA1) gene that is implicated in a wide range of chloroplast functions including the regulation of metabolism and signaling of nitric oxide (NO). A transcriptome analysis reveals that expression of genes involved in metabolism and lateral root development are strongly altered in coe2 seedlings compared with WT. COE2 is expressed in hypocotyls, roots, root hairs, and root caps. Both the accumulation of NO and the growth of lateral roots are enhanced in WT but not in coe2 under nitrogen limitation. These new findings suggest that COE2-dependent signaling not only coordinates gene expression but also promotes chloroplast development and function by modulating root development and absorption of nitrogen compounds.
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Affiliation(s)
- Rui Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (R.W.); (Z.L.); (J.W.); (C.G.); (Y.Z.); (G.B.)
| | - Zhixin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (R.W.); (Z.L.); (J.W.); (C.G.); (Y.Z.); (G.B.)
| | - Jiajing Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (R.W.); (Z.L.); (J.W.); (C.G.); (Y.Z.); (G.B.)
| | - Chenxi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (R.W.); (Z.L.); (J.W.); (C.G.); (Y.Z.); (G.B.)
| | - Yaping Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (R.W.); (Z.L.); (J.W.); (C.G.); (Y.Z.); (G.B.)
| | - George Bawa
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (R.W.); (Z.L.); (J.W.); (C.G.); (Y.Z.); (G.B.)
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland;
| | - Xuwu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China; (R.W.); (Z.L.); (J.W.); (C.G.); (Y.Z.); (G.B.)
- Correspondence:
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284
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Zhang H, Sun X, Dai M. Improving crop drought resistance with plant growth regulators and rhizobacteria: Mechanisms, applications, and perspectives. PLANT COMMUNICATIONS 2022; 3:100228. [PMID: 35059626 PMCID: PMC8760038 DOI: 10.1016/j.xplc.2021.100228] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/20/2021] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
Drought is one of the main abiotic stresses that cause crop yield loss. Improving crop yield under drought stress is a major goal of crop breeding, as it is critical to food security. The mechanism of plant drought resistance has been well studied, and diverse drought resistance genes have been identified in recent years, but transferring this knowledge from the laboratory to field production remains a significant challenge. Recently, some new strategies have become research frontiers owing to their advantages of low cost, convenience, strong field operability, and/or environmental friendliness. Exogenous plant growth regulator (PGR) treatment and microbe-based plant biotechnology have been used to effectively improve crop drought tolerance and preserve yield under drought stress. However, our understanding of the mechanisms by which PGRs regulate plant drought resistance and of plant-microbiome interactions under drought is still incomplete. In this review, we summarize these two strategies reported in recent studies, focusing on the mechanisms by which these exogenous treatments regulate crop drought resistance. Finally, future challenges and directions in crop drought resistance breeding are discussed.
