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Baev V, Gecheva G, Apostolova E, Gozmanova M, Yahubyan G. Exploring the Metatranscriptome of Bacterial Communities of Two Moss Species Thriving in Different Environments-Terrestrial and Aquatic. PLANTS (BASEL, SWITZERLAND) 2024; 13:1210. [PMID: 38732425 PMCID: PMC11085137 DOI: 10.3390/plants13091210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Mosses host diverse bacterial communities essential for their fitness, nutrient acquisition, stress tolerance, and pathogen defense. Understanding the microbiome's taxonomic composition is the first step, but unraveling their functional capabilities is crucial for grasping their ecological significance. Metagenomics characterizes microbial communities by composition, while metatranscriptomics explores gene expression, providing insights into microbiome functionality beyond the structure. Here, we present for the first time a metatranscriptomic study of two moss species, Hypnum cupressiforme (Hedw.) and Platyhypnidium riparioides (Hedw.) Dixon., renowned as key biomonitors of atmospheric and water pollution. Our investigation extends beyond taxonomic profiling and offers a profound exploration of moss bacterial communities. Pseudomonadota and Actinobacteria are the dominant bacterial phyla in both moss species, but their proportions differ. In H. cupressiforme, Actinobacteria make up 62.45% and Pseudomonadota 32.48%, while in P. riparioides, Actinobacteria account for only 25.67% and Pseudomonadota 69.08%. This phylum-level contrast is reflected in genus-level differences. Our study also shows the expression of most genes related to nitrogen cycling across both microbiomes. Additionally, functional annotation highlights disparities in pathway prevalence, including carbon dioxide fixation, photosynthesis, and fatty acid biosynthesis, among others. These findings hint at potential metabolic distinctions between microbial communities associated with different moss species, influenced by their specific genotypes and habitats. The integration of metatranscriptomic data holds promise for enhancing our understanding of bryophyte-microbe partnerships, opening avenues for novel applications in conservation, bioremediation, and sustainable agriculture.
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Affiliation(s)
- Vesselin Baev
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Gana Gecheva
- Department of Ecology and Environmental Conservation, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria;
| | - Elena Apostolova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Mariyana Gozmanova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Galina Yahubyan
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
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Ben Zineb A, Lamine M, Khallef A, Hamdi H, Ahmed T, Al-Jabri H, Alsafran M, Mliki A, Sayadi S, Gargouri M. Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects. Front Microbiol 2024; 15:1362722. [PMID: 38646634 PMCID: PMC11027745 DOI: 10.3389/fmicb.2024.1362722] [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: 12/28/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.
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Affiliation(s)
- Ameni Ben Zineb
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mariem Lamine
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Ahlem Khallef
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Helmi Hamdi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Hareb Al-Jabri
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mohammed Alsafran
- Agricultural Research Station, Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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3
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Wang YW, Bai DS, Zhang Y, Luo XG. The role of afforestation with diverse woody species in enhancing and restructuring the soil microenvironment in polymetallic coal gangue dumps. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:29916-29929. [PMID: 38594563 DOI: 10.1007/s11356-024-33164-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
To elucidate the effects of long-term (20 years) afforestation with different woody plant species on the soil microenvironment in coal gangue polymetallic contaminated areas. This study analyzed the soil physicochemical properties, soil enzyme activities, soil ionophore, bacterial community structure, soil metabolite, and their interaction relationships at different vertical depths. Urease, sucrase, and acid phosphatase activities in the shallow soil layers increased by 4.70-7.45, 3.83-7.64, and 3.27-4.85 times, respectively, after the restoration by the four arboreal plant species compared to the plant-free control soil. Additionally, it reduced the content of available elements in the soil and alleviated the toxicity stress for Cd, Ni, Co, Cr, As, Fe, Cu, U, and Pb. After the long-term restoration of arboreal plants, the richness and Shannon indices of soil bacteria significantly increased by 4.77-23.81% and 2.93-7.93%, respectively, broadening the bacterial ecological niche. The bacterial community structure shaped by different arboreal plants exhibited high similarity, but the community similarity decreased with increasing vertical depth. Soils Zn, U, Sr, S, P, Mg, K, Fe, Cu, Ca, Ba, and pH were identified as important influencing factors for the community structure of Sphingomonas, Pseudarthrobacter, Nocardioides, and Thiobacillus. The metabolites such as sucrose, raffinose, L-valine, D-fructose 2, 6-bisphosphate, and oxoglutaric acid were found to have the greatest effect on the bacterial community in the rhizosphere soils for arboreal plants. The results of the study demonstrated that long-term planting for woody plants in gangue dumps could regulate microbial abundance and symbiotic patterns through the accumulation of rhizosphere metabolites in the soil, increase soil enzyme activity, reduce heavy metal levels, and improve the soil environment in coal gangue dumps.
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Affiliation(s)
- Yi-Wang Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
- Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, 621010, China
| | | | - Yu Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
- Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, 621010, China.
| | - Xue-Gang Luo
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
- Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, 621010, China
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4
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Edwards JD, Krichels AH, Seyfried GS, Dalling J, Kent AD, Yang WH. Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests. MYCORRHIZA 2024; 34:95-105. [PMID: 38183463 PMCID: PMC10998807 DOI: 10.1007/s00572-023-01134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associated Oreomunnea mexicana (Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of the ITS2 (fungi) and 16S rRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.
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Affiliation(s)
- Joseph D Edwards
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.
| | - Alexander H Krichels
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM, 87102, USA
| | - Georgia S Seyfried
- Department of Forest Ecology and Resource Management, Oregon State University, Corvallis, OR, 97331, USA
| | - James Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Angela D Kent
- Department of Natural Resources and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wendy H Yang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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5
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Afridi MS, Kumar A, Javed MA, Dubey A, de Medeiros FHV, Santoyo G. Harnessing root exudates for plant microbiome engineering and stress resistance in plants. Microbiol Res 2024; 279:127564. [PMID: 38071833 DOI: 10.1016/j.micres.2023.127564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
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6
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Ali S, Wright AH, Tanney JB, Renaud JB, Sumarah MW. Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines. J Fungi (Basel) 2024; 10:105. [PMID: 38392777 PMCID: PMC10890244 DOI: 10.3390/jof10020105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.
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Affiliation(s)
- Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main St., Kentville, NS B4N 1J5, Canada
| | - A Harrison Wright
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main St., Kentville, NS B4N 1J5, Canada
| | - Joey B Tanney
- Natural Resources Canada, Pacific Forestry Centre, 506 Burnside Road West, Victoria, BC V8Z 1M5, Canada
| | - Justin B Renaud
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford St., London, ON N5V 4T3, Canada
| | - Mark W Sumarah
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford St., London, ON N5V 4T3, Canada
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Tamang A, Swarnkar M, Kumar P, Kumar D, Pandey SS, Hallan V. Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb. Microbiol Spectr 2023; 11:e0227923. [PMID: 37811959 PMCID: PMC10715050 DOI: 10.1128/spectrum.02279-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.
