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Muhammad M, Wahab A, Waheed A, Mohamed HI, Hakeem KR, Li L, Li WJ. Harnessing bacterial endophytes for environmental resilience and agricultural sustainability. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122201. [PMID: 39142107 DOI: 10.1016/j.jenvman.2024.122201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 08/01/2024] [Accepted: 08/10/2024] [Indexed: 08/16/2024]
Abstract
In the current era of environmental disasters and the necessity of sustainable development, bacterial endophytes have gotten attention for their role in improving agricultural productivity and ecological sustainability. This review explores the multifaceted contributions of bacterial endophytes to plant health and ecosystem sustainability. Bacterial endophytes are invaluable sources of bioactive compounds, promising breakthroughs in medicine and biotechnology. They also serve as natural biocontrol agents, reducing the need for synthetic fertilizers and fostering environmentally friendly agricultural practices. It provides eco-friendly solutions that align with the necessity of sustainability since they can improve pest management, increase crop resilience, and facilitate agricultural production. This review also underscores bacterial endophytes' contribution to promoting sustainable and green industrial productions. It also presented how incorporating these microorganisms into diverse industrial sectors can harmonize humankind with ecological stability. The potential of bacterial endophytes has been largely untapped, presenting an opportunity for pioneering advancements in sustainable industrial applications. Their importance caught attention as they provided innovative solutions to the challenging problems of the new era. This review sheds light on the remarkable potential of bacterial endophytes in various industrial sectors. Further research is imperative to discover their multifaceted potential. It will be essential to delve deeper into their mechanisms, broaden their uses, and examine their long-term impacts.
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Affiliation(s)
- Murad Muhammad
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China.
| | - Abdul Wahab
- University of Chinese Academy of Sciences, Beijing, 100049, China; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
| | - Heba Ibrahim Mohamed
- Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo, 11341, Egypt
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, 21589, Saudi Arabia; Department of Public Health, Daffodil International University, Dhaka, 1341, Bangladesh; University Centre for Research & Development, Chandigarh University, Mohali, Punjab, 140413, India
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Elhady A, Alghanmi L, Abd-Elgawad MMM, Heuer H, Saad MM, Hirt H. Plant-parasitic nematode research in the arid desert landscape: a systematic review of challenges and bridging interventions. FRONTIERS IN PLANT SCIENCE 2024; 15:1432311. [PMID: 39104847 PMCID: PMC11298362 DOI: 10.3389/fpls.2024.1432311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024]
Abstract
Plant-parasitic nematode research in the Middle East and North Africa (MENA) region faces significant challenges rooted in a need for proper assembly, diversity, and a unified and purpose-driven framework. This led to exacerbating their detrimental effects on crop production. This systematic review addresses the current situation and challenges that require targeted interventions to sustainably manage plant-parasitic nematodes and reduce their detrimental impact on agriculture production in the MENA region. We analyzed the nematode-related research conducted within the region over the past three decades to assess available resources and promote diverse research approaches beyond basic morphology-focused surveys. We show that crops are attacked by a diverse spectrum of plant-parasitic nematodes that exceed the global economic threshold limits. In particular, Meloidogyne species exceed the threshold limit by 8 - 14-fold, with a 100% frequency of occurrence in the collected soil samples, posing a catastrophic threat to crop production and the economy. We highlight detrimental agriculture practices in the MENA region, such as transferring soil from established fields to barren land, which enhances the dissemination of plant-parasitic nematodes, disrupting soil ecology and causing significant agricultural challenges in newly cultivated areas. Looking into the behavior of farmers, raising awareness must be accompanied by available solutions, as more practical alternatives are needed to gain the confidence of the farmers. We propose integrating microbial-based products and soil development practices in hygienic farming as resilient and sustainable solutions for nematode management. Increased emphasis is required to diversify the nematode-related research areas to bridge the gaps and facilitate the transition from fundamental knowledge to practical solutions. A cohesive network of nematologists and collaboration with national and international entities is crucial for exchanging knowledge related to legislation against invasive species.
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Affiliation(s)
- Ahmed Elhady
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Linah Alghanmi
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Maged M. Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Alghamdi AK, Parween S, Hirt H, Saad MM. Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina. BMC Genomics 2024; 25:672. [PMID: 38969999 PMCID: PMC11225332 DOI: 10.1186/s12864-024-10555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium's adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.
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Affiliation(s)
- Amal Khalaf Alghamdi
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabiha Parween
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Max Perutz Laboratories, University of Vienna, Vienna, Austria.
| | - Maged M Saad
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Li C, Chen X, Jia Z, Zhai L, Zhang B, Grüters U, Ma S, Qian J, Liu X, Zhang J, Müller C. Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities. Nat Ecol Evol 2024; 8:1270-1284. [PMID: 38849504 DOI: 10.1038/s41559-024-02437-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024]
Abstract
Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Xinli Chen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, USA
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Uwe Grüters
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Jing Qian
- Yangzhou China Grand Canal Museum, Yangzhou, China
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Liebig Centre for Agroecology and Climate Impact Research, Justus-Liebig University, Giessen, Germany
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Bao X, Chong P, He C, Wang X, Zhang F. Mechanism on the promotion of host growth and enhancement of salt tolerance by Bacillaceae isolated from the rhizosphere of Reaumuria soongorica. Front Microbiol 2024; 15:1408622. [PMID: 38881656 PMCID: PMC11176432 DOI: 10.3389/fmicb.2024.1408622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Salt stress is a major abiotic stress that affects the growth of Reaumuria soongorica and many psammophytes in the desert areas of Northwest China. However, various Plant Growth-Promoting Rhizobacteria (PGPR) have been known to play an important role in promoting plant growth and alleviating the damaging effects of salt stress. In this study, three PGPR strains belonging to Bacillaceae were isolated from the rhizosphere of Reaumuria soongorica by morphological and molecular identification. All isolated strains exhibited capabilities of producing IAA, solubilizing phosphate, and fixing nitrogen, and were able to tolerate high levels of NaCl stress, up to 8-12%. The results of the pot-based experiment showed that salt (400 mM NaCl) stress inhibited Reaumuria soongorica seedlings' growth performance as well as biomass production, but after inoculation with strains P2, S37, and S40, the plant's height significantly increased by 26.87, 17.59, and 13.36%, respectively (p < 0.05), and both aboveground and root fresh weight significantly increased by more than 2 times compared to NaCl treatment. Additionally, inoculation with P2, S37, and S40 strains increased the content of photosynthetic pigments, proline, and soluble protein in Reaumuria soongorica seedlings under NaCl stress, while reducing the content of malondialdehyde and soluble sugars. Metabolomic analysis showed that strain S40 induces Reaumuria soongorica seedling leaves metabolome reprogramming to regulate cell metabolism, including plant hormone signal transduction and phenylalanine, tyrosine, and tryptophan biosynthesis pathways. Under NaCl stress, inoculation with strain S40 upregulated differential metabolites in plant hormone signal transduction pathways including plant hormones such as auxins (IAA), cytokinins, and jasmonic acid. The results indicate that inoculation with Bacillaceae can promote the growth of Reaumuria soongorica seedlings under NaCl stress and enhance salt tolerance by increasing the content of photosynthetic pigments, accumulating osmoregulatory substances, regulating plant hormone levels This study contributes to the enrichment of PGPR strains capable of promoting the growth of desert plants and has significant implications for the psammophytes growth and development in desert regions, as well as the effective utilization and transformation of saline-alkali lands.
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Affiliation(s)
- Xinguang Bao
- College of Forest of Gansu Agriculture University, Lanzhou, China
| | - Peifang Chong
- College of Forest of Gansu Agriculture University, Lanzhou, China
| | - Cai He
- Wuwei Academy of Forestry, Wuwei, China
| | - Xueying Wang
- College of Forest of Gansu Agriculture University, Lanzhou, China
| | - Feng Zhang
- College of Forest of Gansu Agriculture University, Lanzhou, China
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6
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Li X, Zheng X, Yadav N, Saha S, Salama ES, Li X, Wang L, Jeon BH. Rational management of the plant microbiome for the Second Green Revolution. PLANT COMMUNICATIONS 2024; 5:100812. [PMID: 38213028 PMCID: PMC11009158 DOI: 10.1016/j.xplc.2024.100812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/06/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.
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Affiliation(s)
- Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Nikita Yadav
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Hermantown, MN 55811, USA; Department of Biotechnology, Brainware University, Barasat, Kolkata 700125, West Bengal, India
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea.