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Affiliation(s)
- Hui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaopeng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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285
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Chen C, Huang Z, Huang P, Li K, Zeng J, Wen Y, Li B, Zhao J, Wu P. Urogenital Microbiota:Potentially Important Determinant of PD-L1 Expression in Male Patients with Non-muscle Invasive Bladder Cancer. BMC Microbiol 2022; 22:7. [PMID: 34983384 PMCID: PMC8725255 DOI: 10.1186/s12866-021-02407-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/29/2021] [Indexed: 02/06/2023] Open
Abstract
Background Urogenital microbiota may be associated with the recurrence of bladder cancer, but the underlying mechanism remains unclear. The notion that microbiota can upregulate PD-L1 expression in certain epithelial tumors to promote immune escape has been demonstrated. Thus, we hypothesized that the urogenital microbiota may be involved in the recurrence and progression of non-muscle invasive bladder cancer (NMIBC) by upregulating the PD-L1 expression. To test this hypothesis, we investigated the relationship between urogenital microbial community and PD-L1 expression in male patients with NMIBC. Results 16S rRNA gene sequencing was performed to analyse the composition of urogenital microbiota, and the expression of PD-L1 in cancerous tissues was detected by immunohistochemistry. The subjects (aged 43–79 years) were divided into PD-L1-positive group (Group P, n = 9) and PD-L1-negative group (Group N, n = 19) respectively based on their PD-L1 immunohistochemical results. No statistically significant differences were found in the demographic characteristics between group P and N. We observed that group P exhibited higher species richness (based on Observed species and Ace index, both P < 0.05). Furthermore, subgroup analysis showed that the increase in number of PD-L1 positive cells was accompanied by increased richness of urogenital microbiota. Significantly different composition of urogenital microbiota was found between group P and group N (based on weighted Unifrac and unweighted Unifrac distances metric, both P < 0.05). Enrichment of some bacterial genera (e.g., Leptotrichia, Roseomonas, and Propionibacterium) and decrease of some bacterial genera (e.g., Prevotella and Massilia) were observed in group P as compared with group N. These findings indicated that these genera may affect the expression of PD-L1 through some mechanisms to be studied. Conclusion Our study provided for the first time an overview of the association between urogenital microbiota and PD-L1 expression in male patients with NMIBC, indicating that urogenital microbiota was an important determinant of PD-L1 expression in male NMIBC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02407-8.
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Affiliation(s)
- Chunxiao Chen
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zehai Huang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Pengcheng Huang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kun Li
- The third hospital of mianyang, Sichuan Province, China
| | - Jiarong Zeng
- Department of Urology, Meizhou People's Hospital, Meizhou, China
| | | | - Biao Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Zhao
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.
| | - Peng Wu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China. .,Clinical Microbiota Center, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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286
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Paz-Ares J, Puga MI, Rojas-Triana M, Martinez-Hevia I, Diaz S, Poza-Carrión C, Miñambres M, Leyva A. Plant adaptation to low phosphorus availability: Core signaling, crosstalks, and applied implications. MOLECULAR PLANT 2022; 15:104-124. [PMID: 34954444 DOI: 10.1016/j.molp.2021.12.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/11/2021] [Accepted: 12/20/2021] [Indexed: 05/25/2023]
Abstract
Phosphorus (P) is an essential nutrient for plant growth and reproduction. Plants preferentially absorb P as orthophosphate (Pi), an ion that displays low solubility and that is readily fixed in the soil, making P limitation a condition common to many soils and Pi fertilization an inefficient practice. To cope with Pi limitation, plants have evolved a series of developmental and physiological responses, collectively known as the Pi starvation rescue system (PSR), aimed to improve Pi acquisition and use efficiency (PUE) and protect from Pi-starvation-induced stress. Intensive research has been carried out during the last 20 years to unravel the mechanisms underlying the control of the PSR in plants. Here we review the results of this research effort that have led to the identification and characterization of several core Pi starvation signaling components, including sensors, transcription factors, microRNAs (miRNAs) and miRNA inhibitors, kinases, phosphatases, and components of the proteostasis machinery. We also refer to recent results revealing the existence of intricate signaling interplays between Pi and other nutrients and antagonists, N, Fe, Zn, and As, that have changed the initial single-nutrient-centric view to a more integrated view of nutrient homeostasis. Finally, we discuss advances toward improving PUE and future research priorities.
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Affiliation(s)
- Javier Paz-Ares
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain.
| | - Maria Isabel Puga
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Monica Rojas-Triana
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Iris Martinez-Hevia
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Sergio Diaz
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Cesar Poza-Carrión
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Miguel Miñambres
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Antonio Leyva
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
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287
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Yu S, Ali J, Zhou S, Ren G, Xie H, Xu J, Yu X, Zhou F, Peng S, Ma L, Yuan D, Li Z, Chen D, Zheng R, Zhao Z, Chu C, You A, Wei Y, Zhu S, Gu Q, He G, Li S, Liu G, Liu C, Zhang C, Xiao J, Luo L, Li Z, Zhang Q. From Green Super Rice to green agriculture: Reaping the promise of functional genomics research. MOLECULAR PLANT 2022; 15:9-26. [PMID: 34883279 DOI: 10.1016/j.molp.2021.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.