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Affiliation(s)
- Anish Tamang
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Mohit Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Pawan Kumar
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dinesh Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Shiv Shanker Pandey
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
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8
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Bruto M, Oger PM, Got P, Bernard C, Melayah D, Cloarec LA, Duval C, Escalas A, Duperron S, Guigard L, Leboulanger C, Ader M, Sarazin G, Jézéquel D, Agogué H, Troussellier M, Hugoni M. Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome. Mol Ecol 2023; 32:6824-6838. [PMID: 37901963 DOI: 10.1111/mec.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023]
Abstract
Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co-dominate: a cyanobacterium, Arthrospira fusiformis, and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell-sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non-negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free-living microbiome (i.e. present in the 3-0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free-living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.
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Affiliation(s)
- Maxime Bruto
- VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | - Philippe M Oger
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Patrice Got
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Delphine Melayah
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Lilian A Cloarec
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Charlotte Duval
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Arthur Escalas
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Ludivine Guigard
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | | | - Magali Ader
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon, France
| | - Hélène Agogué
- LIENSs, UMR7266, La Rochelle Université - CNRS, La Rochelle, France
| | | | - Mylène Hugoni
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
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9
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Li Y, Feng F, Mu Q, Li M, Ma L, Wan Q, Jousset A, Liu C, Yu X. Foliar Spraying of Chlorpyrifos Triggers Plant Production of Linolenic Acid Recruiting Rhizosphere Bacterial Sphingomonas sp. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17312-17323. [PMID: 37907425 DOI: 10.1021/acs.est.3c04593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Plants have developed an adaptive strategy for coping with biotic or abiotic stress by recruiting specific microorganisms from the soil pool. Recent studies have shown that the foliar spraying of pesticides causes oxidative stress in plants and leads to changes in the rhizosphere microbiota, but the mechanisms by which these microbiota change and rebuild remain unclear. Herein, we provide for the first-time concrete evidence that rice plants respond to the stress of application of the insecticide chlorpyrifos (CP) by enhancing the release of amino acids, lipids, and nucleotides in root exudates, leading to a shift in rhizosphere bacterial community composition and a strong enrichment of the genus Sphingomonas sp. In order to investigate the underlying mechanisms, we isolated a Sphingomonas representative isolate and demonstrated that it is both attracted by and able to consume linolenic acid, one of the root exudates overproduced after pesticide application. We further show that this strain selectively colonizes roots of treated plants and alleviates pesticide stress by degrading CP and releasing plant-beneficial metabolites. These results indicate a feedback loop between plants and their associated microbiota allowing to respond to pesticide-induced stress.
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Affiliation(s)
- Yong Li
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Fayun Feng
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Qi'er Mu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Mei Li
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Liya Ma
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Qun Wan
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Alexandre Jousset
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023 Jiangsu, China
| | - Xiangyang Yu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng 224002, China
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10
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Aydinoglu F, Kahriman TY, Balci H. Seed bio-priming enhanced salt stress tolerance of maize ( Zea mays L.) seedlings by regulating the antioxidant system and miRNA expression. 3 Biotech 2023; 13:378. [PMID: 37900268 PMCID: PMC10600073 DOI: 10.1007/s13205-023-03802-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023] Open
Abstract
Maize (Zea mays) is moderately sensitive to salt stress. Therefore, increasing salinity in soil causes the arrestment of physiological processes and retention of growth and development, consequently leading to yield loss. Although many strategies have been launched to improve salt stress tolerance, plant growth-promoting rhizobacteria (PGPR) are considered the most promising approach due to being more environmentally friendly and agronomically sustainable than chemicals. Therefore, this study aims to investigate the potential of Bacillus spp. and the role of microRNA-mediated genetic regulation in maize subjected to seed bio-priming application to mitigate salt stress effects. To this end, maize seeds were bio-primed with the vegetative form of B. pumilus, B. licheniformis, and B. coagulans both individually or combined, subsequently treated to NaCl, and the seedlings were screened morphologically, physiologically, and transcriptionally. The study revealed that seed bio-priming with B. licheniformis reduced the stress effects of maize seedlings by increasing catalase (CAT) and ascorbate peroxidase (APX) activities by 2.5- and 3-fold, respectively, tolerating the decrease in chlorophyll content (CC), upregulating miR160d expression which led to a 36% increase in root fresh weight (RFW) and a 39% increase in shoot fresh weight (SFW). In conclusion, Bacillus spp. successfully alleviated salt stress effects on maize by modulating antioxidant enzymes and miRNA expression.
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Affiliation(s)
- Fatma Aydinoglu
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
| | - Taha Yunus Kahriman
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
| | - Huseyin Balci
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
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11
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Benmrid B, Ghoulam C, Zeroual Y, Kouisni L, Bargaz A. Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems. Commun Biol 2023; 6:1016. [PMID: 37803170 PMCID: PMC10558546 DOI: 10.1038/s42003-023-05399-5] [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: 05/12/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.
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Affiliation(s)
- Bouchra Benmrid
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| | - Cherki Ghoulam
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco
- Agrobiotechnology & Bioengineering Center, Research Unit CNRST labeled, Cadi Ayyad University, Faculty of Sciences and Techniques, 40000, Marrakech, Morocco
| | - Youssef Zeroual
- Situation Innovation - OCP Group, Jorf Lasfar, 24025, Morocco
| | - Lamfeddal Kouisni
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laayoune, Morocco
| | - Adnane Bargaz
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
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12
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Badmi R, Gogoi A, Doyle Prestwich B. Secondary Metabolites and Their Role in Strawberry Defense. PLANTS (BASEL, SWITZERLAND) 2023; 12:3240. [PMID: 37765404 PMCID: PMC10537498 DOI: 10.3390/plants12183240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/21/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Strawberry is a high-value commercial crop and a model for the economically important Rosaceae family. Strawberry is vulnerable to attack by many pathogens that can affect different parts of the plant, including the shoot, root, flowers, and berries. To restrict pathogen growth, strawberry produce a repertoire of secondary metabolites that have an important role in defense against diseases. Terpenes, allergen-like pathogenesis-related proteins, and flavonoids are three of the most important metabolites involved in strawberry defense. Genes involved in the biosynthesis of secondary metabolites are induced upon pathogen attack in strawberry, suggesting their transcriptional activation leads to a higher accumulation of the final compounds. The production of secondary metabolites is also influenced by the beneficial microbes associated with the plant and its environmental factors. Given the importance of the secondary metabolite pathways in strawberry defense, we provide a comprehensive overview of their literature and their role in the defense responses of strawberry. We focus on terpenoids, allergens, and flavonoids, and discuss their involvement in the strawberry microbiome in the context of defense responses. We discuss how the biosynthetic genes of these metabolites could be potential targets for gene editing through CRISPR-Cas9 techniques for strawberry crop improvement.
