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Li Z, Lin Y, Song F, Zheng R, Huang Q. Isolation and characterization of Paenibacillus peoriae JC-3jx from Dendrobium nobile. Biotechniques 2024; 76:192-202. [PMID: 38469872 DOI: 10.2144/btn-2023-0083] [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: 03/13/2024] Open
Abstract
Dendrobium is a rich source of high-value natural components. Endophytic fungi are well studied, yet bacteria research is limited. In this study, endophytic bacteria from Dendrobium nobile were isolated using an improved method, showing inhibition of pathogens and growth promotion. JC-3jx, identified as Paenibacillus peoriae, exhibited significant inhibitory activity against tested fungi and bacteria, including Escherichia coli. JC-3jx also promoted corn seed rooting and Dendrobium growth, highlighting its excellent biocontrol and growth-promoting potential.
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Affiliation(s)
- ZhiPing Li
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - Yuan Lin
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - FeiFei Song
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - RuoNan Zheng
- Department of Health Food, Fujian Vocational College of Bioengineering, Fuzhou, 350000, PR China
| | - QinGeng Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, 350108, PR China
- Qingyuan One Alive Institute of Biological Research Co., Ltd, Qingyuan, 500112, PR China
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Han Z, Zhang Y, Di C, Bi H, Pan K. Application of Rice Straw Inhibits Clubroot Disease by Regulating the Microbial Community in Soil. Microorganisms 2024; 12:717. [PMID: 38674661 PMCID: PMC11051980 DOI: 10.3390/microorganisms12040717] [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: 01/16/2024] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Straw return is an effective agricultural management practice for alleviating soil sickness, but only a few studies have focused on the incorporation of straw with deep plowing and rotary tillage practices in vegetable production. To determine the effects of rice straw return on Chinese cabbage clubroot, a field experiment for three consecutive years in the same area was performed. Soil microbial high-throughput sequencing, quantitative real-time polymerase chain reaction (PCR) and other methods were used to detect Chinese cabbage plant growth, clubroot occurrence, soil chemical properties and soil microbial diversity and abundance. The results showed that straw addition could significantly reduce the clubroot disease incidence. Through Illumina Miseq sequencing, the diversity of the fungi decreased obviously. The relative abundance of the phyla Proteobacteria and Firmicutes was strikingly reduced, while that of Chloroflexi was significantly increased. Redundancy analysis suggests that soil properties may also affect the soil microbial composition; changes in the microbial structure of bacteria and fungi were associated with the available phosphorus. In conclusion, the continuous addition of rice straw can promote the growth and control the occurrence of clubroot, which is closely related to the microbial composition, and the inhibition effect is proportional to the age of addition.
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Affiliation(s)
- Zhe Han
- Institute of Agricultural Remote Sensing and Information, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Z.H.); (H.B.)
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Program, Harbin 150086, China
| | - Yiping Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (C.D.)
| | - Chengqian Di
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (C.D.)
| | - Hongwen Bi
- Institute of Agricultural Remote Sensing and Information, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (Z.H.); (H.B.)
| | - Kai Pan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (C.D.)
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Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024:S0966-842X(24)00043-X. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.
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Affiliation(s)
- Chiara A Berruto
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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Shi H, Yang J, Li Q, PinChu C, Song Z, Yang H, Luo Y, Liu C, Fan W. Diversity and correlation analysis of different root exudates on the regulation of microbial structure and function in soil planted with Panax notoginseng. Front Microbiol 2023; 14:1282689. [PMID: 38125568 PMCID: PMC10731274 DOI: 10.3389/fmicb.2023.1282689] [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: 08/28/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction Specific interactions between root exudates and soil microorganisms has been proposed as one of the reasons accounting for the continuous cropping obstacle (CCO) of Panax notoginseng. However, rotation of other crops on soils planted with P. notoginseng (SPP) did not show CCO, suggesting that root exudates of different crops differentially regulate soil microorganisms in SPP. Methods Here, we investigated the microbial community structure and specific interaction mechanisms of the root exudates of the four plant species, P. notoginseng (Pn), Zea mays (Zm), Nicotiana tabacum (Nt) and Perilla frutescens (Pf), in SPP by static soil culture experiment. Results The results showed that the chemical diversity of root exudates varied significantly among the four plant species. Pn had the highest number of unique root exudates, followed by Nt, Zm and Pf. Terpenoids, flavonoids, alkaloids and phenolic acids were the most abundant differentially accumulated metabolites (DAMs) in Pn, Nt, Zm and Pf, respectively. However, lipids were the most abundant common DAMs among Zm Nt and Pf. Pn root exudates decreased the relative abundance of bacteria, but increased that of fungi. While specific DAMs in Pn enriched Phenylobacterium_zucineum, Sphingobium_yanoikuyae, Ophiostoma_ulmi and functional pathways of Nucleotide excision repair, Streptomycin biosynthesis, Cell cycle-Caulobacter and Glycolysis/Gluconeogenesis, it inhibited Paraburkholderia _caledonica and Ralstonia_pickettii. However, common DAMs in Zm, Nt and Pf had opposite effects. Moreover, common DAMs in Zm, Nt and Pf enriched Ralstonia_pseudosolanacearum and functional pathway of Xylene degradation; unique DAMs in Zm enriched Talaromyces_purcureogeneus, while inhibiting Fusarium_tricinctum and functional pathways of Nucleotide excision repair and Alanine, aspartate and glutamate metabolism; unique DAMs in Pf enriched Synchytrium_taraxaci. Discussion The core strains identified that interact with different root exudates will provide key clues for regulation of soil microorganisms in P. notoginseng cultivation to alleviate CCO.
