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Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024:S0966-842X(24)00043-X. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.
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Affiliation(s)
- Chiara A Berruto
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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Du X, Liu N, Yan B, Li Y, Liu M, Huang Y. Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron. THE ISME JOURNAL 2024; 18:wrad041. [PMID: 38366066 PMCID: PMC10881299 DOI: 10.1093/ismejo/wrad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/25/2023] [Accepted: 12/26/2024] [Indexed: 02/18/2024]
Abstract
Microorganisms living in soil maintain intricate interactions among themselves, forming the soil microbiota that influences the rhizosphere microbiome and plant growth. However, the mechanisms underlying the soil microbial interactions remain unclear. Streptomyces and Mesorhizobium are commonly found in soil and serve as plant growth-promoting rhizobacteria (PGPR). Here, we identified an unprecedented interaction between the colonies of red-soil-derived Streptomyces sp. FXJ1.4098 and Mesorhizobium sp. BAC0120 and referred to it as "proximity-based defensive mutualism (PBDM)." We found that metabolite-mediated iron competition and sharing between the two microorganisms were responsible for PBDM. Streptomyces sp. FXJ1.4098 produced a highly diffusible siderophore, desferrioxamine, which made iron unavailable to co-cultured Mesorhizobium sp. BAC0120, thereby inhibiting its growth. Streptomyces sp. FXJ1.4098 also released poorly diffusible iron-porphyrin complexes, which could be utilized by Mesorhizobium sp. BAC0120, thereby restoring the growth of nearby Mesorhizobium sp. BAC0120. Furthermore, in ternary interactions, the PBDM strategy contributed to the protection of Mesorhizobium sp. BAC0120 close to Streptomyces sp. FXJ1.4098 from other microbial competitors, resulting in the coexistence of these two PGPR. A scale-up pairwise interaction screening suggested that the PBDM strategy may be common between Mesorhizobium and red-soil-derived Streptomyces. These results demonstrate the key role of iron in complex microbial interactions and provide novel insights into the coexistence of PGPR in soil.
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Affiliation(s)
- Xueyuan Du
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
- National Engineering Laboratory for Site Remediation Technologies, BCEG Environmental Remediation Co., Ltd., Beijing 100015, P. R. China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
| | - Bingfa Yan
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
| | - Yisong Li
- School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
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Zong G, Cao G, Fu J, Zhang P, Chen X, Yan W, Xin L, Wang Z, Xu Y, Zhang R. Novel mechanism of hydrogen peroxide for promoting efficient natamycin synthesis in Streptomyces. Microbiol Spectr 2023; 11:e0087923. [PMID: 37695060 PMCID: PMC10580950 DOI: 10.1128/spectrum.00879-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/21/2023] [Indexed: 09/12/2023] Open
Abstract
The mechanism of regulation of natamycin biosynthesis by Streptomyces in response to oxidative stress is unclear. Here, we first show cholesterol oxidase SgnE, which catalyzes the formation of H2O2 from sterols, triggered a series of redox-dependent interactions to stimulate natamycin production in S. gilvosporeus. In response to reactive oxygen species, residues Cys212 and Cys221 of the H2O2-sensing consensus sequence of OxyR were oxidized, resulting in conformational changes in the protein: OxyR extended its DNA-binding domain to interact with four motifs of promoter p sgnM . This acted as a redox-dependent switch to turn on/off gene transcription of sgnM, which encodes a cluster-situated regulator, by controlling the affinity between OxyR and p sgnM , thus regulating the expression of 12 genes in the natamycin biosynthesis gene cluster. OxyR cooperates with SgnR, another cluster-situated regulator and an upstream regulatory factor of SgnM, synergistically modulated natamycin biosynthesis by masking/unmasking the -35 region of p sgnM depending on the redox state of OxyR in response to the intracellular H2O2 concentration. IMPORTANCE Cholesterol oxidase SgnE is an indispensable factor, with an unclear mechanism, for natamycin biosynthesis in Streptomyces. Oxidative stress has been attributed to the natamycin biosynthesis. Here, we show that SgnE catalyzes the formation of H2O2 from sterols and triggers a series of redox-dependent interactions to stimulate natamycin production in S. gilvosporeus. OxyR, which cooperates with SgnR, acted as a redox-dependent switch to turn on/off gene transcription of sgnM, which encodes a cluster-situated regulator, by masking/unmasking its -35 region, to control the natamycin biosynthesis gene cluster. This work provides a novel perspective on the crosstalk between intracellular ROS homeostasis and natamycin biosynthesis. Application of these findings will improve antibiotic yields via control of the intracellular redox pressure in Streptomyces.