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Affiliation(s)
- Raghuram Badmi
- School of Biological Earth and Environmental Sciences, University College Cork, T23 TK30 Cork, Ireland;
| | - Anupam Gogoi
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research (NIBIO), 1433 Ås, Norway
| | - Barbara Doyle Prestwich
- School of Biological Earth and Environmental Sciences, University College Cork, T23 TK30 Cork, Ireland;
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13
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Mesny F, Hacquard S, Thomma BPHJ. Co-evolution within the plant holobiont drives host performance. EMBO Rep 2023; 24:e57455. [PMID: 37471099 PMCID: PMC10481671 DOI: 10.15252/embr.202357455] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.
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Affiliation(s)
- Fantin Mesny
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Stéphane Hacquard
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Bart PHJ Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
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14
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Monteoliva MI, Ruiz OA, Li F. Editorial: Legumes and their microbiome in climate change mitigation. FRONTIERS IN PLANT SCIENCE 2023; 14:1220535. [PMID: 37377800 PMCID: PMC10291733 DOI: 10.3389/fpls.2023.1220535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023]
Affiliation(s)
- Mariela I. Monteoliva
- Instituto de Fisiología y Recursos genéticos Vegetales, Unidad de Estudios Agropecuarios (IFRGV-UDEA), Instituto Nacional de Tecnología Agropecuaria (INTA), Concejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Facultad de Ciencias Agropecuarias, Universidad Católica de Córdoba (UCC), Córdoba, Argentina
| | - Oscar A. Ruiz
- Universidad Nacional de San Martín (UNSAM), San Martín, Argentina
- Instituto Tecnológico de Chascomús (INTECH), CONICET, Chascomús, Argentina
| | - Fadong Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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15
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Patel R, Soni M, Soyantar B, Shivangi S, Sutariya S, Saraf M, Goswami D. A clash of quorum sensing vs quorum sensing inhibitors: an overview and risk of resistance. Arch Microbiol 2023; 205:107. [PMID: 36881156 DOI: 10.1007/s00203-023-03442-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Indiscriminate use of antibiotics to treat microbial pathogens has caused emergence of multiple drug resistant strains. Most infectious diseases are caused by microbes that are capable of intercommunication using signaling molecules, which is known as quorum sensing (QS). Such pathogens express their pathogenicity through various QS-regulated virulence factors. Interference of QS could lead to decisive results in controlling such pathogenicity. Hence, QS inhibition has become an attractive new approach for the development of novel drugs. Many quorum sensing inhibitors (QSIs) of diverse origins have been reported. It is imperative that more such anti-QS compounds be found and studied, as they have significant effect on microbial pathogenicity. This review attempts to give a brief account of QS mechanism, its inhibition and describes some compounds with anti-QS potential. Also discussed is the possibility of emergence of quorum sensing resistance.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Mansi Soni
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Bilv Soyantar
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Suruchi Shivangi
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Swati Sutariya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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16
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Afridi MS, Ali S, Salam A, César Terra W, Hafeez A, Ali B, S AlTami M, Ameen F, Ercisli S, Marc RA, Medeiros FHV, Karunakaran R. Plant Microbiome Engineering: Hopes or Hypes. BIOLOGY 2022; 11:biology11121782. [PMID: 36552290 PMCID: PMC9774975 DOI: 10.3390/biology11121782] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Willian César Terra
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Aqsa Hafeez
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Mona S AlTami
- Biology Department, College of Science, Qassim University, Burydah 52571, Saudi Arabia
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 Calea Mănă ̧stur Street, 400372 Cluj-Napoca, Romania
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, (UFLA), Lavras 37200-900, MG, Brazil
| | - Rohini Karunakaran
- Unit of Biochemistry, Centre of Excellence for Biomaterials Engineering, Faculty of Medicine, AIMST University, Semeling, Bedong 08100, Malaysia
- Department of Computational Biology, Institute of Bioinformatics, Saveetha School of Engineering (SSE), SIMATS, Thandalam, Chennai 602105, Tamil Nadu, India
- Centre of Excellence for Biomaterials Science, AIMST University, Semeling, Bedong 08100, Malaysia
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17
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Uroz S, Geisler O, Fauchery L, Lami R, Rodrigues AMS, Morin E, Leveau JHJ, Oger P. Genomic and transcriptomic characterization of the Collimonas quorum sensing genes and regulon. FEMS Microbiol Ecol 2022; 98:6679101. [PMID: 36040340 DOI: 10.1093/femsec/fiac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/13/2022] [Accepted: 08/26/2022] [Indexed: 01/21/2023] Open
Abstract
Collimonads are well-adapted to nutrient-poor environments. They are known to hydrolyse chitin, produce antifungal metabolites, weather minerals, and are effective biocontrol agents protecting plants from fungal diseases. The production of N-acyl homoserine lactones (AHLs) was suggested to be a conserved trait of collimonads, but little is known about the genes that underlie this production or the genes that are controlled by AHLs. To improve our understanding of the role of AHLs in the ecology of collimonads, we carried out transcriptomic analyses, combined with chemical and functional assays, on strain Collimonas pratensis PMB3(1). The main AHLs produced by this strain were identified as 3-hydroxy-hexa- and octa-noyl-homoserine lactone. Genome analysis permitted to identify putative genes coding for the autoinducer synthase (colI) and cognate transcriptional regulator (colR). The ability to produce AHLs was lost in ΔcolI and ΔcolR mutants. Functional assays revealed that the two mutants metabolized glucose, formate, oxalate, and leucine better than the wild-type (WT) strain. Transcriptome sequencing analyses revealed an up-regulation of different metabolic pathways and of motility in the QS-mutants compared to the WT strain. Overall, our results provide insights into the role of the AHL-dependent regulation system of Collimonas in environment colonization, metabolism readjustment, and microbial interactions.
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Affiliation(s)
- Stephane Uroz
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France.,INRAE, UR1138 "Biogéochimie des écosystèmes forestiers", F-54280 Champenoux, France
| | - Océane Geisler
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM, USR3579), Fédération de Recherche FR3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Alice M S Rodrigues
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM, USR3579), Fédération de Recherche FR3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136 "Interactions Arbres-Microorganismes", F-54280 Champenoux, France
| | - Johan H J Leveau
- Department of Plant Pathology, University of California - Davis, Davis, CA 95616, United States
| | - Philippe Oger
- Université Lyon, INSA de Lyon, CNRS UMR 5240, F-69622 Villeurbanne, France
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18
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The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont. Int J Mol Sci 2022; 23:ijms232112952. [PMID: 36361736 PMCID: PMC9655247 DOI: 10.3390/ijms232112952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/26/2022] Open
Abstract
How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria–Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.
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19
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Hamdan MF, Karlson CKS, Teoh EY, Lau SE, Tan BC. Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022. [PMID: 36235491 DOI: 10.1007/s44187-022-00009-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Climate change poses a serious threat to global agricultural activity and food production. Plant genome editing technologies have been widely used to develop crop varieties with superior qualities or can tolerate adverse environmental conditions. Unlike conventional breeding techniques (e.g., selective breeding and mutation breeding), modern genome editing tools offer more targeted and specific alterations of the plant genome and could significantly speed up the progress of developing crops with desired traits, such as higher yield and/or stronger resilience to the changing environment. In this review, we discuss the current development and future applications of genome editing technologies in mitigating the impacts of biotic and abiotic stresses on agriculture. We focus specifically on the CRISPR/Cas system, which has been the center of attention in the last few years as a revolutionary genome-editing tool in various species. We also conducted a bibliographic analysis on CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and potential in the CRISPR/Cas-related plant research. In addition, this review article outlines the current shortcomings and challenges of employing genome editing technologies in agriculture with notes on future prospective. We believe combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices.