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Čaušević S, Dubey M, Morales M, Salazar G, Sentchilo V, Carraro N, Ruscheweyh HJ, Sunagawa S, van der Meer JR. Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions. Nat Commun 2024; 15:2557. [PMID: 38519488 PMCID: PMC10959995 DOI: 10.1038/s41467-024-46933-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.
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Affiliation(s)
- Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Guillem Salazar
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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8
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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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9
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Salse J, Barnard RL, Veneault-Fourrey C, Rouached H. Strategies for breeding crops for future environments. TRENDS IN PLANT SCIENCE 2024; 29:303-318. [PMID: 37833181 DOI: 10.1016/j.tplants.2023.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/27/2023] [Accepted: 08/08/2023] [Indexed: 10/15/2023]
Abstract
The green revolution successfully increased agricultural output in the early 1960s by relying primarily on three pillars: plant breeding, irrigation, and chemical fertilization. Today, the need to reduce the use of chemical fertilizers, water scarcity, and future environmental changes, together with a growing population, requires innovative strategies to adapt to a new context and prevent food shortages. Therefore, scientists from around the world are directing their efforts to breed crops for future environments to sustainably produce more nutritious food. Herein, we propose scientific avenues to be reinforced in selecting varieties, including crop wild relatives, either for monoculture or mixed cropping systems, taking advantage of plant-microbial interactions, while considering the diversity of organisms associated with crops and unlocking combinatorial nutritional stresses.
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Affiliation(s)
- Jérôme Salse
- UCA-INRAE UMR 1095 Genetics, Diversity, and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Romain L Barnard
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, Unité Mixte de Recherche Interactions Arbres-Microorganismes, F-54000 Nancy, France
| | - Hatem Rouached
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA; The Plant Resilience Institute, Michigan State University, East Lansing, MI 48823, USA.
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10
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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11
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Zhao J, Yu X, Zhang C, Hou L, Wu N, Zhang W, Wang Y, Yao B, Delaplace P, Tian J. Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168847. [PMID: 38036127 DOI: 10.1016/j.scitotenv.2023.168847] [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: 08/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.
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Affiliation(s)
- Jintong Zhao
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoxia Yu
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, Jiangxi 330000, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan, Academy of Agricultural Sciences, Sanya 572000, China
| | - Ligang Hou
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pierre Delaplace
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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12
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Alahmad A, Harir M, Fochesato S, Tulumello J, Walker A, Barakat M, Ndour PMS, Schmitt-Kopplin P, Cournac L, Laplaze L, Heulin T, Achouak W. Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet. MICROBIOME 2024; 12:1. [PMID: 38167150 PMCID: PMC10763007 DOI: 10.1186/s40168-023-01727-3] [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: 08/09/2023] [Accepted: 11/19/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities. RESULTS Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The ß-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines. CONCLUSIONS This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.
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Affiliation(s)
- Abdelrahman Alahmad
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
- UniLaSalle, SFR NORVEGE FED 4277, AGHYLE Rouen UP 2018.C101, 3 Rue du Tronquet, 76130, Mont-Saint- Aignan, France
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Sylvain Fochesato
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Mohamed Barakat
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Papa Mamadou Sitor Ndour
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- UCEIV-ULCO, 50 Rue Ferdinand Buisson, 62228, Calais, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Laurent Cournac
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Laurent Laplaze
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LMI LAPSE, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Thierry Heulin
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
| | - Wafa Achouak
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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Feng L, Li Q, Zhou D, Jia M, Liu Z, Hou Z, Ren Q, Ji S, Sang S, Lu S, Yu J. B. subtilis CNBG-PGPR-1 induces methionine to regulate ethylene pathway and ROS scavenging for improving salt tolerance of tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:193-211. [PMID: 37812678 DOI: 10.1111/tpj.16489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/10/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
Soil salinity severely threatens plant growth and crop yields. The utilization of PGPR is an effective strategy for enhancing plant salt tolerance, but the mechanisms involved in this process have rarely been reported. In this study, we investigated the effects of Bacillus subtilis CNBG-PGPR-1 on improving plant salt tolerance and elucidated the molecular pathways involved. The results showed that CNBG-PGPR-1 significantly improved the cellular homeostasis and photosynthetic efficiency of leaves and reduced ion toxicity and osmotic stress caused by salt in tomato. Transcriptome analysis uncovered that CNBG-PGPR-1 enhanced plant salt tolerance through the activation of complex molecular pathways, with plant hormone signal transduction playing an important role. Comparative analysis and pharmacological experiments confirmed that the ethylene pathway was closely related to the beneficial effect of CNBG-PGPR-1 on improving plant salt tolerance. Furthermore, we found that methionine, a precursor of ethylene synthesis, significantly accumulated in response to CNBG-PGPR-1 in tomato. Exogenous L-methionine largely mimicked the beneficial effects of CNBG-PGPR-1 and activated the expression of ethylene pathway-related genes, indicating CNBG-PGPR-1 induces methionine accumulation to regulate the ethylene pathway in tomato. Finally, CNBG-PGPR-1 reduced salt-induced ROS by activating ROS scavenger-encoding genes, mainly involved in GSH metabolism and POD-related genes, which were also closely linked to methionine metabolism. Overall, our studies demonstrate that CNBG-PGPR-1-induced methionine is a key regulator in enhancing plant salt tolerance through the ethylene pathway and ROS scavenging, providing a novel understanding of the mechanism by which beneficial microbes improve plant salt tolerance.
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Affiliation(s)
- Liuchun Feng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Qi Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Dongqin Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Mingyun Jia
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Zhuangzhuang Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Zhaoqi Hou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Quanjin Ren
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Shengdong Ji
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shifei Sang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shipeng Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Jinping Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
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15
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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16
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Modolon F, Schultz J, Duarte G, Vilela CLS, Thomas T, Peixoto RS. In situ devices can culture the microbial dark matter of corals. iScience 2023; 26:108374. [PMID: 38162026 PMCID: PMC10755713 DOI: 10.1016/j.isci.2023.108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/16/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024] Open
Abstract
Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.
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Affiliation(s)
- Flúvio Modolon
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Júnia Schultz
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Gustavo Duarte
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raquel Silva Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
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17
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Yang H, Zhang X, Qiu X, Chen J, Wang Y, Zhang G, Jia S, Shen X, Ye W, Yan Z. Fusarium Wilt Invasion Results in a Strong Impact on Strawberry Microbiomes. PLANTS (BASEL, SWITZERLAND) 2023; 12:4153. [PMID: 38140478 PMCID: PMC10747085 DOI: 10.3390/plants12244153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Plant-endophytic microbes affect plant growth, development, nutrition, and resistance to pathogens. However, how endophytic microbial communities change in different strawberry plant compartments after Fusarium pathogen infection has remained elusive. In this study, 16S and internal transcribed spacer rRNA amplicon sequencing were used to systematically investigate changes in the bacterial and fungal diversity and composition in the endophytic compartments (roots, stems, and leaves) of healthy strawberries and strawberries with Fusarium wilt, respectively. The analysis of the diversity, structure, and composition of the bacterial and fungal communities revealed a strong effect of pathogen invasion on the endophytic communities. The bacterial and fungal community diversity was lower in the Fusarium-infected endophytic compartments than in the healthy samples. The relative abundance of certain bacterial and fungal genera also changed after Fusarium wilt infection. The relative abundance of the beneficial bacterial genera Bacillus, Bradyrhizobium, Methylophilus, Sphingobium, Lactobacillus, and Streptomyces, as well as fungal genera Acremonium, Penicillium, Talaromyces, and Trichoderma, were higher in the healthy samples than in the Fusarium wilt samples. The relative abundance of Fusarium in the infected samples was significantly higher than that in the healthy samples, consistent with the field observations and culture isolation results for strawberry wilt. Our findings provide a theoretical basis for the isolation, identification, and control of strawberry wilt disease.
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Affiliation(s)
- Hongjun Yang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Xu Zhang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Xiaohong Qiu
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
| | - Jiajia Chen
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China;
| | - Yuanhua Wang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Geng Zhang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Sizhen Jia
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
| | - Xiangqi Shen
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
| | - Wenwu Ye
- Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhiming Yan
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China; (H.Y.); (X.Q.); (Y.W.); (G.Z.); (S.J.); (X.S.)