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Affiliation(s)
- Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shaochuan Zhou
- Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guangjun Ren
- Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Huaan Xie
- Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Fasong Zhou
- China National Seed Group Co., Ltd, Beijing, China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangyong Ma
- China National Rice Research Institute, Hangzhou, China
| | | | - Zefu Li
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Dazhou Chen
- Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | | | | | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Aiqing You
- Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yu Wei
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Susong Zhu
- Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Qiongyao Gu
- Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Shigui Li
- Sichuan Agricultural University, Chengdu, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Changhua Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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288
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Chen P, He W, Shen Y, Zhu L, Yao X, Sun R, Dai C, Sun B, Chen Y. Interspecific Neighbor Stimulates Peanut Growth Through Modulating Root Endophytic Microbial Community Construction. FRONTIERS IN PLANT SCIENCE 2022; 13:830666. [PMID: 35310651 PMCID: PMC8928431 DOI: 10.3389/fpls.2022.830666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/07/2022] [Indexed: 05/04/2023]
Abstract
Plants have evolved the capability to respond to interspecific neighbors by changing morphological performance and reshaping belowground microbiota. However, whether neighboring plants influence the microbial colonization of the host's root and further affect host performance is less understood. In this study, using 16S rRNA high-throughput sequencing of peanut (Arachis hypogaea L.) roots from over 5 years of mono- and intercropping field systems, we found that neighbor maize can alter the peanut root microbial composition and re-shape microbial community assembly. Interspecific maize coexistence increased the colonization of genera Bradyrhizobium and Streptomyces in intercropped peanut roots. Through endophytic bacterial isolation and isolate back inoculation experiments, we demonstrated that the functional potentials of available nutrient accumulation and phytohormones production from Bradyrhizobium and Streptomyces endowed them with the ability to act as keystones in the microbial network to benefit peanut growth and production with neighbor competition. Our results support the idea that plants establish a plant-endophytic microbial holobiont through root selective filtration to enhance host competitive dominance, and provide a promising direction to develop modern diversified planting for harnessing crop microbiomes for the promotion of crop growth and productivity in sustainable agriculture.
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Affiliation(s)
- Pin Chen
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wei He
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yi Shen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lingyue Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiangzhi Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ruibo Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Chuanchao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yan Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Yan Chen,
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289
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Chen J, Li N, Chang J, Ren K, Zhou J, Yang G. Taxonomic Structure of Rhizosphere Bacterial Communities and Its Association With the Accumulation of Alkaloidal Metabolites in Sophora flavescens. Front Microbiol 2022; 12:781316. [PMID: 34970241 PMCID: PMC8712762 DOI: 10.3389/fmicb.2021.781316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Plant secondary metabolites (SMs) play a crucial role in plant defense against pathogens and adaptation to environmental stresses, some of which are produced from medicinal plants and are the material basis of clinical efficacy and vital indicators for quality evaluation of corresponding medicinal materials. The influence of plant microbiota on plant nutrient uptake, production, and stress tolerance has been revealed, but the associations between plant microbiota and the accumulation of SMs in medicinal plants remain largely unknown. Plant SMs can vary among individuals, which could be partly ascribed to the shift in microbial community associated with the plant host. In the present study, we sampled fine roots and rhizosphere soils of Sophora flavescens grown in four well-separated cities/counties in China and determined the taxonomic composition of rhizosphere bacterial communities using Illumina 16S amplicon sequencing. In addition, the association of the rhizosphere bacterial microbiota with the accumulation of alkaloids in the roots of S. flavescens was analyzed. The results showed that S. flavescens hosted distinct bacterial communities in the rhizosphere across geographic locations and plant ages, also indicating that geographic location was a larger source of variation than plant age. Moreover, redundancy analysis revealed that spatial, climatic (mean annual temperature and precipitation), and edaphic factors (pH and available N and P) were the key drivers that shape the rhizosphere bacterial communities. Furthermore, the results of the Mantel test demonstrated that the rhizosphere bacterial microbiota was remarkably correlated with the contents of oxymatrine, sophoridine, and matrine + oxymatrine in roots. Specific taxa belonging to Actinobacteria and Chloroflexi were identified as potential beneficial bacteria associated with the total accumulation of matrine and oxymatrine by a random forest machine learning algorithm. Finally, the structural equation modeling indicated that the Actinobacteria phylum had a direct effect on the total accumulation of matrine and oxymatrine. The present study addresses the association between the rhizosphere bacterial communities and the accumulation of alkaloids in the medicinal plant S. flavescens. Our findings may provide a basis for the quality improvement and sustainable utilization of this medicinal plant thorough rhizosphere microbiota manipulation.
