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Gao W, Chen X, He J, Sha A, Ren Y, Wu P, Li Q. The impact of kaolin mining activities on bacterial diversity and community structure in the rhizosphere soil of three local plants. Front Microbiol 2024; 15:1424687. [PMID: 39314884 PMCID: PMC11417686 DOI: 10.3389/fmicb.2024.1424687] [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: 04/28/2024] [Accepted: 07/22/2024] [Indexed: 09/25/2024] Open
Abstract
Introduction Thus far, the impact of kaolin mining activities on the surrounding native plants and rhizosphere microecology has not been fully understood. Methods In this study, we used 16S rRNA high-throughput sequencing to examine the impact of kaolin mining on the rhizosphere bacterial communities and functions of three local plant species: Conyza bonariensis, Artemisia annua, and Dodonaea viscosa. Results The results showed that kaolin mining significantly reduced the diversity of rhizosphere bacteria in these plants, as indicated by the Shannon, Simpson, Chao1, and observed species indices (p < 0.05). Kaolin mining had an impact on the recruitment of three rhizosphere bacteria native to the area: Actinoplanes, RB41, and Mycobacterium. These bacteria were found to be more abundant in the rhizosphere soil of three local plants than in bulk soil, yet the mining of kaolin caused a decrease in their abundance (p < 0.05). Interestingly, Ralstonia was enriched in the rhizosphere of these plants found in kaolin mining areas, suggesting its resilience to environmental stress. Furthermore, the three plants had different dominant rhizosphere bacterial populations in kaolin mining areas, such as Nocardioides, Pseudarthrobacter, and Sphingomonas, likely due to the unique microecology of the plant rhizosphere. Kaolin mining activities also caused a shift in the functional diversity of rhizosphere bacteria in the three local plants, with each plant displaying different functions to cope with kaolin mining-induced stress, such as increased abundance of the GlpM family and glucan-binding domain. Discussion This study is the first to investigate the effects of kaolin mining on the rhizosphere microecology of local plants, thus contributing to the establishment of soil microecological health monitoring indicators to better control soil pollution in kaolin mining areas.
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Affiliation(s)
- Wei Gao
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Xiaodie Chen
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Jing He
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Ajia Sha
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Yuanhang Ren
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
| | - Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Qiang Li
- Clinical Medical College and Affiliated Hospital of Chengdu University, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, Sichuan, China
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Jeong GJ, Khan F, Tabassum N, Jo DM, Jung WK, Kim YM. Roles of Pseudomonas aeruginosa siderophores in interaction with prokaryotic and eukaryotic organisms. Res Microbiol 2024; 175:104211. [PMID: 38734157 DOI: 10.1016/j.resmic.2024.104211] [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: 11/19/2023] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that produces two types of siderophores, pyoverdine and pyochelin, that play pivotal roles in iron scavenging from the environment and host cells. P. aeruginosa siderophores can serve as virulence factors and perform various functions. Several bacterial and fungal species are likely to interact with P. aeruginosa due to its ubiquity in soil and water as well as its potential to cause infections in plants, animals, and humans. Siderophores produced by P. aeruginosa play critical roles in iron scavenging for prokaryotic species (bacteria) and eukaryotic hosts (fungi, animals, insects, invertebrates, and plants) as well. This review provides a comprehensive discussion of the role of P. aeruginosa siderophores in interaction with prokaryotes and eukaryotes as well as their underlying mechanisms of action. The evolutionary relationship between P. aeruginosa siderophore recognition receptors, such as FpvA, FpvB, and FptA, and those of other bacterial species has also been investigated.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Institute of Fisheries Science, Pukyong National University. Busan 48513, Republic of Korea; International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Du-Min Jo
- National Marine Biodiversity Institute of Korea, Seochun, Chungcheongnam-do, 33662, Republic of Korea
| | - Won-Kyo Jung
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence and New-senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
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Spooren J, van Bentum S, Thomashow LS, Pieterse CMJ, Weller DM, Berendsen RL. Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:1-30. [PMID: 38857541 DOI: 10.1146/annurev-phyto-021622-100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.