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Affiliation(s)
- Mohd Fadhli Hamdan
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chou Khai Soong Karlson
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Ee Yang Teoh
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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20
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Afridi MS, Fakhar A, Kumar A, Ali S, Medeiros FHV, Muneer MA, Ali H, Saleem M. Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 2022; 265:127199. [PMID: 36137486 DOI: 10.1016/j.micres.2022.127199] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022]
Abstract
The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ali Fakhar
- Division of Applied Science, Gyeongsang National University, South Korea
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Sher Ali
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hina Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA
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21
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Korenblum E, Massalha H, Aharoni A. Plant-microbe interactions in the rhizosphere via a circular metabolic economy. THE PLANT CELL 2022; 34:3168-3182. [PMID: 35678568 PMCID: PMC9421461 DOI: 10.1093/plcell/koac163] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/25/2022] [Indexed: 05/30/2023]
Abstract
Chemical exchange often serves as the first step in plant-microbe interactions and exchanges of various signals, nutrients, and metabolites continue throughout the interaction. Here, we highlight the role of metabolite exchanges and metabolic crosstalk in the microbiome-root-shoot-environment nexus. Roots secret a diverse set of metabolites; this assortment of root exudates, including secondary metabolites such as benzoxazinoids, coumarins, flavonoids, indolic compounds, and terpenes, shapes the rhizosphere microbiome. In turn, the rhizosphere microbiome affects plant growth and defense. These inter-kingdom chemical interactions are based on a metabolic circular economy, a seemingly wasteless system in which rhizosphere members exchange (i.e. consume, reuse, and redesign) metabolites. This review also describes the recently discovered phenomenon "Systemically Induced Root Exudation of Metabolites" in which the rhizosphere microbiome governs plant metabolism by inducing systemic responses that shift the metabolic profiles of root exudates. Metabolic exchange in the rhizosphere is based on chemical gradients that form specific microhabitats for microbial colonization and we describe recently developed high-resolution methods to study chemical interactions in the rhizosphere. Finally, we propose an action plan to advance the metabolic circular economy in the rhizosphere for sustainable solutions to the cumulative degradation of soil health in agricultural lands.
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Affiliation(s)
| | - Hassan Massalha
- Theory of Condensed Matter Group, Cavendish Laboratory, Wellcome Sanger Institute, University of Cambridge, Cambridge CB2 1TN, UK
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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22
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The potential of mineral weathering of halophilic-endophytic bacteria isolated from Suaeda salsa and Spartina anglica. Arch Microbiol 2022; 204:561. [PMID: 35978053 PMCID: PMC9385829 DOI: 10.1007/s00203-022-03129-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 11/02/2022]
Abstract
Bacteria have the abilities of salt tolerant, mineral weathering and plant growth promoting can promote the growth of plants in saline lands. However, few reports of the mineral weathering capacity of halophilic-endophytic bacteria, raising the question of whether the halophilic-endophytic weathering bacteria are fundamentally distinct from those in plants communities. In this study, we isolated and characterized halophilic bacterial strains from the roots and leaves of Suaeda salsa and Spartina anglica with respect to their mineral weathering pattern, role in the promoting plant growth, community structure, and their changes in these two plants. Using improved Gibbson medium, we obtained 156 halophilic bacterial strains, among which 92 and 64 strains were isolated from the S. salsa and S. anglica samples, respectively. The rock weathering patterns of the isolates were characterized using batch cultures that measure the quantity of Si, Al, K, and Fe released from crystal biotite under aerobic conditions. Significantly, the biomass and capacity of the mineral weathering of the halophilic-endophytic bacteria were different in the plants. The abundance of the halophilic-endophytic bacterials in the Suaeda salsa was significantly greater than Spartina anglica, whereas the mineral weathering bacterial in the Suaeda salsa was similar to the Spartina anglica. Furthermore, the proportion of plant growth-promoting bacteria in the Suaeda salsa was higher than Spartina anglica. Phylogenetic analyses show that the weathered minerals were inhabited by specific functional groups of bacteria (Halomonas, Acinetobacter, Burkholderia, Alcaligenes, Sphingobium, Arthrobacter, Chryseobacterium, Paenibacillus, Microbacterium, Ensifer, Ralstonia and Enterobacter) that contribute to the mineral weathering. The changes in halophilic endophytes weathering communities between the two plants were attributable not only to major bacterial groups but also to a change in the minor population structure.
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23
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Alvarenga DO, Rousk K. Unraveling host-microbe interactions and ecosystem functions in moss-bacteria symbioses. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4473-4486. [PMID: 35728619 DOI: 10.1093/jxb/erac091] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Mosses are non-vascular plants usually found in moist and shaded areas, with great ecological importance in several ecosystems. This is especially true in northern latitudes, where mosses are responsible for up to 100% of primary production in some ecosystems. Mosses establish symbiotic associations with unique bacteria that play key roles in the carbon and nitrogen cycles. For instance, in boreal environments, more than 35% of the nitrogen fixed by diazotrophic symbionts in peatlands is transferred to mosses, directly affecting carbon fixation by the hosts, while moss-associated methanotrophic bacteria contribute 10-30% of moss carbon. Further, half of ecosystem N input may derive from moss-cyanobacteria associations in pristine ecosystems. Moss-bacteria interactions have consequences on a global scale since northern environments sequester 20% of all the carbon generated by forests in the world and stock at least 32% of global terrestrial carbon. Different moss hosts influence bacteria in distinct ways, which suggests that threats to mosses also threaten unique microbial communities with important ecological and biogeochemical consequences. Since their origin ~500 Ma, mosses have interacted with bacteria, making these associations ideal models for understanding the evolution of plant-microbe associations and their contribution to biogeochemical cycles.
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Affiliation(s)
- Danillo O Alvarenga
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
- Centre for Permafrost, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Kathrin Rousk
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
- Centre for Permafrost, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
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24
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Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
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Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
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25
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Koyro HW, Huchzermeyer B. From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity. PLANTS 2022; 11:plants11131654. [PMID: 35807605 PMCID: PMC9269222 DOI: 10.3390/plants11131654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022]
Abstract
Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.
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Affiliation(s)
- Hans-Werner Koyro
- Institute of Plantecology, Justus-Liebig-University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
- Correspondence:
| | - Bernhard Huchzermeyer
- Institute of Botany, Leibniz Universitaet Hannover, Herrenhaeuser Str. 2, 30416 Hannover, Germany; or
- AK Biotechnology, VDI-BV-Hannover, Hanomagstr. 12, 30449 Hannover, Germany
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26
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Nerva L, Garcia JF, Favaretto F, Giudice G, Moffa L, Sandrini M, Cantu D, Zanzotto A, Gardiman M, Velasco R, Gambino G, Chitarra W. The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2682-2697. [PMID: 35106548 DOI: 10.1093/jxb/erac032] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.