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Affiliation(s)
- Jie Chen
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Na Li
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Jiayu Chang
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Kaida Ren
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Jiangtao Zhou
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
| | - Guan'e Yang
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, China
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290
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Tayyab M, Islam W, Noman A, Pang Z, Li S, Lin S, Wenxiong L, Hua Z. Sugarcane cultivars manipulate rhizosphere bacterial communities' structure and composition of agriculturally important keystone taxa. 3 Biotech 2022; 12:32. [PMID: 35070622 PMCID: PMC8724486 DOI: 10.1007/s13205-021-03091-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/09/2021] [Indexed: 01/03/2023] Open
Abstract
Different sugarcane cultivars are grown to produce renewable energy and sugar in China. However, we have a limited awareness of the interactive influence of varying sugarcane cultivars on rhizosphere bacterial structure and diversity. Assessing cultivar choice impact on soil bacterial communities is vital since bacterial taxa are frequently impacted by planting performance. Employing high-throughput Illumina sequencing, we examined bacterial communities' assemblage in the rhizosphere of six Chinese sugarcane cultivars (Regan14-62, Guitang 08-120, Haizhe 22, Guitang 08-1180, Taitang 22 and Liucheng 05-136). Our results indicated that different sugarcane cultivars have no significant influence on the Shannon index; however, their impact on richness was substantial. There was a difference in the bacterial community structure that is also associated with a change in the community composition, as determined by the DESeq2 results, suggesting that "Haizhe 22 (HZ22)" had a completely different beta diversity as compared to other five cultivars by enriching abundance of Firmicutes, Proteobacteria, Gemmatimonadetes, Saccharibacteria and Bacteroidetes and reducing the quantity of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes, respectively. The HZ22 rhizosphere significantly enriched six genera (e.g., Devosia, Mizugakiibacter, Mycobacterium, Nakamurella, Rhizomicrobium, and Virgibacillus) relative to other varieties, suggesting an important role in plant disease tolerance and growth development, including soil nutrient cycling and bioremediation. Analysis of similarity (ANOSIM) and correlation analysis revealed that cultivars, soil organic matter, pH and soil moisture were central factors influencing bacterial composition. These findings may help in selection of plant cultivars capable of supporting highly abundant specific beneficial microbial groups, improving plant disease resistance, growth stimulation, and soil bioremediation capabilities, further leading to improvements in breeding strategies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03091-1.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Waqar Islam
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ali Noman
- Department of Botany, Govt. College University Faisalabad, Faisalabad, Pakistan
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shiyan Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lin Wenxiong
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhang Hua
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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291
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Dong H, Sun H, Jiang L, Ma D, Fan S. Characteristics of root‐associated bacterial community and nitrogen biochemical properties of two
Japonica
rice cultivars with different yields. Food Energy Secur 2021. [DOI: 10.1002/fes3.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Hangyu Dong
- Key Laboratory of Northeast Rice Biology and Breeding Rice Research Institute Shenyang Agricultural University Shenyang China
- Agronomy College Shenyang Agricultural University Shenyang China
| | - Haoyuan Sun
- Key Laboratory of Northeast Rice Biology and Breeding Rice Research Institute Shenyang Agricultural University Shenyang China
- Agronomy College Shenyang Agricultural University Shenyang China
| | - Linlin Jiang
- Key Laboratory of Northeast Rice Biology and Breeding Rice Research Institute Shenyang Agricultural University Shenyang China
- Agronomy College Shenyang Agricultural University Shenyang China
| | - Dianrong Ma