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Affiliation(s)
- Jelle Spooren
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Sietske van Bentum
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Linda S Thomashow
- Wheat Health, Genetics and Quality Research Unit, US Department of Agriculture, Agricultural Research Service, Pullman, Washington, USA;
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - David M Weller
- Wheat Health, Genetics and Quality Research Unit, US Department of Agriculture, Agricultural Research Service, Pullman, Washington, USA;
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
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Wang G, Li Z, Yang B, Yang H, Zhang Y, Zeng Q, Yan C, He Y, Peng Y, Wang W, Chen B, Du G. The effect of white grub (Maladera Verticalis) larvae feeding on rhizosphere microbial characterization of aerobic rice (Oryza sativa L.) in Puer City, Yunnan Province, China. BMC Microbiol 2024; 24:123. [PMID: 38622504 PMCID: PMC11017655 DOI: 10.1186/s12866-024-03265-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Rhizosphere microorganisms are vital in plants' growth and development and these beneficial microbes are recruited to the root-zone soil when experiencing various environmental stresses. However, the effect of white grub (Maladera verticalis) larvae feeding on the structure and function of rhizosphere microbial communities of aerobic rice (Oryza sativa L.) is unclear. RESULTS In this study, we compared physicochemical properties, enzyme activities, and microbial communities using 18 samples under healthy and M. verticalis larvae-feeding aerobic rice rhizosphere soils at the Yunnan of China. 16 S rRNA and ITS amplicons were sequenced using Illumina high throughput sequencing. M. verticalis larvae feeding on aerobic rice can influence rhizosphere soil physicochemical properties and enzyme activities, which also change rhizosphere microbial communities. The healthy and M. verticalis larvae-feeding aerobic rice rhizosphere soil microorganisms had distinct genus signatures, such as possible_genus_04 and Knoellia genera in healthy aerobic rice rhizosphere soils and norank_f__SC - I-84 and norank_f__Roseiflexaceae genera in M. verticalis larvae-feeding aerobic rice rhizosphere soils. The pathway of the metabolism of terpenoids and polyketides and carbohydrate metabolism in rhizosphere bacteria were significantly decreased after M. verticalis larvae feeding. Fungal parasite-wood saprotroph and fungal parasites were significantly decreased after M. verticalis larvae feeding, and plant pathogen-wood saprotroph and animal pathogen-undefined saprotroph were increased after larvae feeding. Additionally, the relative abundance of Bradyrhizobium and Talaromyces genera gradually increased with the elevation of the larvae density. Bacterial and fungal communities significantly correlated with soil physicochemical properties and enzyme activities, respectively. CONCLUSIONS Based on the results we provide new insight for understanding the adaptation of aerobic rice to M. verticalis larvae feeding via regulating the rhizosphere environment, which would allow us to facilitate translation to more effective measures.
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Affiliation(s)
- Guang Wang
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhengfei Li
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Baoyun Yang
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Huquan Yang
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Yujie Zhang
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Qingping Zeng
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Chaojianping Yan
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Yanyan He
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
- School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yuejin Peng
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Wenqian Wang
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Bin Chen
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Guangzu Du
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China.
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Spescha A, Zwyssig M, Hess Hermida M, Moix A, Bruno P, Enkerli J, Campos-Herrera R, Grabenweger G, Maurhofer M. When Competitors Join Forces: Consortia of Entomopathogenic Microorganisms Increase Killing Speed and Mortality in Leaf- and Root-Feeding Insect Hosts. MICROBIAL ECOLOGY 2023; 86:1947-1960. [PMID: 36849610 PMCID: PMC10497674 DOI: 10.1007/s00248-023-02191-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Combining different biocontrol agents (BCA) is an approach to increase efficacy and reliability of biological control. If several BCA are applied together, they have to be compatible and ideally work together. We studied the interaction of a previously selected BCA consortium of entomopathogenic pseudomonads (Pseudomonas chlororaphis), nematodes (Steinernema feltiae associated with Xenorhabdus bovienii), and fungi (Metarhizium brunneum). We monitored the infection course in a leaf- (Pieris brassicae) and a root-feeding (Diabrotica balteata) pest insect after simultaneous application of the three BCA as well as their interactions inside the larvae in a laboratory setting. The triple combination caused the highest mortality and increased killing speed compared to single applications against both pests. Improved efficacy against P. brassicae was mainly caused by the pseudomonad-nematode combination, whereas the nematode-fungus combination accelerated killing of D. balteata. Co-monitoring of the three BCA and the nematode-associated Xenorhabdus symbionts revealed that the four organisms are able to co-infect the same larva. However, with advancing decay of the cadaver there is increasing competition and cadaver colonization is clearly dominated by the pseudomonads, which are known for their high competitivity in the plant rhizosphere. Altogether, the combination of the three BCA increased killing efficacy against a Coleopteran and a Lepidopteran pest which indicates that this consortium could be applied successfully against a variety of insect pests.