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
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18
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Du C, Xu R, Zhao X, Liu Y, Zhou X, Zhang W, Zhou X, Hu N, Zhang Y, Sun Z, Wang Z. Association between host nitrogen absorption and root-associated microbial community in field-grown wheat. Appl Microbiol Biotechnol 2023; 107:7347-7364. [PMID: 37747613 DOI: 10.1007/s00253-023-12787-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/08/2023] [Accepted: 09/02/2023] [Indexed: 09/26/2023]
Abstract
Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.
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Affiliation(s)
- Chenghang Du
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Runlai Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xuan Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ying Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaohan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanqing Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaonan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Naiyue Hu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yinghua Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhencai Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhimin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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19
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Sarker PK, Paul AS, Karmoker D. Mitigating climate change and pandemic impacts on global food security: dual sustainable agriculture approach (2S approach). PLANTA 2023; 258:104. [PMID: 37878120 DOI: 10.1007/s00425-023-04257-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/01/2023] [Indexed: 10/26/2023]
Abstract
MAIN CONCLUSION Simultaneous application of two sustainability approaches such as the application of biofertilizers to GM plants and microbe bioengineering to enhance physiological response and beneficial interaction with GM plants may have a significant impact on strengthening global food security amid climate change and the pandemic. The second sustainable development goal (SDG 02, Zero Hunger) aims global agricultural sustainability and food security challenges. The agriculture sector has been an integral part of developing countries for millions of farmers and their families. Their contribution provides stability of raw matter related to food availability. But climate change, higher population growth and worldwide pandemics are the main obstacles to food quality, higher crop productivity and global food security. Scientists are concerned with the manifestation of agriculture sustainability in the modern crop management approach to resolving the issues. It is the only way to higher yield productivity by protecting the environment, conserving natural resources, and slowing climate change. Several strategies can be an option to implement, yet the proposed two sustainability approach or 2S approach will be the significant way toward the goal of zero hunger. The first sustainability approach is an application of genetically modified (S1: GMO) Plants and the other is an application of beneficiary plant growth-promoting microbes (S2: Biofertilizers) to the plants for both higher crops and maintenance of the environment. This study summarizes the essential points of S1 and S2 for the widespread utilization of the 2S approach in agriculture and recommends the potential alternatives to be implemented to produce food for all. Simultaneous application of the 2S approach can defeat all threats to gain sustainability in agriculture.
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Affiliation(s)
- Protup Kumer Sarker
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, 470-1192, Japan.
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Dhaka, Bangladesh.
| | - Archi Sundar Paul
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Dhaka, Bangladesh
- Graduate School of Biomedical Sciences, Medical College of Wisconsin's, Milwaukee, WI53226, USA
| | - Dola Karmoker
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Dhaka, Bangladesh
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20
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Liu C, Jiang M, Yuan MM, Wang E, Bai Y, Crowther TW, Zhou J, Ma Z, Zhang L, Wang Y, Ding J, Liu W, Sun B, Shen R, Zhang J, Liang Y. Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils. NATURE FOOD 2023; 4:912-924. [PMID: 37783790 DOI: 10.1038/s43016-023-00848-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to crops. Here we found that a synthetic community composed of highly Al-resistant bacterial strains isolated from the rice rhizosphere increased rice yield by 26.36% in acidic fields. The synthetic community harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation. The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil. These findings highlight the potential of microbial tools for advancing sustainable agriculture in acidic soils.
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Affiliation(s)
- Chaoyang Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Meitong Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengting Maggie Yuan
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhiyuan Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Li Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jixian Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wuxing Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
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21
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Khan AL. The phytomicrobiome: solving plant stress tolerance under climate change. FRONTIERS IN PLANT SCIENCE 2023; 14:1219366. [PMID: 37746004 PMCID: PMC10513501 DOI: 10.3389/fpls.2023.1219366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.
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Affiliation(s)
- Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Houston, TX, United States
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22
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Alhammad BA, Zaheer MS, Ali HH, Hameed A, Ghanem KZ, Seleiman MF. Effect of Co-Application of Azospirillum brasilense and Rhizobium pisi on Wheat Performance and Soil Nutrient Status under Deficit and Partial Root Drying Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:3141. [PMID: 37687389 PMCID: PMC10489886 DOI: 10.3390/plants12173141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/15/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Water management techniques are improving at the farm level, but they are not enough to deal with the limited availability of water and increased crop yields. Soil microbes play a vital role in nitrogen fixation, improving soil fertility and enhancing plant growth hormones under drought conditions. Therefore, this study was conducted to investigate the impact of water management combined with Azospirillum brasilense and Rhizobium pisi on wheat crop productivity and soil properties in dry regions. Three water management techniques were compared, normal irrigation as a control (C), deficit irrigation (DI), and partial root drying irrigation (PRD), together with the interaction of plant-growth-promoting rhizobacteria (PGPR). Experiments were conducted with six treatments in total: T1 = C + No PGPR, T2 = C + PGPR, T3 = DI + No PGPR, T4 = DI + PGPR, T5 = PRD + No PGPR, and T6 = PRD + PGPR. The highest grain yield was achieved in the control irrigation treatment using seeds inoculated with rhizobacteria, followed by control treatment without any inoculation, and the lowest was recorded with deficit irrigation without rhizobacteria inoculated in the seeds. However, PRD irrigation resulted in significantly higher plant growth and grain yield than the DI treatment. PGPR inoculation combined with PRD resulted in a 22% and 20% higher number of grains per spike, a 19% and 21% higher grain yield, and a 25% and 22% higher crop growth rate compared to rhizobacteria inoculation combined with the DI system in 2021-22 and 2022-23, respectively. This increase was due to the higher production of growth hormones and higher leaf area index under water-limited conditions. A greater leaf area index leads to a higher chlorophyll content and higher food production for plant growth.
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Affiliation(s)
- Bushra Ahmed Alhammad
- Biology Department, College of Science and Humanity Studies, Prince Sattam Bin Abdulaziz University, P.O. Box 292, Riyadh 11942, Saudi Arabia;
| | - Muhammad Saqlain Zaheer
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Hafiz Haider Ali
- Department of Agriculture, Government College University, Lahore 54000, Pakistan;
| | - Akhtar Hameed
- Institute of Plant Protection, MNS University of Agriculture Multan, Multan 61000, Pakistan;
| | - Kholoud Z. Ghanem
- Department of Biological Science, College of Science and Humanities, Shaqra University, Riyadh 11961, Saudi Arabia;
| | - Mahmoud F. Seleiman
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Department of Crop Sciences, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt
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23
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Proietti S, Falconieri GS, Bertini L, Pascale A, Bizzarri E, Morales-Sanfrutos J, Sabidó E, Ruocco M, Monti MM, Russo A, Dziurka K, Ceci M, Loreto F, Caruso C. Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4225-4243. [PMID: 37094092 PMCID: PMC10400115 DOI: 10.1093/jxb/erad148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/21/2023] [Indexed: 05/03/2023]
Abstract
Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring in tomato interacting with the beneficial fungus Beauveria bassiana. The tomato leaf proteome revealed perturbed molecular pathways during the establishment of the plant-fungus relationship. In the early stages of colonization (5-7 d), proteins related to defense responses to the fungus were down-regulated and proteins related to calcium transport were up-regulated. At later time points (12-19 d after colonization), up-regulation of molecular pathways linked to protein/amino acid turnover and to biosynthesis of energy compounds suggests beneficial interaction enhancing plant growth and development. At the later stage, the profile of leaf hormones and related compounds was also investigated, highlighting up-regulation of those related to plant growth and defense. Finally, B. bassiana colonization was found to improve plant resistance to Botrytis cinerea, impacting plant oxidative damage. Overall, our findings further expand current knowledge on the possible mechanisms underlying the beneficial role of B. bassiana in tomato plants.