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Affiliation(s)
- Luca Nerva
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, One Shields Ave, Davis, CA 95618, USA
| | - Francesco Favaretto
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- University of Padova, Department of Agronomy, Animals, Food, Natural Resources and Environment (DAFNAE), Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Gaetano Giudice
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- University of Milano, Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DiSAA), Via Celoria 2, 20133, Milano, Italy
| | - Loredana Moffa
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100 Udine, Italy
| | - Marco Sandrini
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100 Udine, Italy
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, One Shields Ave, Davis, CA 95618, USA
| | - Alessandro Zanzotto
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Massimo Gardiman
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Riccardo Velasco
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Walter Chitarra
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
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27
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28
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Harnessing phytomicrobiome signals for phytopathogenic stress management. J Biosci 2022. [DOI: 10.1007/s12038-021-00240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Hidden Earthstar Diversity in the Jharkhand State of India. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Kim JY, Loo EPI, Pang TY, Lercher M, Frommer WB, Wudick MM. Cellular export of sugars and amino acids: role in feeding other cells and organisms. PLANT PHYSIOLOGY 2021; 187:1893-1914. [PMID: 34015139 PMCID: PMC8644676 DOI: 10.1093/plphys/kiab228] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/29/2021] [Indexed: 05/20/2023]
Abstract
Sucrose, hexoses, and raffinose play key roles in the plant metabolism. Sucrose and raffinose, produced by photosynthesis, are translocated from leaves to flowers, developing seeds and roots. Translocation occurs in the sieve elements or sieve tubes of angiosperms. But how is sucrose loaded into and unloaded from the sieve elements? There seem to be two principal routes: one through plasmodesmata and one via the apoplasm. The best-studied transporters are the H+/SUCROSE TRANSPORTERs (SUTs) in the sieve element-companion cell complex. Sucrose is delivered to SUTs by SWEET sugar uniporters that release these key metabolites into the apoplasmic space. The H+/amino acid permeases and the UmamiT amino acid transporters are hypothesized to play analogous roles as the SUT-SWEET pair to transport amino acids. SWEETs and UmamiTs also act in many other important processes-for example, seed filling, nectar secretion, and pollen nutrition. We present information on cell type-specific enrichment of SWEET and UmamiT family members and propose several members to play redundant roles in the efflux of sucrose and amino acids across different cell types in the leaf. Pathogens hijack SWEETs and thus represent a major susceptibility of the plant. Here, we provide an update on the status of research on intercellular and long-distance translocation of key metabolites such as sucrose and amino acids, communication of the plants with the root microbiota via root exudates, discuss the existence of transporters for other important metabolites and provide potential perspectives that may direct future research activities.
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Affiliation(s)
- Ji-Yun Kim
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Eliza P -I Loo
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Tin Yau Pang
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Martin Lercher
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Michael M Wudick
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Author for communication:
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31
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Kang L, He D, Wang H, Han G, Lv H, Xiao W, Zhang Z, Yan Z, Huang L. "Breeding on Mountains" Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants ( Ligusticum chuanxiong Hort.). FRONTIERS IN PLANT SCIENCE 2021; 12:740456. [PMID: 34858448 PMCID: PMC8631752 DOI: 10.3389/fpls.2021.740456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/04/2021] [Indexed: 05/05/2023]
Abstract
"Breeding on mountains, cultivation in dam areas" is a unique propagation method for the vegetatively propagated plant Ligusticum chuanxiong, including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on L. chuanxiong and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in L. chuanxiong increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of L. chuanxiong, while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant Gibberella, Phoma, Pericona, Paraphoma, and Neocosmospora. The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.
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Affiliation(s)
- Lei Kang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dongmei He
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory Breeding Base of Dao-di Herbs, Center for Post-doctoral Research, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hai Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guiqi Han
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hongyang Lv
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wanting Xiao
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhanling Zhang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, Center for Post-doctoral Research, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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32
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Dominant woody plants alter soil microbial community composition during succession. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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33
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Sportes A, Hériché M, Boussageon R, Noceto PA, van Tuinen D, Wipf D, Courty PE. A historical perspective on mycorrhizal mutualism emphasizing arbuscular mycorrhizas and their emerging challenges. MYCORRHIZA 2021; 31:637-653. [PMID: 34657204 DOI: 10.1007/s00572-021-01053-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Arbuscular mycorrhiza, one of the oldest interactions on earth (~ 450 million years old) and a first-class partner for plants to colonize emerged land, is considered one of the most pervasive ecological relationships on the globe. Despite how important and old this interaction is, its discovery was very recent compared to the long story of land plant evolution. The story of the arbuscular mycorrhiza cannot be addressed apart from the history, controversies, and speculations about mycorrhiza in its broad sense. The chronicle of mycorrhizal research is marked by multiple key milestones such as the initial description of a "persistent epiderm and pellicular wall structure" by Hartig; the introduction of the "Symbiotismus" and "Mycorrhiza" concepts by Frank; the description of diverse root-fungal morphologies; the first description of arbuscules by Gallaud; Mosse's pivotal statement of the beneficial nature of the arbuscular mycorrhizal symbiosis; the impact of molecular tools on the taxonomy of mycorrhizal fungi as well as the development of in vitro root organ cultures for producing axenic arbuscular mycorrhizal fungi (AMF). An appreciation of the story - full of twists and turns - of the arbuscular mycorrhiza, going from the roots of mycorrhiza history, along with the discovery of different mycorrhiza types such as ectomycorrhiza, can improve research to help face our days' challenge of developing sustainable agriculture that integrates the arbuscular mycorrhiza and its ecosystem services.
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Affiliation(s)
- Antoine Sportes
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Mathilde Hériché
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Raphaël Boussageon
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Antoine Noceto
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Diederik van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pierre Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France.
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34
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Deng Z, Zhang J, Li J, Zhang X. Application of Deep Learning in Plant-Microbiota Association Analysis. Front Genet 2021; 12:697090. [PMID: 34691142 PMCID: PMC8531731 DOI: 10.3389/fgene.2021.697090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/31/2021] [Indexed: 01/04/2023] Open
Abstract
Unraveling the association between microbiome and plant phenotype can illustrate the effect of microbiome on host and then guide the agriculture management. Adequate identification of species and appropriate choice of models are two challenges in microbiome data analysis. Computational models of microbiome data could help in association analysis between the microbiome and plant host. The deep learning methods have been widely used to learn the microbiome data due to their powerful strength of handling the complex, sparse, noisy, and high-dimensional data. Here, we review the analytic strategies in the microbiome data analysis and describe the applications of deep learning models for plant–microbiome correlation studies. We also introduce the application cases of different models in plant–microbiome correlation analysis and discuss how to adapt the models on the critical steps in data processing. From the aspect of data processing manner, model structure, and operating principle, most deep learning models are suitable for the plant microbiome data analysis. The ability of feature representation and pattern recognition is the advantage of deep learning methods in modeling and interpretation for association analysis. Based on published computational experiments, the convolutional neural network and graph neural networks could be recommended for plant microbiome analysis.