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Affiliation(s)
- Anna Spescha
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
| | - Maria Zwyssig
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Mathias Hess Hermida
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Research Group Extension Arable Crops, Agroscope, Zurich, Switzerland
| | - Aurélie Moix
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Pamela Bruno
- Division of Agricultural Entomology, Department of Crop Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jürg Enkerli
- Research Group Molecular Ecology, Agroscope, Zurich, Switzerland
| | - Raquel Campos-Herrera
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC, Universidad de La Rioja, Gobierno de La Rioja, Logroño, Spain
| | | | - Monika Maurhofer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
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Garrido-Sanz D, Vesga P, Heiman CM, Altenried A, Keel C, Vacheron J. Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens. THE ISME JOURNAL 2023; 17:1369-1381. [PMID: 37311938 PMCID: PMC10432460 DOI: 10.1038/s41396-023-01451-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
Strains belonging to the Pseudomonas protegens phylogenomic subgroup have long been known for their beneficial association with plant roots, notably antagonising soilborne phytopathogens. Interestingly, they can also infect and kill pest insects, emphasising their interest as biocontrol agents. In the present study, we used all available Pseudomonas genomes to reassess the phylogeny of this subgroup. Clustering analysis revealed the presence of 12 distinct species, many of which were previously unknown. The differences between these species also extend to the phenotypic level. Most of the species were able to antagonise two soilborne phytopathogens, Fusarium graminearum and Pythium ultimum, and to kill the plant pest insect Pieris brassicae in feeding and systemic infection assays. However, four strains failed to do so, likely as a consequence of adaptation to particular niches. The absence of the insecticidal Fit toxin explained the non-pathogenic behaviour of the four strains towards Pieris brassicae. Further analyses of the Fit toxin genomic island evidence that the loss of this toxin is related to non-insecticidal niche specialisation. This work expands the knowledge on the growing Pseudomonas protegens subgroup and suggests that loss of phytopathogen inhibition and pest insect killing abilities in some of these bacteria may be linked to species diversification processes involving adaptation to particular niches. Our work sheds light on the important ecological consequences of gain and loss dynamics for functions involved in pathogenic host interactions of environmental bacteria.
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Affiliation(s)
- Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Pilar Vesga
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Aline Altenried
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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8
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Abstract
Prokaryotic and eukaryotic microbial symbiotic communities span through kingdoms. The vast microbial gene pool extends the host genome and supports adaptations to changing environmental conditions. Plants are versatile hosts for the symbionts, carrying microbes on the surface, inside tissues, and even within the cells. Insects are equally abundantly colonized by microbial symbionts on the exoskeleton, in the gut, in the hemocoel, and inside the cells. The insect gut is a prolific environment, but it is selective on the microbial species that enter with food. Plants and insects are often highly dependent on each other and frequently interact. Regardless of the accumulating evidence on the microbiomes of both organisms, it remains unclear how much they exchange and modify each other's microbiomes. In this review, we approach this question from the point of view of herbivores that feed on plants, with a special focus on the forest ecosystems. After a brief introduction to the subject, we concentrate on the plant microbiome, the overlap between plant and insect microbial communities, and how the exchange and modification of microbiomes affects the fitness of each host.
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9
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Ogier JC, Akhurst R, Boemare N, Gaudriault S. The endosymbiont and the second bacterial circle of entomopathogenic nematodes. Trends Microbiol 2023; 31:629-643. [PMID: 36801155 DOI: 10.1016/j.tim.2023.01.004] [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: 07/20/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/19/2023]
Abstract
Single host-symbiont interactions should be reconsidered from the perspective of the pathobiome. We revisit here the interactions between entomopathogenic nematodes (EPNs) and their microbiota. We first describe the discovery of these EPNs and their bacterial endosymbionts. We also consider EPN-like nematodes and their putative symbionts. Recent high-throughput sequencing studies have shown that EPNs and EPN-like nematodes are also associated with other bacterial communities, referred to here as the second bacterial circle of EPNs. Current findings suggest that some members of this second bacterial circle contribute to the pathogenic success of nematodes. We suggest that the endosymbiont and the second bacterial circle delimit an EPN pathobiome.
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Affiliation(s)
| | | | - Noël Boemare
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
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10
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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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11
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Hamze R, Nuvoli MT, Pirino C, Ruiu L. Compatibility of the bacterial entomopathogen Pseudomonas protegens with the natural predator Chrysoperla carnea (Neuroptera: Chrysopidae). J Invertebr Pathol 2022; 194:107828. [PMID: 36087780 DOI: 10.1016/j.jip.2022.107828] [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: 07/14/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/15/2022]
Abstract
The susceptibility of the green lacewing Chrysoperla carnea to the soil-dwelling bacterial entomopathogen Pseudomonas protegens CHA0 was investigated in this study. Laboratory bioassays were conducted on larval instars exposed to different bacterial concentrations by both direct feeding and indirectly by offering a pre-treated insect prey. Potential toxicity was assessed through dose-response bioassays, while possible sublethal effects were evaluated on immature development time and the reproductive performance (fecundity) of adults emerging from treated juveniles. As a result, no significant effects were observed on larval survival and development in a comparison between treated and untreated (control) groups. No significant impact on adult emergence and no detrimental effects on female fecundity were detected. Everything considered, the use of P. protegens in the agroecosystem appears to be compatible with chrysopids.