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Affiliation(s)
- Silvia Proietti
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Gaia Salvatore Falconieri
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Laura Bertini
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Alberto Pascale
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Elisabetta Bizzarri
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Julia Morales-Sanfrutos
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Spain
| | - Michelina Ruocco
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
| | - Maurilia M Monti
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
| | - Assunta Russo
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
| | - Kinga Dziurka
- Department of Biotechnology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marcello Ceci
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Francesco Loreto
- Department of Biology, Via Cinthia, University of Naples Federico II, 80126, Naples, Italy
| | - Carla Caruso
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
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24
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Alves MJG, Mendonça JJ, Vitalino GM, Oliveira JP, Carvalho EX, Fracetto FJC, Fracetto GGM, Lira Junior MA. Screening Digitaria eriantha cv. Suvernola Endophytic Bacteria for Maize Growth Promotion. PLANTS (BASEL, SWITZERLAND) 2023; 12:2589. [PMID: 37514205 PMCID: PMC10385894 DOI: 10.3390/plants12142589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The search for sustainable agriculture has increased interest in using endophytic bacteria to reduce fertilizer use and increase stress resilience. Stress-adapted plants are a potential source of these bacteria. Some species of these plants have not yet been evaluated for this, such as pangolão grass, from which we considered endophytic bacteria as potential plant growth promoters. Bacteria from the root, colm, leaves, and rhizospheric soil were isolated, and 132 strains were evaluated for their in vitro biological nitrogen fixation, IAA and siderophores production, and phosphate solubilization. Each mechanism was also assessed under low N availability, water stress, and low-solubility Fe and P sources in maize greenhouse experiments. All strains synthesized IAA; 63 grew on N-free media, 114 synthesized siderophores, and 46 solubilized P, while 19 presented all four mechanisms. Overall, these strains had better performance than commercial inoculant in all experiments. Still, in vitro responses were not good predictors of in vivo effects, which indicates that the former should not be used for strain selection, since this could lead to not testing strains with good plant growth promotion potential. Their heterologous growth promotion in maize reinforces the potential of stress-adapted plant species as potential sources of strains for inoculants.
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Affiliation(s)
- Michelle J G Alves
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife 52171-900, Brazil
| | - Johny Jesus Mendonça
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife 52171-900, Brazil
- Programa de Pós-Graduação em Ciência do Solo, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Gisely Moreira Vitalino
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife 52171-900, Brazil
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25
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Nadarajah K, Abdul Rahman NSN. The Microbial Connection to Sustainable Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:2307. [PMID: 37375932 DOI: 10.3390/plants12122307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.
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Affiliation(s)
- Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Nur Sabrina Natasha Abdul Rahman
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
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26
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Xu S, Cao J, Wu M, Xu Y, Wu Y, Shang K, Ma B, Zhang L, Chen D, Liu X, Yan X, Xu J. Enhancing the Thermotolerance of Isochrysis zhangjiangensis Through Co-culturing With Algoriphagus marincola. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10219-2. [PMID: 37289264 DOI: 10.1007/s10126-023-10219-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
Isochrysis zhangjiangensis is an important microalgal species used as bait in aquaculture. However, its optimal cultivation temperature is around 25 °C, limiting its use in summer when temperature is higher. To overcome this limitation, we aimed to develop a consortia of I. zhangjiangensis and bacteria that are more resistant to heat stress. Here, six thermotolerance-promoting bacterial strains were isolated from the culture of a heat-tolerant mutant strain of I. zhangjiangensis (IM), and identified as Algoriphagus marincola, Nocardioides sp., Pseudidiomarina sp., Labrenzia alba, Nitratireductor sp., and Staphylococcus haemolyticus. Further, co-culturing I. zhangjiangensis with A. marincola under high temperature conditions increased cell density, chlorophyll a, PSII maximum photochemical efficiency (Fv/Fm), and soluble protein content of microalgae. The presence of A. marincola positively influenced the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and total antioxidant capacity (T-AOC) in I. zhangjiangensis cells, while concurrently reducing the levels of reactive oxygen species (ROS). Additionally, gene expression studies confirmed that co-culturing with A. marincola upregulated the expression of antioxidant-related genes (sod and pod) and stress tolerance genes (heat shock protein genes). Our findings indicate that A. marincola effectively helps I. zhangjiangensis withstand high temperature stress, leading to improved yield of microalgae during high temperature conditions. The thermotolerance-promoting bacteria can be exploited as potential inoculants for enhancing the productivity and sustainability of bait microalgae in aquaculture.
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Affiliation(s)
- Simin Xu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Jiayi Cao
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Minnan Wu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Yijun Xu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Yuanyuan Wu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China
- Laizhou Bay Marine Technology Co., Ltd, Yantai, 261400, Shandong, China
| | - Kaixi Shang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Bin Ma
- Laizhou Bay Marine Technology Co., Ltd, Yantai, 261400, Shandong, China
| | - Lin Zhang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Deshui Chen
- Fujian Dalai Seed Science and Technology Co., Ltd, Ningde, 352101, Fujian, China
| | - Xinyu Liu
- Laizhou Bay Marine Technology Co., Ltd, Yantai, 261400, Shandong, China
| | - Xiaojun Yan
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jilin Xu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, Zhejiang, China.
- Fujian Dalai Seed Science and Technology Co., Ltd, Ningde, 352101, Fujian, China.
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Blilou I, Hirt H. Desert plants to stop desertification: To succeed, reforestation projects to reclaim once fertile lands need to consider the local abiotic, biotic, and social factors: To succeed, reforestation projects to reclaim once fertile lands need to consider the local abiotic, biotic, and social factors. EMBO Rep 2023; 24:e56687. [PMID: 36579758 PMCID: PMC9900327 DOI: 10.15252/embr.202256687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Understanding the intricate relationship between plants, desert soils, and desert-specific microbiomes would increase the success chances for reforestation projects to reclaim lands lost to desertification.
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Affiliation(s)
- Ikram Blilou
- Center for Desert AgricultureKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Heribert Hirt
- Center for Desert AgricultureKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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28
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Andrić S, Rigolet A, Argüelles Arias A, Steels S, Hoff G, Balleux G, Ongena L, Höfte M, Meyer T, Ongena M. Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor. THE ISME JOURNAL 2023; 17:263-275. [PMID: 36357782 PMCID: PMC9860033 DOI: 10.1038/s41396-022-01337-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022]
Abstract
Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.
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Affiliation(s)
- Sofija Andrić
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Augustin Rigolet
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Anthony Argüelles Arias
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Sébastien Steels
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Grégory Hoff
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.5477.10000000120346234Present Address: Ecology and Biodiversity, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Guillaume Balleux
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Loïc Ongena
- grid.4861.b0000 0001 0805 7253Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Monica Höfte
- grid.5342.00000 0001 2069 7798Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thibault Meyer
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.7849.20000 0001 2150 7757Present Address: UMR Ecologie Microbienne, F-69622, University of Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
| | - Marc Ongena
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Espinosa-Urgel M. Connecting environmental and evolutionary microbiology for the development of new agrobiotechnological tools. Environ Microbiol 2023; 25:87-90. [PMID: 36519350 PMCID: PMC10087822 DOI: 10.1111/1462-2920.16197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, Spain
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30
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Anand U, Vaishnav A, Sharma SK, Sahu J, Ahmad S, Sunita K, Suresh S, Dey A, Bontempi E, Singh AK, Proćków J, Shukla AK. Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156641. [PMID: 35700781 DOI: 10.1016/j.scitotenv.2022.156641] [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: 01/17/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Anukool Vaishnav
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh 281406, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Sushil K Sharma
- National Agriculturally Important Microbial Culture Collection (NAIMCC), ICAR-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM), Mau 275 103, Uttar Pradesh, India.
| | - Jagajjit Sahu
- GyanArras Academy, Gothapatna, Malipada, Bhubaneswar, Odisha 751029, India
| | - Sarfaraz Ahmad
- Department of Botany, Jai Prakash University, Saran, Chhapra 841301, Bihar, India
| | - Kumari Sunita
- Department of Botany, Faculty of Science, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh 273009, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal 462 003, Madhya Pradesh, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College, (A Constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur 812007, Bihar, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland.
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya (affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya) 224123, Uttar Pradesh, India.
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Mohamad OAA, Liu YH, Huang Y, Li L, Ma JB, Egamberdieva D, Gao L, Fang BZ, Hatab S, Jiang HC, Li WJ. The Metabolic Potential of Endophytic Actinobacteria Associated with Medicinal Plant Thymus roseus as a Plant-Growth Stimulator. Microorganisms 2022; 10:microorganisms10091802. [PMID: 36144404 PMCID: PMC9505248 DOI: 10.3390/microorganisms10091802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
Bio-fertilizer practice considers not only economical but also environmentally friendly, sustainable agriculture. Endophytes can play important beneficiary roles in plant development, directly, indirectly, or synergistically. In this study, the majority of our endophytic actinobacteria were able to possess direct plant growth-promoting (PGP) traits, including auxin (88%), ammonia (96%), siderophore production (94%), and phosphate solubilization (24%), along with cell-wall degrading enzymes such as protease (75%), cellulase (81%), lipase (81%), and chitinase (18%). About 45% of tested strains have an inhibitory effect on the phytopathogen Fusarium oxysporum, followed by 26% for Verticillium dahlia. Overall, our results showed that strains XIEG63 and XIEG55 were the potent strains with various PGP traits that caused a higher significant increase (p ≤ 0.05) in length and biomass in the aerial part and roots of tomato and cotton, compared to the uninoculated plants. Our data showed that the greatest inhibition percentages of two phytopathogens were achieved due to treatment with strains XIEG05, XIEG07, XIEG45, and XIEG51. The GC-MS analysis showed that most of the compounds were mainly alkanes, fatty acid esters, phenols, alkenes, and aromatic chemicals and have been reported to have antifungal activity. Our investigation emphasizes that endophytic actinobacteria associated with medicinal plants might help reduce the use of chemical fertilization and potentially lead to increased agricultural productivity and sustainability.