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Affiliation(s)
- Zhiyu Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Zhang
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Junya Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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35
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Schaedel M, Hidrobo G, Grossman J. From Microns to Meters: Exploring Advances in Legume Microbiome Diversity for Agroecosystem Benefits. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.668195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Legumes are of primary importance for agroecosystems because they provide protein-rich foods and enhance soil fertility through fixed atmospheric nitrogen. The legume-rhizobia symbiosis that makes this possible has been extensively studied, from basic research on biochemical signaling to practical applications in cropping systems. While rhizobia are the most-studied group of associated microorganisms, the functional benefit they confer to their legume hosts by fixing nitrogen is not performed in isolation. Indeed, non-rhizobia members of the rhizosphere and nodule microbiome are now understood to contribute in multiple ways to nodule formation, legume fitness, and other agroecosystem services. In this review, we summarize advances contributing to our understanding of the diversity and composition of bacterial members of the belowground legume microbiome. We also highlight applied work in legume food and forage crops that link microbial community composition with plant functional benefits. Ultimately, further research will assist in the development of multi-species microbial inoculants and cropping systems that maximize plant nutrient benefits, while reducing sources of agricultural pollution.
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Zhu L, Zhang Y, Cui X, Zhu Y, Dai Q, Chen H, Liu G, Yao R, Yang Z. Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense. Microbiol Spectr 2021; 9:e0075621. [PMID: 34406815 PMCID: PMC8552726 DOI: 10.1128/spectrum.00756-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.
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Affiliation(s)
- Lifeng Zhu
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yongyong Zhang
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Xinyuan Cui
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yudong Zhu
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Qinlong Dai
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Hua Chen
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Guoqi Liu
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Ran Yao
- College of Life Sciences, Nanjing Norma University, Nanjing, China
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Sauer S, Dlugosch L, Kammerer DR, Stintzing FC, Simon M. The Microbiome of the Medicinal Plants Achillea millefolium L. and Hamamelis virginiana L. Front Microbiol 2021; 12:696398. [PMID: 34354692 PMCID: PMC8329415 DOI: 10.3389/fmicb.2021.696398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/22/2021] [Indexed: 01/19/2023] Open
Abstract
In the recent past many studies investigated the microbiome of plants including several medicinal plants (MP). Microbial communities of the associated soil, rhizosphere and the above-ground organs were included, but there is still limited information on their seasonal development, and in particular simultaneous investigations of different plant organs are lacking. Many studies predominantly addressed either the prokaryotic or fungal microbiome. A distinction of epi- and endophytic communities of above-ground plant organs has rarely been made. Therefore, we conducted a comprehensive investigation of the bacterial and fungal microbiome of the MP Achillea millefolium and studied the epi- and endophytic microbial communities of leaves, flower buds and flowers between spring and summer together with the microbiome of the associated soil at one location. Further, we assessed the core microbiome of Achillea from four different locations at distances up to 250 km in southern Germany and Switzerland. In addition, the bacterial and fungal epi- and endophytic leaf microbiome of the arborescent shrub Hamamelis virginiana and the associated soil was investigated at one location. The results show a generally decreasing diversity of both microbial communities from soil to flower of Achillea. The diversity of the bacterial and fungal endophytic leaf communities of Achillea increased from April to July, whereas that of the epiphytic leaf communities decreased. In contrast, the diversity of the fungal communities of both leaf compartments and that of epiphytic bacteria of Hamamelis increased over time indicating plant-specific differences in the temporal development of microbial communities. Both MPs exhibited distinct microbial communities with plant-specific but also common taxa. The core taxa of Achillea constituted a lower fraction of the total number of taxa than of the total abundance of taxa. The results of our study provide a basis to link interactions of the microbiome with their host plant in relation to the production of bioactive compounds.
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Affiliation(s)
- Simon Sauer
- WALA Heilmittel GmbH, Bad Boll, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | | | | | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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Torres N, Yu R, Kurtural SK. Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils. Microorganisms 2021; 9:1273. [PMID: 34207954 PMCID: PMC8230719 DOI: 10.3390/microorganisms9061273] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/05/2022] Open
Abstract
Vineyard-living microbiota affect grapevine health and adaptation to changing environments and determine the biological quality of soils that strongly influence wine quality. However, their abundance and interactions may be affected by vineyard management. The present study was conducted to assess whether the vineyard soil microbiome was altered by the use of biostimulants (arbuscular mycorrhizal fungi (AMF) inoculation vs. non-inoculated) and/or irrigation management (fully irrigated vs. half irrigated). Bacterial and fungal communities in vineyard soils were shaped by both time course and soil management (i.e., the use of biostimulants and irrigation). Regarding alpha diversity, fungal communities were more responsive to treatments, whereas changes in beta diversity were mainly recorded in the bacterial communities. Edaphic factors rarely influence bacterial and fungal communities. Microbial network analyses suggested that the bacterial associations were weaker than the fungal ones under half irrigation and that the inoculation with AMF led to the increase in positive associations between vineyard-soil-living microbes. Altogether, the results highlight the need for more studies on the effect of management practices, especially the addition of AMF on cropping systems, to fully understand the factors that drive their variability, strengthen beneficial microbial networks, and achieve better soil quality, which will improve crop performance.
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Affiliation(s)
| | | | - S. Kaan Kurtural
- Department of Viticulture and Enology, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA; (N.T.); (R.Y.)
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Vannini C, Domingo G, Fiorilli V, Seco DG, Novero M, Marsoni M, Wisniewski-Dye F, Bracale M, Moulin L, Bonfante P. Proteomic analysis reveals how pairing of a Mycorrhizal fungus with plant growth-promoting bacteria modulates growth and defense in wheat. PLANT, CELL & ENVIRONMENT 2021; 44:1946-1960. [PMID: 33675052 DOI: 10.1111/pce.14039] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Plants rely on their microbiota for improving the nutritional status and environmental stress tolerance. Previous studies mainly focused on bipartite interactions (a plant challenged by a single microbe), while plant responses to multiple microbes have received limited attention. Here, we investigated local and systemic changes induced in wheat by two plant growth-promoting bacteria (PGPB), Azospirillum brasilense and Paraburkholderia graminis, either alone or together with an arbuscular mycorrhizal fungus (AMF). We conducted phenotypic, proteomic, and biochemical analyses to investigate bipartite (wheat-PGPB) and tripartite (wheat-PGPB-AMF) interactions, also upon a leaf pathogen infection. Results revealed that only AMF and A. brasilense promoted plant growth by activating photosynthesis and N assimilation which led to increased glucose and amino acid content. The bioprotective effect of the PGPB-AMF interactions on infected wheat plants depended on the PGPB-AMF combinations, which caused specific phenotypic and proteomic responses (elicitation of defense related proteins, immune response and jasmonic acid biosynthesis). In the whole, wheat responses strongly depended on the inoculum composition (single vs. multiple microbes) and the investigated organs (roots vs. leaf). Our findings showed that AMF is the best-performing microbe, suggesting its presence as the crucial one for synthetic microbial community development.