- Key Laboratory of Northeast Rice Biology and Breeding Rice Research Institute Shenyang Agricultural University Shenyang China
- Agronomy College Shenyang Agricultural University Shenyang China
| | - Shuxiu Fan
- Agronomy College Shenyang Agricultural University Shenyang China
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292
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Ju Z, Du X, Feng K, Li S, Gu S, Jin D, Deng Y. The Succession of Bacterial Community Attached on Biodegradable Plastic Mulches During the Degradation in Soil. Front Microbiol 2021; 12:785737. [PMID: 35046914 PMCID: PMC8762578 DOI: 10.3389/fmicb.2021.785737] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
Despite the increasing application of biodegradable plastic mulches (BDMs) in agriculture, the colonization and succession of the attached microbial community on BDMs during their degradation processes remain poorly characterized. Here, we buried four types of commonly used BDMs, including pure polylactic acid (PLA), pure polybutylene adipate terephthalate (PBAT), and two mixtures of PLA and PBAT (85:15 and 15:85 w/w), and one classic polyethylene (PE) mulch in soil for 5 months. Both plastic components and incubation time significantly shaped the β-diversities of microbiota on the plastic mulches (p < 0.001). Meanwhile, the microbial compositions and community structures on BDMs were significantly different from PE mulch, and when excluding PE mulch, the microbiota varied more with time than by the composition of the four BDMs. The orders Burkholderiales and Pseudonocardiales were dominant on most BDMs across different time points. The genus Ramlibacter was revealed as a common biomarker for both PLA and PBAT by random-forest model, and all biomarkers for the BDMs belonged to the dominant order Burkholderiales. In addition, degradation-related and pathogen-related functional taxa were enriched in all mulches among all 40 functional groups, while surprisingly, potential pathogens were detected at higher levels on BDMs than PE. For community assembly on all mulches, the drift and dispersal processes played more important roles than selection, and in particular, the contribution of stochastic drift increased during the degradation process of BDMs while selection decreased, while the opposite trend was observed with PE mulch. Overall, our results demonstrated some degradation species and pathogens were specifically enriched on BDMs, though stochastic processes also had important impacts on the community assembly. It suggested that, similar to conventional plastic mulch, the increased usage of BDMs could lead to potential hazards to crops and human health.
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Affiliation(s)
- Zhicheng Ju
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Decai Jin
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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293
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Wu R, Wang L, Xie J, Zhang Z. Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics. Front Microbiol 2021; 12:758794. [PMID: 34975785 PMCID: PMC8718803 DOI: 10.3389/fmicb.2021.758794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022] Open
Abstract
Wolf spiders (Lycosidae) are crucial component of integrated pest management programs and the characteristics of their gut microbiota are known to play important roles in improving fitness and survival of the host. However, there are only few studies of the gut microbiota among closely related species of wolf spider. Whether wolf spiders gut microbiota vary with habitats remains unknown. Here, we used shotgun metagenomic sequencing to compare the gut microbiota of two wolf spider species, Pardosa agraria and P. laura from farmland and woodland ecosystems, respectively. The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. Approximately 27.3% of the gut microbiota of P. agraria comprises Proteobacteria, and approximately 34.4% of the gut microbiota of P. laura comprises Firmicutes. We assembled microbial genomes and found that the gut microbiota of P. laura are enriched in genes for carbohydrate metabolism. In contrast, those of P. agraria showed a higher proportion of genes encoding acetyltransferase, an enzyme involved in resistance to antibiotics. We reconstructed three high-quality and species-level microbial genomes: Vulcaniibacterium thermophilum, Anoxybacillus flavithermus and an unknown bacterium belonging to the family Simkaniaceae. Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders.