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Affiliation(s)
- Gongli Zong
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, China
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Jiafang Fu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Peipei Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Xi Chen
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Wenxiu Yan
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Lulu Xin
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Zhongxue Wang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, China
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Dow L, Gallart M, Ramarajan M, Law SR, Thatcher LF. Streptomyces and their specialised metabolites for phytopathogen control - comparative in vitro and in planta metabolic approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1151912. [PMID: 37389291 PMCID: PMC10301723 DOI: 10.3389/fpls.2023.1151912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
In the search for new crop protection microbial biocontrol agents, isolates from the genus Streptomyces are commonly found with promising attributes. Streptomyces are natural soil dwellers and have evolved as plant symbionts producing specialised metabolites with antibiotic and antifungal activities. Streptomyces biocontrol strains can effectively suppress plant pathogens via direct antimicrobial activity, but also induce plant resistance through indirect biosynthetic pathways. The investigation of factors stimulating the production and release of Streptomyces bioactive compounds is commonly conducted in vitro, between Streptomyces sp. and a plant pathogen. However, recent research is starting to shed light on the behaviour of these biocontrol agents in planta, where the biotic and abiotic conditions share little similarity to those of controlled laboratory conditions. With a focus on specialised metabolites, this review details (i) the various methods by which Streptomyces biocontrol agents employ specialised metabolites as an additional line of defence against plant pathogens, (ii) the signals shared in the tripartite system of plant, pathogen and biocontrol agent, and (iii) an outlook on new approaches to expedite the identification and ecological understanding of these metabolites under a crop protection lens.
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Affiliation(s)
- Lachlan Dow
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Microbiomes for One Systems Health Future Science Platform, Acton, ACT, Australia
| | - Marta Gallart
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Advanced Engineering Biology Future Science Platform, Acton, ACT, Australia
| | - Margaret Ramarajan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
| | - Simon R. Law
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Microbiomes for One Systems Health Future Science Platform, Acton, ACT, Australia
| | - Louise F. Thatcher
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Microbiomes for One Systems Health Future Science Platform, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Advanced Engineering Biology Future Science Platform, Acton, ACT, Australia
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Qu L, Dai K, Wang J, Cao L, Rao Z, Han R. Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita. Front Microbiol 2023; 14:1168179. [PMID: 37303801 PMCID: PMC10247985 DOI: 10.3389/fmicb.2023.1168179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops. Methods To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods. Results Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents. Discussion These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.
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Shen F, Wang G, Liu X, Zhu S. Exogenous inoculation of endophyte Penicillium sp. alleviated pineapple internal browning during storage. Heliyon 2023; 9:e16258. [PMID: 37234623 PMCID: PMC10205634 DOI: 10.1016/j.heliyon.2023.e16258] [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: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Pineapple is ranked sixth in terms of global fruit production and the most traded tropical fruit worldwide. Internal browning (IB), a physiological disorder of pineapple fruit after harvest, limits the export and industry development of pineapple. Evidence confirmed that endophyte played a pivotal role in plant disease. This study investigated the relationship between endophyte fungi community structure, population abundance in healthy and IB pineapple fruit; as well as the effect of endophyte Penicillium sp. inoculation on pineapple IB. Intended to explore a new effective measure for controlling IB and reducing postharvest losses in pineapple by an economical and environmentally friendly approach. We found the abundance of endophyte fungi in healthy pineapple fruit was different from that in IB fruit by high-throughput sequencing. The results emphasized that the endophyte Penicillium sp. inoculation dramatically alleviated pineapple IB intensity and severity, delayed crown withering and fruit yellowing, and maintained the exterior quality traits during the postharvest period at 20 °C. Penicillium sp. retarded H2O2 accumulation and increased the total phenols level in pineapple. Application of Penicillium sp. also maintained the higher antioxidant capacity by increasing antioxidant enzyme activity and ascorbic acids levels, regulated of the homeostasis of endogenous hormones, and increased the abundance of Penicillium sp. in the fruit. In summary, Penicillium sp. retarded the occurrence of IB and enhanced the storability of pineapple at postharvest, and this economical and environmentally friendly technology is convenient to spread in agriculture.