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Affiliation(s)
- Candida Vannini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
| | | | - Mara Novero
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
| | - Milena Marsoni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Florence Wisniewski-Dye
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgroSup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Marcella Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Lionel Moulin
- IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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Impact of Application of Abscisic Acid, Benzothiadiazole and Chitosan on Berry Quality Characteristics and Plant Associated Microbial Communities of Vitis vinifera L var. Mouhtaro Plants. SUSTAINABILITY 2021. [DOI: 10.3390/su13115802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The phenolic profile of the grape berries is a key quality factor for the red grapevine varieties and several techniques have been applied to improve it. An innovative technique is the application of resistance elicitors and phytohormones. In the present study, leaves and berries of a Greek red indigenous variety (Mouhtaro) sprayed with two elicitors, benzothiadiazole and chitosan and a plant hormone abscisic acid, during veraison. Physicochemical and phenolic characteristics of the berries and microbial communities of rhizosphere, phyllosphere and carposphere were analyzed at harvest. Differences in the microbial communities on different plant compartments were observed after the application of the plant activators. Chitosan treatment increased the abundance of the beneficial lactic acid bacteria, while the abscisic acid treatment decreased the presence of spoilage fungi on the carposphere. Treatments differentiate total phenolics, anthocyanins and in the chemical characteristics of grape must with chitosan treated grapes had increased anthocyanins and skin-derived phenolics that correlated positively with the microbial taxa that was discriminant by LefSe analysis. This research provides an overview of the effect of plant activators on the microbial ecology and grape quality of the Greek variety Mouhtaro and presents the potential of new and innovative approaches in the field of sustainable viticulture.
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The Coevolution of Plants and Microbes Underpins Sustainable Agriculture. Microorganisms 2021; 9:microorganisms9051036. [PMID: 34065848 PMCID: PMC8151373 DOI: 10.3390/microorganisms9051036] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.
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Tsiknia M, Tsikou D, Papadopoulou KK, Ehaliotis C. Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant - microbiome - soil continuum. FEMS Microbiol Ecol 2021; 97:5957530. [PMID: 33155054 DOI: 10.1093/femsec/fiaa222] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/03/2020] [Indexed: 01/02/2023] Open
Abstract
Mutualistic relationships of legume plants with, either bacteria (like rhizobia) or fungi (like arbuscular mycorrhizal fungi), have been investigated intensively, usually as bi-partite interactions. However, diverse symbiotic interactions take place simultaneously or sequentially under field conditions. Their collective, but not additive, contribution to plant growth and performance remains hard to predict, and appears to be furthermore affected by crop species and genotype, non-symbiotic microbial interactions and environmental variables. The challenge is: (i) to unravel the complex overlapping mechanisms that operate between the microbial symbionts as well as between them, their hosts and the rhizosphere (ii) to understand the dynamics of the respective mechanisms in evolutionary and ecological terms. The target for agriculture, food security and the environment, is to use this insight as a solid basis for developing new integrated technologies, practices and strategies for the efficient use of beneficial microbes in legumes and other plants. We review recent advances in our understanding of the symbiotic interactions in legumes roots brought about with the aid of molecular and bioinformatics tools. We go through single symbiont-host interactions, proceed to tripartite symbiont-host interactions, appraise interactions of symbiotic and associative microbiomes with plants in the root-rhizoplane-soil continuum of habitats and end up by examining attempts to validate community ecology principles in the legume-microbe-soil biosystem.
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Affiliation(s)
- Myrto Tsiknia
- Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75 st., Athens 11855, Greece
| | - Daniela Tsikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Kalliope K Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Constantinos Ehaliotis
- Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75 st., Athens 11855, Greece
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Peng X, Xie J, Li W, Xie H, Cai Y, Ding X. Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures. PLoS One 2021; 16:e0246687. [PMID: 33556120 PMCID: PMC7870070 DOI: 10.1371/journal.pone.0246687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/23/2021] [Indexed: 11/18/2022] Open
Abstract
Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.
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Affiliation(s)
- Xiaojue Peng
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Jian Xie
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Wenzhuo Li
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Xia Ding
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
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Middleton H, Yergeau É, Monard C, Combier JP, El Amrani A. Rhizospheric Plant-Microbe Interactions: miRNAs as a Key Mediator. TRENDS IN PLANT SCIENCE 2021; 26:132-141. [PMID: 33036916 DOI: 10.1016/j.tplants.2020.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 05/20/2023]
Abstract
The importance of microorganisms in plant development, nutrition, and stress resistance is unquestioned and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of the plant microbiota is often described as host driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through coevolution, plants and microbes have developed cross-kingdom communication channels. Here, we propose that miRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, miRNAs as a promising tool for novel holobiont engineering.
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Affiliation(s)
- Harriet Middleton
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France.
| | - Étienne Yergeau
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada
| | - Cécile Monard
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Vegetales, UMR 5546, UPS, CNRS, Auzeville-Tolosane 31320, France
| | - Abdelhak El Amrani
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
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45
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Chaudhary T, Gera R, Shukla P. Emerging Molecular Tools for Engineering Phytomicrobiome. Indian J Microbiol 2021; 61:116-124. [PMID: 33927453 DOI: 10.1007/s12088-020-00915-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022] Open
Abstract
Microbial plant interaction plays a major role in the sustainability of plants. The understanding of phytomicrobiome interactions enables the gene-editing tools for the construction of the microbial consortia. In this interaction, microbes share several common secondary metabolites and terpenoid metabolic pathways with their host plants that ensure a direct connection between the microbiome and associated plant metabolome. In this way, the CRISPR-mediated gene-editing tool provides an attractive approach to accomplish the creation of microbial consortia. On the other hand, the genetic manipulation of the host plant with the help of CRISPR-Cas9 can facilitate the characterization and identification of the genetic determinants. It leads to the enhancement of microbial capacity for more trait improvement. Many plant characteristics like phytovolatilization, phytoextraction, phytodesalination and phytodegradation are targeted by these approaches. Alternatively, chemical communications by PGPB are accomplished by the exchange of different signal molecules. For example, quorum-sensing is the way of the cell to cell communication in bacteria that lead to the detection of metabolites produced by pathogens during adverse conditions and also helpful in devising some tactics towards understanding plant immunity. Along with quorum-sensing, different volatile organic compounds and N-acyl homoserine lactones play a significant role in cell to cell communication by microbe to plant and among the plants respectively. Therefore, it is necessary to get details of all the significant approaches that are useful in exploring cell to cell communications. In this review, we have described gene-editing tools and the cell to cell communication process by quorum-sensing based signaling. These signaling processes via CRISPR- Cas9 mediated gene editing can improve the microbe-plant community in adverse climatic conditions.