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Affiliation(s)
- Runbiao Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Luyu Wang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Jianping Xie
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Zhisheng Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- *Correspondence: Zhisheng Zhang, , orcid.org/0000-0002-9304-1789
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294
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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295
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Zheng Y, Chiang TY, Huang CL, Feng XY, Yrjälä K, Gong X. The Predominance of Proteobacteria and Cyanobacteria in the Cycas dolichophylla Coralloid Roots Revealed by 16S rRNA Metabarcoding. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721060175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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296
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Zhang P, Spaepen S, Bai Y, Hacquard S, Garrido-Oter R. Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME COMMUNICATIONS 2021; 1:73. [PMID: 37938657 PMCID: PMC9723543 DOI: 10.1038/s43705-021-00077-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/03/2021] [Accepted: 11/18/2021] [Indexed: 09/30/2023]
Abstract
Synthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.
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Affiliation(s)
- Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stjin Spaepen
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Stephane Hacquard
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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297
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Mittelstrass J, Sperone FG, Horton MW. Using transects to disentangle the environmental drivers of plant-microbiome assembly. PLANT, CELL & ENVIRONMENT 2021; 44:3515-3525. [PMID: 34562029 PMCID: PMC9292149 DOI: 10.1111/pce.14190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental heterogeneity is a major driver of plant-microbiome assembly, but the specific climate and soil conditions that are involved remain poorly understood. To better understand plant microbiome formation, we examined the bacteria and fungi that colonize wild strawberry (Fragaria vesca) plants in North American and European populations. Using transects as replicates, we found strong overlap among the environmental conditions that best predict the overall similarity and richness of the plant microbiome, including soil nutrients that replicate across continents. Temperature is also among the main predictors of diversity for both bacteria and fungi in both the leaf and, unexpectedly, the root microbiome. Our results indicate that a small number of environmental factors, and their interactions, consistently contribute to plant microbiome formation, which has implications for predicting the contributions of microbes to plant productivity in ever-changing environments.
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Affiliation(s)
- Jana Mittelstrass
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - F. Gianluca Sperone
- Department of Environmental Science and GeologyWayne State UniversityDetroitMichiganUSA
| | - Matthew W. Horton
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
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298
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Yu RP, Lambers H, Callaway RM, Wright AJ, Li L. Belowground facilitation and trait matching: two or three to tango? TRENDS IN PLANT SCIENCE 2021; 26:1227-1235. [PMID: 34400074 DOI: 10.1016/j.tplants.2021.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/15/2021] [Accepted: 07/24/2021] [Indexed: 05/12/2023]
Abstract
High biodiversity increases ecosystem functions; however, belowground facilitation remains poorly understood in this context. Here, we explore mechanisms that operate via 'giving-receiving feedbacks' for belowground facilitation. These include direct effects via root exudates, signals, and root trait plasticity, and indirect biotic facilitation via the effects of root exudates on soil biota and feedback from biota to plants. We then highlight that these two- or three-way mechanisms must affect biodiversity-ecosystem function relationships via specific combinations of matching traits. To tango requires a powerful affinity and harmony between well-matched partners, and such matches link belowground facilitation to the effect of biodiversity on function. Such matching underpins applications in intercropping, forestry, and pasture systems, in which diversity contributes to greater productivity and sustainability.
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Affiliation(s)
- Rui-Peng Yu
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, 2 Yuan Ming Yuan West Road, Beijing 100193, PR China
| | - Hans Lambers
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia; National Academy of Agriculture Green Development, China Agricultural University, 2 Yuan Ming Yuan West Road, Beijing 100193, PR China
| | - Ragan M Callaway
- Division of Biological Sciences and Institute on Ecosystems, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Alexandra J Wright
- Department of Biological Sciences, California State University Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Long Li
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, 2 Yuan Ming Yuan West Road, Beijing 100193, PR China.