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Affiliation(s)
- Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Department of Biological, Marine Sciences and Environmental Agriculture, Institute for Post Graduate Environmental Studies, Arish University, Al-Arish 45511, Egypt
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish 45511, Egypt
- Correspondence: (O.A.A.M.); (L.L.); (W.-J.L.)
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Yin Huang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Correspondence: (O.A.A.M.); (L.L.); (W.-J.L.)
| | - Jin-Biao Ma
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Dilfuza Egamberdieva
- Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan
- Institute of Fundamental and Applied Research, National Research University (TIIAME), Tashkent 100000, Uzbekistan
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Shaimaa Hatab
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish 45511, Egypt
- Faculty of Organic Agriculture, Heliopolis University, Cairo 2834, Egypt
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Correspondence: (O.A.A.M.); (L.L.); (W.-J.L.)
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32
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Mawarda PC, Le Roux X, Acosta MU, van Elsas JD, Salles JF. The impact of protozoa addition on the survivability of Bacillus inoculants and soil microbiome dynamics. ISME COMMUNICATIONS 2022; 2:82. [PMID: 37938668 PMCID: PMC9723691 DOI: 10.1038/s43705-022-00166-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 10/06/2023]
Abstract
Protists' selective predation of bacterial cells is an important regulator of soil microbiomes, which might influence the success of bacterial releases in soils. For instance, the survival and activity of introduced bacteria can be affected by selective grazing on resident communities or the inoculant, but this remains poorly understood. Here, we investigated the impact of the introduction in the soil of two protozoa species, Rosculus terrestris ECOP02 and/or Cerocomonas lenta ECOP01, on the survival of the inoculants Bacillus mycoides M2E15 (BM) or B. pumilus ECOB02 (BP). We also evaluated the impact of bacterial inoculation with or without protozoan addition on the abundance and diversity of native soil bacterial and protist communities. While the addition of both protozoa decreased the survival of BM, their presence contrarily increased the BP abundance. Protists' selective predation governs the establishment of these bacterial inoculants via modifying the soil microbiome structure and the total bacterial abundance. In the BP experiment, the presence of the introduced protozoa altered the soil community structures and decreased soil bacterial abundance at the end of the experiment, favouring the invader survival. Meanwhile, the introduced protozoa did not modify the soil community structures in the BM experiment and reduced the BM + Protozoa inoculants' effect on total soil bacterial abundance. Our study reinforces the view that, provided added protozoa do not feed preferentially on bacterial inoculants, their predatory behaviour can be used to steer the soil microbiome to improve the success of bacterial inoculations by reducing resource competition with the resident soil microbial communities.
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Affiliation(s)
- Panji Cahya Mawarda
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
- Research Center for Environment and Clean Technology, National Research and Innovation Agency Republic of Indonesia (BRIN), Komplek LIPI Bandung, Jalan Sangkuriang Gedung 50, Bandung, 40135, Indonesia.
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, INRAE, CNRS, Université de Lyon, Université Lyon 1, UMR INRAE 1418, UMR CNRS 5557, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne, France
| | - Melissa Uribe Acosta
- Plant-Microbe Interactions Group, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Pollution Diagnostics and Control Group (GDCON), Biology Institute, University Research Campus (SIU), University of Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
| | - Jan Dirk van Elsas
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Joana Falcão Salles
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Shekhawat K, Almeida-Trapp M, García-Ramírez GX, Hirt H. Beat the heat: plant- and microbe-mediated strategies for crop thermotolerance. TRENDS IN PLANT SCIENCE 2022; 27:802-813. [PMID: 35331665 DOI: 10.1016/j.tplants.2022.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/30/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Heat stress (HS) affects plant growth and development, and reduces crop yield. To combat HS, plants have evolved several sophisticated strategies. The primary HS response in plants involves the activation of heat-shock transcription factors and heat-shock proteins (HSPs). Plants also deploy more advanced epigenetic mechanisms in response to recurring HS conditions. In addition, beneficial microbes can reprogram the plant epitranscriptome to induce thermotolerance, and have the potential to improve crop yield productivity by mitigating HS-induced inhibition of growth and development. We summarize the latest advances in plant epigenetic regulation and highlight microbe-mediated thermotolerance in plants.
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Affiliation(s)
- Kirti Shekhawat
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Marilia Almeida-Trapp
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Gabriel X García-Ramírez
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia; Max Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria.
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34
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Schmitz L, Yan Z, Schneijderberg M, de Roij M, Pijnenburg R, Zheng Q, Franken C, Dechesne A, Trindade LM, van Velzen R, Bisseling T, Geurts R, Cheng X. Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome. THE ISME JOURNAL 2022; 16:1907-1920. [PMID: 35444261 PMCID: PMC9296610 DOI: 10.1038/s41396-022-01238-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 02/06/2023]
Abstract
The root bacterial microbiome is important for the general health of the plant. Additionally, it can enhance tolerance to abiotic stresses, exemplified by plant species found in extreme ecological niches like deserts. These complex microbe-plant interactions can be simplified by constructing synthetic bacterial communities or SynComs from the root microbiome. Furthermore, SynComs can be applied as biocontrol agents to protect crops against abiotic stresses such as high salinity. However, there is little knowledge on the design of a SynCom that offers a consistent protection against salt stress for plants growing in a natural and, therefore, non-sterile soil which is more realistic to an agricultural setting. Here we show that a SynCom of five bacterial strains, originating from the root of the desert plant Indigofera argentea, protected tomato plants growing in a non-sterile substrate against a high salt stress. This phenotype correlated with the differential expression of salt stress related genes and ion accumulation in tomato. Quantification of the SynCom strains indicated a low penetrance into the natural soil used as the non-sterile substrate. Our results demonstrate how a desert microbiome could be engineered into a simplified SynCom that protected tomato plants growing in a natural soil against an abiotic stress.
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Affiliation(s)
- Lucas Schmitz
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Zhichun Yan
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Martinus Schneijderberg
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Martijn de Roij
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Rick Pijnenburg
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Qi Zheng
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Carolien Franken
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Annemarie Dechesne
- Laboratory of Plant Breeding, Plant Sciences Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Luisa M Trindade
- Laboratory of Plant Breeding, Plant Sciences Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robin van Velzen
- Biosystematics, Plant Sciences Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Rene Geurts
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Xu Cheng
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Plant Sciences Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Kuhl-Nagel T, Rodriguez PA, Gantner I, Chowdhury SP, Schwehn P, Rosenkranz M, Weber B, Schnitzler JP, Kublik S, Schloter M, Rothballer M, Falter-Braun P. Novel Pseudomonas sp. SCA7 Promotes Plant Growth in Two Plant Families and Induces Systemic Resistance in Arabidopsis thaliana. Front Microbiol 2022; 13:923515. [PMID: 35875540 PMCID: PMC9297469 DOI: 10.3389/fmicb.2022.923515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas sp. SCA7, characterized in this study, was isolated from roots of the bread wheat Triticum aestivum. Sequencing and annotation of the complete SCA7 genome revealed that it represents a potential new Pseudomonas sp. with a remarkable repertoire of plant beneficial functions. In vitro and in planta experiments with the reference dicot plant A. thaliana and the original monocot host T. aestivum were conducted to identify the functional properties of SCA7. The isolate was able to colonize roots, modify root architecture, and promote growth in A. thaliana. Moreover, the isolate increased plant fresh weight in T. aestivum under unchallenged conditions. Gene expression analysis of SCA7-inoculated A. thaliana indicated a role of SCA7 in nutrient uptake and priming of plants. Moreover, confrontational assays of SCA7 with fungal and bacterial plant pathogens revealed growth restriction of the pathogens by SCA7 in direct as well as indirect contact. The latter indicated involvement of microbial volatile organic compounds (mVOCs) in this interaction. Gas chromatography-mass spectrometry (GC-MS) analyses revealed 1-undecene as the major mVOC, and octanal and 1,4-undecadiene as minor abundant compounds in the emission pattern of SCA7. Additionally, SCA7 enhanced resistance of A. thaliana against infection with the plant pathogen Pseudomonas syringae pv. tomato DC3000. In line with these results, SA- and JA/ET-related gene expression in A. thaliana during infection with Pst DC3000 was upregulated upon treatment with SCA7, indicating the ability of SCA7 to induce systemic resistance. The thorough characterization of the novel Pseudomonas sp. SCA7 showed a remarkable genomic and functional potential of plant beneficial traits, rendering it a promising candidate for application as a biocontrol or a biostimulation agent.