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Affiliation(s)
- Twinkle Chaudhary
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 India
| | - Rajesh Gera
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 India.,Present Address: School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
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Sun A, Jiao XY, Chen Q, Trivedi P, Li Z, Li F, Zheng Y, Lin Y, Hu HW, He JZ. Fertilization alters protistan consumers and parasites in crop-associated microbiomes. Environ Microbiol 2021; 23:2169-2183. [PMID: 33400366 DOI: 10.1111/1462-2920.15385] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/03/2021] [Indexed: 12/12/2022]
Abstract
Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant-soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.
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Affiliation(s)
- Anqi Sun
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Xiao-Yan Jiao
- College of Resource and Environment, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Qinglin Chen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Zixin Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Yong Zheng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Yongxin Lin
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.,School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.,School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
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Santander C, Aroca R, Cartes P, Vidal G, Cornejo P. Aquaporins and cation transporters are differentially regulated by two arbuscular mycorrhizal fungi strains in lettuce cultivars growing under salinity conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:396-409. [PMID: 33248899 DOI: 10.1016/j.plaphy.2020.11.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/17/2020] [Indexed: 05/02/2023]
Abstract
The aim was to identify the effects of AM symbiosis on the expression patterns of genes associated with K+ and Na+ compartmentalization and translocation and on K+/Na+ homeostasis in some lettuce (Lactuca sativa) cultivars as well as the effects of the relative abundance of plant AQPs on plant water status. Two AM fungi species (Funneliformis mosseae and Claroideoglomus lamellosum) isolated from the hyper-arid Atacama Desert (northern Chile) were inoculated to two lettuce cultivars (Grand Rapids and Lollo Bionda), and watered with 0 and 60 mM NaCl. At 60 days of plant growth, the AM symbiotic development, biomass production, nutrient content (Pi, Na+, K+), physiological parameters, gene expressions of ion channels and transporters (NHX and HKT1), and aquaporins proteins abundance (phosphorylated and non-phosphorylated) were evaluated. Salinity increased the AM root colonization by both inocula. AM lettuce plants showed an improved growth, increased relative water content and improved of K/Na ratio in root. In Grand Rapids cultivar, the high efficiency of photosystem II was higher than Lollo Bionda cultivar; on the contrary, stomatal conductance was higher in Lollo Bionda. Nevertheless, both parameters were increased by AM colonization. In the same way, LsaHKT1;1, LsaHKT1;6, LsaNHX2, LsaNHX4, LsaNHX6 and LsaNHX8 genes and aquaporins PIP2 were up-regulated differentially by both AM fungi. The improved plant growth was closely related to a higher water status due to increased PIP2 abundance, as well as to the upregulation of LsaNHX gene expression, which concomitantly improved plant nutrition and K+/Na+ homeostasis maintenance.
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Affiliation(s)
- Christian Santander
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental, CIMYSA, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile; Universidad Arturo Prat, Centro de Investigación y Desarrollo en Recursos Hídricos (CIDERH), Vivar 493 2nd floor, Iquique, Chile
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain
| | - Paula Cartes
- Scientific and Technological Bioresource Nucleus, BIOREN-UFRO, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - Gladys Vidal
- Grupo de Ingeniería y Biotecnología Ambiental, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Concepción, Chile
| | - Pablo Cornejo
- Centro de Investigación en Micorrizas y Sustentabilidad Agroambiental, CIMYSA, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile.
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Brunel C, Pouteau R, Dawson W, Pester M, Ramirez KS, van Kleunen M. Towards Unraveling Macroecological Patterns in Rhizosphere Microbiomes. TRENDS IN PLANT SCIENCE 2020; 25:1017-1029. [PMID: 32467065 DOI: 10.1016/j.tplants.2020.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/18/2020] [Accepted: 04/28/2020] [Indexed: 05/26/2023]
Abstract
It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further involves a hierarchy of constraints with varying strengths across spatial and temporal scales. However, our knowledge of rhizosphere microbiomes is largely based on single-location and time-point studies. Consequently, it remains difficult to predict patterns at large landscape scales, and we lack a clear understanding of how the rhizosphere microbiome forms and is maintained by drivers beyond the influence of the plant. By synthesizing recent literature and collating data on rhizosphere microbiomes, we point out the opportunities and challenges offered by advances in molecular biology, bioinformatics, and data availability. Specifically, we highlight the use of exact sequence variants, coupled with existing and newly generated data to decipher the rules of rhizosphere community assembly across large spatial and taxonomic scales.
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Affiliation(s)
- Caroline Brunel
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, 318000 Taizhou, China; IRD, IPME, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France.
| | - Robin Pouteau
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, 318000 Taizhou, China; AMAP, IRD, CNRS, CIRAD, INRA, Université de Montpellier, 34398 Montpellier Cedex 05, France
| | - Wayne Dawson
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Michael Pester
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany; Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, 38106 Braunschweig, Germany
| | - Kelly S Ramirez
- Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; University of Texas at El Paso, Department of Biological Sciences, 500 W University Ave, El Paso, TX 79968, USA
| | - Mark van Kleunen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, 318000 Taizhou, China; Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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49
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Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL. The Plant Microbiome: From Ecology to Reductionism and Beyond. Annu Rev Microbiol 2020; 74:81-100. [PMID: 32530732 DOI: 10.1146/annurev-micro-022620-014327] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Sarah Gilbert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Paulo José Pereira Lima Teixeira
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Bettenfeld P, Fontaine F, Trouvelot S, Fernandez O, Courty PE. Woody Plant Declines. What's Wrong with the Microbiome? TRENDS IN PLANT SCIENCE 2020; 25:381-394. [PMID: 31983620 DOI: 10.1016/j.tplants.2019.12.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Woody plant (WP) declines have multifactorial determinants as well as a biological and economic reality. The vascular system of WPs involved in the transport of carbon, nitrogen, and water from sources to sinks has a seasonal activity, which places it at a central position for mediating plant-environment interactions from nutrient cycling to community assembly and for regulating a variety of processes. To limit effects and to fight against declines, we propose: (i) to consider the WP and its associated microbiota as an holobiont and as a set of functions; (ii) to consider simultaneously, without looking at what comes first, the physiological or pathogenic disorders; and (iii) to define pragmatic strategies, including preventive and curative agronomical practices based on microbiota engineering.
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Affiliation(s)
- Pauline Bettenfeld
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France; SFR Condorcet CNRS 3417, Université de Reims Champagne-Ardenne, Unité Résistance Induite et Bioprotection des Plantes EA4707, Reims, France
| | - Florence Fontaine
- SFR Condorcet CNRS 3417, Université de Reims Champagne-Ardenne, Unité Résistance Induite et Bioprotection des Plantes EA4707, Reims, France
| | - Sophie Trouvelot
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Olivier Fernandez
- SFR Condorcet CNRS 3417, Université de Reims Champagne-Ardenne, Unité Résistance Induite et Bioprotection des Plantes EA4707, Reims, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France.
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