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299
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Fu R, Feng H, Dini-Andreote F, Wang Z, Bo C, Cao W, Yang K, Liu M, Yang T, Shen Q, Xu Y, Wei Z. Modulation of the Tomato Rhizosphere Microbiome via Changes in Root Exudation Mediated by the Ethylene Receptor NR. Microorganisms 2021; 9:2456. [PMID: 34946058 PMCID: PMC8705318 DOI: 10.3390/microorganisms9122456] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
Plant hormones have been recently shown to exert an indirect influence on the recruitment of plant-associated microbiomes. However, it remains unclear the extent to which the disruption of the ethylene (ET) signaling pathway affects the assembly and functioning of plant-root microbiomes. In this study, the Never-ripe tomato mutant (Nr) was profiled for differences compared to the wild type (control). Tomato plants were subjected to root exudate profiling and the characterization of bacterial and fungal communities. Compared to the control, Nr revealed differences in the composition of root exudates, including lower amounts of esculetin, gallic acid, L-fucose, eicosapentaenoic acid, and higher amounts of β-aldehyde. Interestingly, Nr significantly differed in the composition and functioning of the rhizosphere bacterial community. We also identified the taxa that occurred at relatively higher abundances in Nr, including the genus Lysobacter, which displayed a significant negative correlation with changes in eicosapentaenoic acid and esculetin, and a significant positive correlation with changes in β-aldehyde. Taken together, our study provides evidence that a mutation in the ET receptor exerts predictable changes in the root-associated microbial taxa of tomato plants. These indirect effects can potentially be explored towards new strategies to engineer beneficial plant microbiomes via targeted changes in plant genetics and physiology.
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Affiliation(s)
- Ruixin Fu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16801, USA;
| | - Zhen Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Chunbin Bo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Wenhui Cao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Keming Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
| | - Tianjie Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Yangchun Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
| | - Zhong Wei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (R.F.); (H.F.); (Z.W.); (C.B.); (W.C.); (K.Y.); (Q.S.); (Y.X.); (Z.W.)
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Armanhi JSL, de Souza RSC, Biazotti BB, Yassitepe JEDCT, Arruda P. Modulating Drought Stress Response of Maize by a Synthetic Bacterial Community. Front Microbiol 2021; 12:747541. [PMID: 34745050 PMCID: PMC8566980 DOI: 10.3389/fmicb.2021.747541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/20/2021] [Indexed: 01/21/2023] Open
Abstract
Plant perception and responses to environmental stresses are known to encompass a complex set of mechanisms in which the microbiome is involved. Knowledge about plant physiological responses is therefore critical for understanding the contribution of the microbiome to plant resilience. However, as plant growth is a dynamic process, a major hurdle is to find appropriate tools to effectively measure temporal variations of different plant physiological parameters. Here, we used a non-invasive real-time phenotyping platform in a one-to-one (plant–sensors) set up to investigate the impact of a synthetic community (SynCom) harboring plant-beneficial bacteria on the physiology and response of three commercial maize hybrids to drought stress (DS). SynCom inoculation significantly reduced yield loss and modulated vital physiological traits. SynCom-inoculated plants displayed lower leaf temperature, reduced turgor loss under severe DS and a faster recovery upon rehydration, likely as a result of sap flow modulation and better water usage. Microbiome profiling revealed that SynCom bacterial members were able to robustly colonize mature plants and recruit soil/seed-borne beneficial microbes. The high-resolution temporal data allowed us to record instant plant responses to daily environmental fluctuations, thus revealing the impact of the microbiome in modulating maize physiology, resilience to drought, and crop productivity.
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Affiliation(s)
- 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
| | - 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
| | - Bárbara Bort Biazotti
- 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
| | | | - 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
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