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Affiliation(s)
| | | | | | - Shijiang Zhu
- Corresponding author. 483 Wushan Road, Tianhe District, South China Agricultural University, Guangzhou, 510640, China.
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Su J, Wang Y, Bai M, Peng T, Li H, Xu HJ, Guo G, Bai H, Rong N, Sahu SK, He H, Liang X, Jin C, Liu W, Strube ML, Gram L, Li Y, Wang E, Liu H, Wu H. Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata 'Chachi'. MICROBIOME 2023; 11:61. [PMID: 36973820 PMCID: PMC10044787 DOI: 10.1186/s40168-023-01504-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The medicinal material quality of Citrus reticulata 'Chachi' differs depending on the bioactive components influenced by the planting area. Environmental factors, such as soil nutrients, the plant-associated microbiome and climatic conditions, play important roles in the accumulation of bioactive components in citrus. However, how these environmental factors mediate the production of bioactive components of medicinal plants remains understudied. RESULTS Here, a multi-omics approach was used to clarify the role of environmental factors such as soil nutrients and the root-associated microbiome on the accumulation of monoterpenes in the peel of C. reticulata 'Chachi' procured from core (geo-authentic product region) and non-core (non-geo-authentic product region) geographical regions. The soil environment (high salinity, Mg, Mn and K) enhanced the monoterpene content by promoting the expression of salt stress-responsive genes and terpene backbone synthase in the host plants from the core region. The microbial effects on the monoterpene accumulation of citrus from the core region were further verified by synthetic community (SynCom) experiments. Rhizosphere microorganisms activated terpene synthesis and promoted monoterpene accumulation through interactions with the host immune system. Endophyte microorganisms derived from soil with the potential for terpene synthesis might enhance monoterpene accumulation in citrus by providing precursors of monoterpenes. CONCLUSIONS Overall, this study demonstrated that both soil properties and the soil microbiome impacted monoterpene production in citrus peel, thus providing an essential basis for increasing fruit quality via reasonable fertilization and precision microbiota management. Video Abstract.
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Affiliation(s)
- Jianmu Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Mei Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Tianhua Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huisi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hui-Juan Xu
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Guifang Guo
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Haiyi Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ning Rong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hanjun He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiangxiu Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Canzhi Jin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Wei Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Yongtao Li
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
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Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
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Ghatak A, Chaturvedi P, Waldherr S, Subbarao GV, Weckwerth W. PANOMICS at the interface of root-soil microbiome and BNI. TRENDS IN PLANT SCIENCE 2023; 28:106-122. [PMID: 36229336 DOI: 10.1016/j.tplants.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.
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Affiliation(s)
- Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Steffen Waldherr
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guntur Venkata Subbarao
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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Quan W, Wang A, Li C, Xie L. Allelopathic potential and allelochemical composition in different soil layers of Rhododendron delavayi forest, southwest China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.963116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Forests habituated by Rhododendron delavayi often lack understory vegetation, which could possibly be a consequence of allelopathy. It is a phenomenon by virtue of which certain plant species produce allelochemicals that affect the growth and behavior of surrounding plants. To elucidate the allelopathic potential and allelochemicals present in the different layers of a R. delavayi forest, extracts obtained from three layers of the forest were used for seed germination bioassays and gas chromatography-mass spectrometry (GC–MS) analysis. Aqueous extracts of the litter and humus layers significantly inhibited the seed germination of R. delavayi, Festuca arundinacea, and Lolium perenne, with the litter layer causing the strongest inhibitory effect. A total of 26 allelochemicals were identified in the litter, humus, and soil layers by GC–MS analysis. The primary allelochemicals in the soil and humus layer were organic acids, while the main allelochemicals in the litter layer were phenolic acids. The redundancy analysis revealed the significance of total nitrogen (TN) and relative water content (RWC) in explaining the distribution of the allelochemicals. The results indicated that the litter layer exerted the maximum allelopathic effect due to presence of maximum amount of allelochemical especially the phenolic acids.