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Affiliation(s)
- Theresa Kuhl-Nagel
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patricia Antonia Rodriguez
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Isabella Gantner
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Soumitra Paul Chowdhury
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patrick Schwehn
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Maaria Rosenkranz
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Baris Weber
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jörg-Peter Schnitzler
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Rothballer
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Pascal Falter-Braun
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
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Yadav R, Chakraborty S, Ramakrishna W. Wheat grain proteomic and protein-metabolite interactions analyses provide insights into plant growth promoting bacteria-arbuscular mycorrhizal fungi-wheat interactions. PLANT CELL REPORTS 2022; 41:1417-1437. [PMID: 35396966 DOI: 10.1007/s00299-022-02866-x] [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: 01/12/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Proteomic, protein-protein and protein-metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant's metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein-protein and protein-metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat-PGPB-AMF interactions leading to higher yield and biofortification.
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Affiliation(s)
- Radheshyam Yadav
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Sudip Chakraborty
- Department of Computational Sciences, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Wusirika Ramakrishna
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India.
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Vázquez MB, Matencio A, Bianchinotti MV, García-Carmona F, López-Nicolás JM. Enhanced production of 2-phenylethanol by salicylic acid and cyclodextrins in cell suspension cultures of the unexplored filamentous fungus Monochaetinula geoffroeana. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:1609-1618. [PMID: 34405402 DOI: 10.1002/jsfa.11497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/03/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND 2-Phenylethanol (PEA) is a higher aromatic alcohol with a rose-like odor, which is used in several industries. Although PEA can be synthesized, consumers are increasingly concerned about the toxicity of chemically synthesized products, and prefer natural aroma compound. PEA occurs naturally in the environment but concentrations are too low to justify extraction. RESULTS The present study offers a novel biological source of PEA: the filamentous fungi Monochaetinula geoffroeana. We report the highest recorded yield of PEA of fungal origin to date: 6.52 g L-1 . The volatility and low water solubility of PEA can affect its use in many industries, for which reason complexation studies of PEA and cyclodextrins were carried out using the phase solubility technique. PEA formed 1:1 stoichiometric inclusion complexes with natural and modified CDs, the highest encapsulation constant being obtained with MβCD (K1:1 = 299.88 L mol-1 ). The complexation process significantly increased the water solubility of PEA. A computational study showed a high degree of correlation between computed scores and experimental values. Furthermore, this study reports the role of salicylic acid as an effective elicitor for improved PEA production by the studied fungi. Supplementation with 10 μmol L-1 salicylic acid increased PEA production from 6.52 to 10.54 g L-1 . CONCLUSION The best treatment to enhance PEA production by M. geoffroeana under laboratory conditions was to use salicylic acid 10 μmol L-1 . Due to the commercial importance of PEA, further investigation is needed to improve PEA production by M. geoffroeana and to optimize culture conditions in order to standardize yields. © 2021 Society of Chemical Industry.
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Affiliation(s)
- María Belén Vázquez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Adrián Matencio
- Dipartimento di Chimica, Università degli studi di Torino, Turin, Italy
| | | | - Francisco García-Carmona
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Murcia, Spain
| | - José Manuel López-Nicolás
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Murcia, Spain
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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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Analysis of seed-associated bacteria and fungi on staple crops using the cultivation and metagenomic approaches. Folia Microbiol (Praha) 2022; 67:351-361. [PMID: 35220558 PMCID: PMC9072454 DOI: 10.1007/s12223-022-00958-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 11/04/2022]
Abstract
AbstractOne of the key factors affecting seed quality is microbial communities residing on and in the seeds. In this study, microbial populations of seeds of conventionally and organically produced wheat, barley, and maize were analyzed using two different approaches: the cultivation method and metagenomics. For cultivation, three basic media were used: DG18 (for fungi), and nutrient agar or tryptic soy agar supplemented with cycloheximide or nystatin (for bacteria). Metagenomic sequencing was performed using the Illumina MiSeq platform. A total of 452 bacterial isolates comprising 36 genera and 5 phyla and 90 fungal isolates comprising 10 genera and 3 phyla were obtained from the seed surfaces. Among bacteria, representatives from the genera Bacillus, Pantoea, Paenibacillus, and Curtobacterium predominated, and among fungi, Aspergillus predominated. A total of 142 fungal OTUs and 201 bacterial OTUs were obtained from all the samples. Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria comprised most of the bacterial OTUs, and Ascomycota comprised most of the fungal OTUs. Only 3 fungal OTUs (representatives of Curvibasidium, Venturia, and Dermateaceae) were exclusively present only within seeds and not on the seed surfaces. Barley seeds had the highest microbial load and richness, whereas corn had the lowest. Wheat and barley shared a higher number of OTUs than either of them did with corn with higher overlap between conventionally grown cereals than between organically grown cereals. Some OTUs were farming specific. This study demonstrates that the microbiome of cereal seeds is greatly dependent on the species of the host and is less affected by agricultural practices.
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Okoroafor PU, Mann L, Amin Ngu K, Zaffar N, Monei NL, Boldt C, Reitz T, Heilmeier H, Wiche O. Impact of Soil Inoculation with Bacillus amyloliquefaciens FZB42 on the Phytoaccumulation of Germanium, Rare Earth Elements, and Potentially Toxic Elements. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030341. [PMID: 35161323 PMCID: PMC8838376 DOI: 10.3390/plants11030341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 05/21/2023]
Abstract
Bioaugmentation promises benefits for agricultural production as well as for remediation and phytomining approaches. Thus, this study investigated the effect of soil inoculation with the commercially available product RhizoVital®42, which contains Bacillus amyloliquefaciens FZB42, on nutrient uptake and plant biomass production as well as on the phytoaccumulation of potentially toxic elements, germanium, and rare earth elements (REEs). Zea mays and Fagopyrum esculentum were selected as model plants, and after harvest, the element uptake was compared between plants grown on inoculated versus reference soil. The results indicate an enrichment of B. amyloliquefaciens in inoculated soils as well as no significant impact on the inherent bacterial community composition. For F. esculentum, inoculation increased the accumulation of most nutrients and As, Cu, Pb, Co, and REEs (significant for Ca, Cu, and Co with 40%, 2042%, and 383%, respectively), while it slightly decreased the uptake of Ge, Cr, and Fe. For Z. mays, soil inoculation decreased the accumulation of Cr, Pb, Co, Ge, and REEs (significant for Co with 57%) but showed an insignificant increased uptake of Cu, As, and nutrient elements. Summarily, the results suggest that bioaugmentation with B. amyloliquefaciens is safe and has the potential to enhance/reduce the phytoaccumulation of some elements and the effects of inoculation are plant specific.