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Affiliation(s)
- Rim Hamze
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Maria Tiziana Nuvoli
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Carolina Pirino
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Luca Ruiu
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100 Sassari, Italy.
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12
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Lee JH, Anderson AJ, Kim YC. Root-Associated Bacteria Are Biocontrol Agents for Multiple Plant Pests. Microorganisms 2022; 10:microorganisms10051053. [PMID: 35630495 PMCID: PMC9146382 DOI: 10.3390/microorganisms10051053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Biological control is an important process for sustainable plant production, and this trait is found in many plant-associated microbes. This study reviews microbes that could be formulated into pesticides active against various microbial plant pathogens as well as damaging insects or nematodes. The focus is on the beneficial microbes that colonize the rhizosphere where, through various mechanisms, they promote healthy plant growth. Although these microbes have adapted to cohabit root tissues without causing disease, they are pathogenic to plant pathogens, including microbes, insects, and nematodes. The cocktail of metabolites released from the beneficial strains inhibits the growth of certain bacterial and fungal plant pathogens and participates in insect and nematode toxicity. There is a reinforcement of plant health through the systemic induction of defenses against pathogen attack and abiotic stress in the plant; metabolites in the beneficial microbial cocktail function in triggering the plant defenses. The review discusses a wide range of metabolites involved in plant protection through biocontrol in the rhizosphere. The focus is on the beneficial firmicutes and pseudomonads, because of the extensive studies with these isolates. The review evaluates how culture conditions can be optimized to provide formulations containing the preformed active metabolites for rapid control, with or without viable microbial cells as plant inocula, to boost plant productivity in field situations.
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Affiliation(s)
- Jang Hoon Lee
- Agricultural Solutions, BASF Korea Ltd., Seoul 04518, Korea;
| | - Anne J. Anderson
- Department of Biological Engineering, Utah State University, Logan, UT 84322, USA;
| | - Young Cheol Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
- Correspondence:
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13
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Zhou F, Wu X, Gao Y, Fan S, Zhou H, Zhang X. Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates. Front Microbiol 2022; 13:878409. [PMID: 35663868 PMCID: PMC9159939 DOI: 10.3389/fmicb.2022.878409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/29/2022] [Indexed: 01/09/2023] Open
Abstract
Application of plant artificial cultivation substrates lead to alteration of rhizosphere environment. Whether this alteration could lead to root microbiome variation was limitedly investigated. This work aims to determine the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates and predict corresponding function of these different root bacterial microbiota. Cucumber root samples cultivated with two artificial cultivation substrates and greenhouse soils were prepared. Subsequently, high throughput sequencing and bioinformatics analysis were applicated to compare the root bacterial diversity of cucumber cultivated in different substrates and their corresponding function. In total, 311,039 sequences were obtained, and they were annotated to 42 operational taxonomic units (OTUs), belonging to 28 genera, 18 families, 12 orders, four classes, and three phyla. The α and β diversity of samples from the two cultivation substrates and greenhouse soils were significantly different. Only 2-3 bacterial species were found to be discrepancy between cucumber root samples from artificial cultivation substrates and from greenhouse soils. The relative abundance of genus Asticcacaulis, Methylophilus, Massilia, Dyella, and Devosia in samples of artificial cultivation substrates was significantly higher than that of soils, while the relative abundance of genus Phenylobacterium, Noviherbaspirillum, and Arenimonas was significantly lower than that of soils. Besides, compared to cucumber root bacterial community cultivated in soils, the abundance of synthetic pathways for flavonoids and flavonols, bile acids, indole alkaloids, lactose, and neolactose increased by 41.6-, 28.7-, 5.9-, and 5.5-fold, respectively, in the bacterial community of the substrate 1-cultivated roots, and the abundance of clavulanic acid, receptor interaction, sesquiterpenoid, bile acid, flavonoid and flavonol, indole alkaloid, lactose, and neolactose synthetic pathways increased by 42.3-, 32.4-, 32.4-, 13.9-, 10.3-, 6.3-, and 5.2-fold, respectively, in the bacterial community of the substrate two-cultivated roots. This paper verified the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates. Besides, the corresponding function difference of these different root bacterial microbiota was predicted. This work would provide theoretical support for discovering microbial resources and building artificial microbial flora.
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Affiliation(s)
| | | | | | | | | | - Xinjian Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji’nan, China
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14
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Matilla MA, Roca A. Multi-host lifestyle in plant-beneficial bacteria: an evolutionary advantage for survival and dispersal? Environ Microbiol 2022; 24:3307-3309. [PMID: 35411622 PMCID: PMC9541277 DOI: 10.1111/1462-2920.16002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Amalia Roca
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, Granada, 18071, Spain
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