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Li Y, He X, Yuan H, Lv G. Differed Growth Stage Dynamics of Root-Associated Bacterial and Fungal Community Structure Associated with Halophytic Plant Lycium ruthenicum. Microorganisms 2022; 10:microorganisms10081644. [PMID: 36014066 PMCID: PMC9414475 DOI: 10.3390/microorganisms10081644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 01/02/2023] Open
Abstract
Lycium ruthenicum, a halophytic shrub, has been used to remediate saline soils in northwest China. However, little is known about its root-associated microbial community and how it may be affected by the plant’s growth cycle. In this study, we investigate the microbial community structure of L. ruthenicum by examining three root compartments (rhizosphere, rhizoplane, and endosphere) during four growth stages (vegetative, flowering, fruiting, and senescence). The microbial community diversity and composition were determined by Illumina MiSeq sequencing of the 16S V3–V4 and 18S ITS regions. Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Acidobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most dominant fungal phyla. The alpha diversity of the bacterial communities was highest in the rhizosphere and decreased from the rhizosphere to the endosphere compartments; the fungal communities did not show a consistent trend. The rhizosphere, rhizoplane, and endosphere had distinct bacterial community structures among the three root compartments and from the bulk soil. Additionally, PERMANOVA indicated that the effect of rhizocompartments explained a large proportion of the total community variation. Differential and biomarker analysis not only revealed that each compartment had unique biomarkers and was enriched for specific bacteria, but also that the biomarkers changed with the plant growth cycle. Fungi were also affected by the rhizocompartment, but to a much less so than bacteria, with significant differences in the community composition along the root compartments observed only during the vegetative and flowering stages. Instead, the growth stages appear to account for most of the fungal community variation as demonstrated by PCoA and NMDS, and supported by differential and biomarker analysis, which revealed that the fungal community composition in the rhizosphere and endosphere were dynamic in response to the growth stage. Many enriched OTUs or biomarkers that were identified in the root compartments were potentially beneficial to the plant, meanwhile, some harmful OTUs were excluded from the root, implying that the host plant can select for beneficial bacteria and fungi, which can promote plant growth or increase salt tolerance. In conclusion, the root compartment and growth stage were both determinant factors in structuring the microbial communities of L. ruthenicum, but the effects were different in bacteria and fungi, suggesting that bacterial and fungal community structures respond differently to these growth factors.
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Affiliation(s)
- Yan Li
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
| | - Xuemin He
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
| | - Hongfei Yuan
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
- Correspondence:
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Oyserman BO, Flores SS, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson JN, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión VJ, Ligterink W, Snoek BL, Medema MH, Raaijmakers JM. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nat Commun 2022; 13:3228. [PMID: 35710629 PMCID: PMC9203511 DOI: 10.1038/s41467-022-30849-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/19/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.
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Affiliation(s)
- Ben O Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Stalin Sarango Flores
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thom Griffioen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Elmar van der Wijk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Lotte Pronk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Wouter Lokhorst
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Azkia Nurfikari
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, Genentech, Inc. South San Francisco, South San Francisco, CA, USA
| | - Mercedeh Movassagh
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Data Sciences Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nejc Stopnisek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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Rani S, Kumar P, Dahiya P, Maheshwari R, Dang AS, Suneja P. Endophytism: A Multidimensional Approach to Plant-Prokaryotic Microbe Interaction. Front Microbiol 2022; 13:861235. [PMID: 35633681 PMCID: PMC9135327 DOI: 10.3389/fmicb.2022.861235] [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: 01/24/2022] [Accepted: 03/11/2022] [Indexed: 11/20/2022] Open
Abstract
Plant growth and development are positively regulated by the endophytic microbiome via both direct and indirect perspectives. Endophytes use phytohormone production to promote plant health along with other added benefits such as nutrient acquisition, nitrogen fixation, and survival under abiotic and biotic stress conditions. The ability of endophytes to penetrate the plant tissues, reside and interact with the host in multiple ways makes them unique. The common assumption that these endophytes interact with plants in a similar manner as the rhizospheric bacteria is a deterring factor to go deeper into their study, and more focus was on symbiotic associations and plant–pathogen reactions. The current focus has shifted on the complexity of relationships between host plants and their endophytic counterparts. It would be gripping to inspect how endophytes influence host gene expression and can be utilized to climb the ladder of “Sustainable agriculture.” Advancements in various molecular techniques have provided an impetus to elucidate the complexity of endophytic microbiome. The present review is focused on canvassing different aspects concerned with the multidimensional interaction of endophytes with plants along with their application.
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Affiliation(s)
- Simran Rani
- Plant Microbe Interaction Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Pradeep Kumar
- Plant Microbe Interaction Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Priyanka Dahiya
- Plant Microbe Interaction Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Rajat Maheshwari
- Plant Microbe Interaction Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Amita Suneja Dang
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Pooja Suneja
- Plant Microbe Interaction Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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