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Affiliation(s)
- Precious Uchenna Okoroafor
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
- Correspondence:
| | - Lotte Mann
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Kerian Amin Ngu
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Nazia Zaffar
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Nthati Lillian Monei
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
- Mining Department, Geology Institute, Tallinn University of Technology, 19086 Tallin, Estonia
| | - Christin Boldt
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research–UFZ, Theodor–Lieser Str. 4, 06120 Halle, Germany;
| | - Hermann Heilmeier
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Oliver Wiche
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
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Shen MC, Zhang YZ, Bo GD, Yang B, Wang P, Ding ZY, Wang ZB, Yang JM, Zhang P, Yuan XL. Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco. Front Bioeng Biotechnol 2022; 9:812316. [PMID: 35087808 PMCID: PMC8787768 DOI: 10.3389/fbioe.2021.812316] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
The overuse of chemical fertilizers has resulted in the degradation of the physicochemical properties and negative changes in the microbial profiles of agricultural soil. These changes have disequilibrated the balance in agricultural ecology, which has resulted in overloaded land with low fertility and planting obstacles. To protect the agricultural soil from the effects of unsustainable fertilization strategies, experiments of the reduction of nitrogen fertilization at 10, 20, and 30% were implemented. In this study, the bacterial responses to the reduction of nitrogen fertilizer were investigated. The bacterial communities of the fertilizer-reducing treatments (D10F, D20F, and D30F) were different from those of the control group (CK). The alpha diversity was significantly increased in D20F compared to that of the CK. The analysis of beta diversity revealed variation of the bacterial communities between fertilizer-reducing treatments and CK, when the clusters of D10F, D20F, and D30F were separated. Chemical fertilizers played dominant roles in changing the bacterial community of D20F. Meanwhile, pH, soil organic matter, and six enzymes (soil sucrase, catalase, polyphenol oxidase, urease, acid phosphatase, and nitrite reductase) were responsible for the variation of the bacterial communities in fertilizer-reducing treatments. Moreover, four of the top 20 genera (unidentified JG30-KF-AS9, JG30-KF-CM45, Streptomyces, and Elsterales) were considered as key bacteria, which contributed to the variation of bacterial communities between fertilizer-reducing treatments and CK. These findings provide a theoretical basis for a fertilizer-reducing strategy in sustainable agriculture, and potentially contribute to the utilization of agricultural resources through screening plant beneficial bacteria from native low-fertility soil.
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Affiliation(s)
- Min-Chong Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yu-Zhen Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guo-Dong Bo
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bin Yang
- Shandong Qingdao Tobacco Co., Ltd., Qingdao, China
| | - Peng Wang
- Shandong Qingdao Tobacco Co., Ltd., Qingdao, China
| | | | - Zhao-Bao Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jian-Ming Yang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Peng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xiao-Long Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Karthikeyan A. Establishment of Ailanthus tryphysa (Dennst.) Alston inoculated with beneficial microbes in barren laterite rocks. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100061. [PMID: 34841351 PMCID: PMC8610305 DOI: 10.1016/j.crmicr.2021.100061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/30/2021] [Accepted: 08/17/2021] [Indexed: 10/25/2022] Open
Abstract
Developing countries including India are using laterite bricks extracted from laterite rocks for building construction. Laterite rocks are found barren usually as they are not fit for cultivation. Extraction of laterite bricks from these barren laterite rocks causing land degradation and posing environmental threats in the laterite excavated lands. Hence, planting or establishing of trees on laterite rocks can prevent land degradation and environmental problems. In this study, it was decided to establish Ailanthus tryphysa (Dennst.) Alston a multipurpose native tree species of India on laterite rocks with suitable beneficial microbes as growth promotors. The laterite soils dug out from laterite rocks were tested and found that the soils have lack of beneficial microbes and poor in major nutrients (N, P, K). Therefore the beneficial microbes, arbuscular mycorrhizal fungi and growth promoting bacteria were used for A. tryphysa as they are one of the important soil properties. The laterite soils were also used as potting media for the seedlings of A. tryphysa in nursery and thereafter the cultured beneficial microbes were inoculated in to the seedlings and maintained for three months. After three months the seedlings were planted at laterite rocks and monitored for their growth and survival. The results of the experiment showed that beneficial microbes inoculated seedlings improved the growth, biomass, tissue nutrient content and 95% of survival rate after twelve months in laterite rocks. These results confirmed that the beneficial microbes have successfully established the A. tryphysa seedlings in laterite rocks through transfer of essential nutrients.
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Reducing Drought Stress in Plants by Encapsulating Plant Growth-Promoting Bacteria with Polysaccharides. Int J Mol Sci 2021; 22:ijms222312979. [PMID: 34884785 PMCID: PMC8657635 DOI: 10.3390/ijms222312979] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 01/02/2023] Open
Abstract
Drought is a major abiotic stress imposed by climate change that affects crop production and soil microbial functions. Plants respond to water deficits at the morphological, biochemical, and physiological levels, and invoke different adaptation mechanisms to tolerate drought stress. Plant growth-promoting bacteria (PGPB) can help to alleviate drought stress in plants through various strategies, including phytohormone production, the solubilization of mineral nutrients, and the production of 1-aminocyclopropane-1-carboxylate deaminase and osmolytes. However, PGPB populations and functions are influenced by adverse soil factors, such as drought. Therefore, maintaining the viability and stability of PGPB applied to arid soils requires that the PGPB have to be protected by suitable coatings. The encapsulation of PGPB is one of the newest and most efficient techniques for protecting beneficial bacteria against unfavorable soil conditions. Coatings made from polysaccharides, such as sodium alginate, chitosan, starch, cellulose, and their derivatives, can absorb and retain substantial amounts of water in the interstitial sites of their structures, thereby promoting bacterial survival and better plant growth.
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Zvinavashe AT, Mardad I, Mhada M, Kouisni L, Marelli B. Engineering the Plant Microenvironment To Facilitate Plant-Growth-Promoting Microbe Association. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13270-13285. [PMID: 33929839 DOI: 10.1021/acs.jafc.1c00138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
New technologies that enhance soil biodiversity and minimize the use of scarce resources while boosting crop production are highly sought to mitigate the increasing threats that climate change, population growth, and desertification pose on the food infrastructure. In particular, solutions based on plant-growth-promoting bacteria (PGPB) bring merits of self-replication, low environmental impact, tolerance to biotic and abiotic stressors, and reduction of inputs, such as fertilizers. However, challenges in facilitating PGPB delivery in the soil still persist and include survival to desiccation, precise delivery, programmable resuscitation, competition with the indigenous rhizosphere, and soil structure. These factors play a critical role in microbial root association and development of a beneficial plant microbiome. Engineering the seed microenvironment with protein and polysaccharides is one proposed way to deliver PGPB precisely and effectively in the seed spermosphere. In this review, we will cover new advancements in the precise and scalable delivery of microbial inoculants, also highlighting the latest development of multifunctional rhizobacteria solutions that have beneficial impact on not only legumes but also cereals. To conclude, we will discuss the role that legislators and policymakers play in promoting the adoption of new technologies that can enhance the sustainability of crop production.
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Affiliation(s)
- Augustine T Zvinavashe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ilham Mardad
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco
| | - Manal Mhada
- African integrated Plant and Soil Group (AiPlaS), AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco
| | - Lamfeddal Kouisni
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University (ASARI-UM6P), 70000 Laayoune, Morocco
| | - Benedetto Marelli
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance. Proc Natl Acad Sci U S A 2021; 118:2107417118. [PMID: 34772809 PMCID: PMC8609655 DOI: 10.1073/pnas.2107417118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/22/2022] Open
Abstract
Although plant growth–promoting bacteria (PGPB) enhance the performance of plants, only a few mechanisms have been identified so far. We show that the sulfur metabolisms in both PGPB Enterobacter sp. SA187 and Arabidopsis plants play a key role in plant salt stress tolerance. Salt stress induces a sulfur starvation response in plants that is attenuated by SA187. Arabidopsis sulfur metabolic mutants are hypersensitive to salt stress but can be rescued by SA187. Most plant sulfur metabolism occurs in chloroplasts and is linked to stress-induced accumulation of reactive oxygen species that is suppressed by SA187. This work reveals that plant salt stress tolerance requires the coordinated regulation of the sulfur metabolic pathways in both beneficial microbe and host plant. Enterobacter sp. SA187 is a root endophytic bacterium that maintains growth and yield of plants under abiotic stress conditions. In this work, we compared the metabolic wirings of Arabidopsis and SA187 in the free-living and endophytic interaction states. The interaction of SA187 with Arabidopsis induced massive changes in bacterial gene expression for chemotaxis, flagellar biosynthesis, quorum sensing, and biofilm formation. Besides modification of the bacterial carbon and energy metabolism, various nutrient and metabolite transporters and the entire sulfur pathway were up-regulated. Under salt stress, Arabidopsis resembled plants under sulfate starvation but not when colonized by SA187, which reprogramed the sulfur regulon of Arabidopsis. In accordance, salt hypersensitivity of multiple Arabidopsis sulfur metabolism mutants was partially or completely rescued by SA187 as much as by the addition of sulfate, L-cysteine, or L-methionine. Many components of the sulfur metabolism that are localized in the chloroplast were partially rescued by SA187. Finally, salt-induced accumulation of reactive oxygen species as well as the hypersensitivity of LSU mutants were suppressed by SA187. LSUs encode a central regulator linking sulfur metabolism to chloroplast superoxide dismutase activity. The coordinated regulation of the sulfur metabolic pathways in both the beneficial microorganism and the host plant is required for salt stress tolerance in Arabidopsis and might be a common mechanism utilized by different beneficial microbes to mitigate the harmful effects of different abiotic stresses on plants.
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Sun X, Pei J, Zhao L, Ahmad B, Huang LF. Fighting climate change: soil bacteria communities and topography play a role in plant colonization of desert areas. Environ Microbiol 2021; 23:6876-6894. [PMID: 34693620 DOI: 10.1111/1462-2920.15799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022]
Abstract
Global warming has exacerbated desertification in arid regions. Exploring the environmental variables and microbial communities that drive the dynamics of geographic patterns of desert crops is important for large-scale standardization of crops that can control desertification. Here, predictions based on future climate data from CMIP6 show that a steady expand in the suitable production areas for three desert plants (Cistanche deserticola, Cynomorium songaricum and Cistanche salsa) under global warming, demonstrating their high adaptability to future climate change. We examined the biogeography of three desert plant soil bacteria communities and assessed the environmental factors affecting the community assembly process. The α-diversity significantly decreased along elevated latitudes, indicating that the soil bacterial communities of the three species have latitude diversity patterns. The neutral community model evaluated 66.6% of the explained variance of the bacterial community in the soil of desert plants and Modified Stochasticity Ratio <0.5, suggesting that deterministic processes dominate the assembly of bacterial communities in three desert plants. Moreover, topography (longitude, elevation) and precipitation as well as key OTUs (OTU4911: Streptomyces eurythermus and OTU4672: Streptomyces flaveus) drive the colonization of three desert plants. This research offers a promising solution for desert management in arid areas under global warming.
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Affiliation(s)
- Xiao Sun
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, 611137, China.,Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Lei Zhao
- Central Medical District of Chinese PLA General Hospital, Beijing, 100193, China
| | - Bashir Ahmad
- Center for Biotechnology & Microbiology, University of Peshawar, Peshawar, 25000, Pakistan
| | - Lin-Fang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
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Plant Growth-Promoting Rhizobacteria as a Green Alternative for Sustainable Agriculture. SUSTAINABILITY 2021. [DOI: 10.3390/su131910986] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Environmental stress is a major challenge for sustainable food production as it reduces yield by generating reactive oxygen species (ROS) which pose a threat to cell organelles and biomolecules such as proteins, DNA, enzymes, and others, leading to apoptosis. Plant growth-promoting rhizobacteria (PGPR) offers an eco-friendly and green alternative to synthetic agrochemicals and conventional agricultural practices in accomplishing sustainable agriculture by boosting growth and stress tolerance in plants. PGPR inhabit the rhizosphere of soil and exhibit positive interaction with plant roots. These organisms render multifaceted benefits to plants by several mechanisms such as the release of phytohormones, nitrogen fixation, solubilization of mineral phosphates, siderophore production for iron sequestration, protection against various pathogens, and stress. PGPR has the potential to curb the adverse effects of various stresses such as salinity, drought, heavy metals, floods, and other stresses on plants by inducing the production of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. Genetically engineered PGPR strains play significant roles to alleviate the abiotic stress to improve crop productivity. Thus, the present review will focus on the impact of PGPR on stress resistance, plant growth promotion, and induction of antioxidant systems in plants.
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Hori Y, Fujita H, Hiruma K, Narisawa K, Toju H. Synergistic and Offset Effects of Fungal Species Combinations on Plant Performance. Front Microbiol 2021; 12:713180. [PMID: 34594312 PMCID: PMC8478078 DOI: 10.3389/fmicb.2021.713180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022] Open
Abstract
In natural and agricultural ecosystems, survival and growth of plants depend substantially on residing microbes in the endosphere and rhizosphere. Although numerous studies have reported the presence of plant-growth promoting bacteria and fungi in below-ground biomes, it remains a major challenge to understand how sets of microbial species positively or negatively affect plants' performance. By conducting a series of single- and dual-inoculation experiments of 13 plant-associated fungi targeting a Brassicaceae plant species (Brassica rapa var. perviridis), we here systematically evaluated how microbial effects on plants depend on presence/absence of co-occurring microbes. The comparison of single- and dual-inoculation experiments showed that combinations of the fungal isolates with the highest plant-growth promoting effects in single inoculations did not have highly positive impacts on plant performance traits (e.g., shoot dry weight). In contrast, pairs of fungi with small/moderate contributions to plant growth in single-inoculation contexts showed the greatest effects on plants among the 78 fungal pairs examined. These results on the offset and synergistic effects of pairs of microbes suggest that inoculation experiments of single microbial species/isolates can result in the overestimation or underestimation of microbial functions in multi-species contexts. Because keeping single-microbe systems under outdoor conditions is impractical, designing sets of microbes that can maximize performance of crop plants is an important step for the use of microbial functions in sustainable agriculture.
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Affiliation(s)
- Yoshie Hori
- Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Kei Hiruma
- Graduate School of Arts and Sciences, Multi-Disciplinary Sciences Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Kyoto, Japan
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Synek L, Rawat A, L'Haridon F, Weisskopf L, Saad MM, Hirt H. Multiple strategies of plant colonization by beneficial endophytic Enterobacter sp. SA187. Environ Microbiol 2021; 23:6223-6240. [PMID: 34472197 DOI: 10.1111/1462-2920.15747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/29/2022]
Abstract
Although many endophytic plant growth-promoting rhizobacteria have been identified, relatively little is still known about the mechanisms by which they enter plants and promote plant growth. The beneficial endophyte Enterobacter sp. SA187 was shown to maintain the productivity of crops in extreme agricultural conditions. Here we present that roots of its natural host (Indigofera argentea), alfalfa, tomato, wheat, barley and Arabidopsis are all efficiently colonized by SA187. Detailed analysis of the colonization process in Arabidopsis showed that colonization already starts during seed germination, where seed-coat mucilage supports SA187 proliferation. The meristematic zone of growing roots attracts SA187, allowing epiphytic colonization in the elongation zone. Unlike primary roots, lateral roots are significantly less epiphytically colonized by SA187. Root endophytic colonization was found to occur by passive entry of SA187 at lateral-root bases. However, SA187 also actively penetrates the root epidermis by enzymatic disruption of plant cell wall material. In contrast to roots, endophytic colonization of shoots occurs via stomata, whereby SA187 can actively re-open stomata similarly to pathogenic bacteria. In summary, several entry strategies were identified that allow SA187 to establish itself as a beneficial endophyte in several plant species, supporting its use as a plant growth-promoting bacterium in agriculture systems.
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Affiliation(s)
- Lukas Synek
- Darwin 21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Institute of Experimental Botany, Czech Academy of Sciences, Rozvojova 263, Prague, 165 02, Czech Republic
| | - Anamika Rawat
- Darwin 21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Floriane L'Haridon
- Department of Biology, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Maged M Saad
- Darwin 21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Heribert Hirt
- Darwin 21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, Vienna, 1030, Austria
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Meisner A, Wepner B, Kostic T, van Overbeek LS, Bunthof CJ, de Souza RSC, Olivares M, Sanz Y, Lange L, Fischer D, Sessitsch A, Smidt H. Calling for a systems approach in microbiome research and innovation. Curr Opin Biotechnol 2021; 73:171-178. [PMID: 34479027 DOI: 10.1016/j.copbio.2021.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 12/23/2022]
Abstract
Microbiomes are all around us in natural and cultivated ecosystems, for example, soils, plants, animals and our own body. Microbiomes are essential players of biotechnological applications, and their functions drive human, animal, plant and environmental health. The rapidly developing microbiome research landscape was studied by a global mapping excercise and bibliometric analysis. Although microbiome research is performed in many different science fields, using similar concepts within and across fields, microbiomes are mostly investigated one ecosystem at-a-time. In order to fully understand microbiome impacts and leverage microbial functions, research needs to adopt a systems approach connecting microbiomes and research initiatives in divergent fields to create understanding on how microbiomes can be modulated for desirable functions as a basis of sustainable, circular bioeconomy.
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Affiliation(s)
- Annelein Meisner
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Beatrix Wepner
- AIT Austrian Institute of Technology, Center for Innovation Systems & Policy, Giefinggasse 4, Vienna, 1210, Austria
| | - Tanja Kostic
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Leo S van Overbeek
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Christine J Bunthof
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Lene Lange
- BioEconomy, Research & Advisory, Karensgade 5, Valby, 2500, Denmark
| | - Doreen Fischer
- Helmholtz Zentrum München, National Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstaedter Landstr. 1, Neuherberg, Munich, D-85764, Germany
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.
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