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Affiliation(s)
- Huineng Shi
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Jianli Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Qi Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Cier PinChu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Zhanhua Song
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Honglei Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Yu Luo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Chunlan Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
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Park HE, Nebert L, King RM, Busby P, Myers JR. Influence of organic plant breeding on the rhizosphere microbiome of common bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1251919. [PMID: 37954997 PMCID: PMC10634438 DOI: 10.3389/fpls.2023.1251919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023]
Abstract
Introduction We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history. Methods Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set. Results Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens. Discussion The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.
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Affiliation(s)
- Hayley E. Park
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Lucas Nebert
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Ryan M. King
- National Clonal Germplasm Repository, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Posy Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - James R. Myers
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
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Gruppuso L, Receveur JP, Fenoglio S, Bona F, Benbow ME. Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways. MICROBIAL ECOLOGY 2023; 86:1499-1512. [PMID: 36646914 PMCID: PMC10497695 DOI: 10.1007/s00248-023-02169-y] [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: 06/20/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.
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Affiliation(s)
- L Gruppuso
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy.
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy.
| | - J P Receveur
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - S Fenoglio
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - F Bona
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - M E Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
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Ding J, Wang N, Liu P, Liu B, Zhu Y, Mao J, Wang Y, Ding X, Yang H, Wei Y, Li J, Ding GC. Bacterial wilt suppressive composts: Significance of rhizosphere microbiome. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 169:179-185. [PMID: 37453305 DOI: 10.1016/j.wasman.2023.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Composts are often suppressive to several plant diseases, including the devastating bacterial wilt caused by Ralstonia solanacearum. However, the underlying mechanisms are still unclear. Herein, we carried out an experiment with 38 composts collected from different factories in China to study the interlinking among bacterial wilt suppression, the physicochemical properties and bacterial community of the compost, and bacterial community in the rhizosphere of tomato fertilized by compost. Totally 26 composts were suppressive to bacterial wilt, while six composts stimulated the disease. The control efficiency was neither correlated with physicochemical properties (TC, TN, P and K, pH or GI) nor bacterial community of compost, but with rhizosphere bacterial community (r = 0.17, p = 0.016). The control efficiency was also positive correlated with taxa (Rhizobium, Aeromicrobium) known suppressive to R. solanacearum. The mushroom spent or cow manure, from which the two composts were 100% and 77% in control efficiencies against bacterial wilt respectively were subject to a pilot-scale composting reaction. The reproduced composts from mushroom spent or cow manure were only 57% and 23% effective on the control of bacterial wilt, respectively. The analysis of bacterial communities revealed that the relative abundances of R. solanacearum were 28.4% for the control, but only 7.8%-7.9% for compost fertilized tomatoes. The compost from mushroom spent also exerted a strong effect on rhizosphere bacterial community. Taken together, most composts were suppressive to bacterial wilt possibly also by modifying rhizosphere bacterial community towards inhibiting the colonization of R. solanacearum and selecting for beneficial genera of Proteobacteria, Bacteroidetes and Actinobacteria.
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Affiliation(s)
- Jia Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ning Wang
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Pingping Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Baoju Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Yuelin Zhu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Jing Mao
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Yue Wang
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Xiaoyan Ding
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Hefa Yang
- Quzhou Experimental Station, China Agricultural University, 057250 Hebei Province, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China.
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Zhang X, Zhao W, Kou Y, Fang K, Liu Y, He H, Liu Q. The contrasting responses of abundant and rare microbial community structures and co-occurrence networks to secondary forest succession in the subalpine region. Front Microbiol 2023; 14:1177239. [PMID: 37250033 PMCID: PMC10213230 DOI: 10.3389/fmicb.2023.1177239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Knowledge of variations in abundant and rare soil microbial communities and interactions during secondary forest succession is lacking. Soil samples were gathered from different secondary successional stages (grassland, shrubland, and secondary forest) to study the responses of abundant and rare bacterial and fungal communities, interactions and driving factors to secondary forest succession by Illumina sequencing of the 16S and ITS rRNA genes. The results showed that the α-diversities (Shannon index) of abundant bacteria and fungi revealed no significant changes during secondary forest succession, but increased significantly for rare bacteria. The abundant and rare bacterial and fungal β-diversities changed significantly during secondary forest succession. Network analysis showed no obvious changes in the topological properties (nodes, links, and average degree) of abundant microbial networks during secondary forest succession. In contrast, these properties of the rare microbial networks in the secondary forest were higher than those in the grassland and shrubland, indicating that rare microbial networks are more responsive to secondary forest succession than abundant microorganisms. Additionally, rare microbial networks revealed more microbial interactions and greater network complexity than abundant microbial networks due to their higher numbers of nodes and links. The keystone species differed between the abundant and rare microbial networks and consisted of 1 and 48 keystone taxa in the abundant and rare microbial networks, respectively. Soil TP was the most important influencing factor of abundant and rare bacterial communities. Successional stages and plant richness had the most important influences on abundant and rare fungal communities, respectively. C:P, SM and N:P were mainly related to abundant and rare microbial network topological properties. Our study indicates that abundant and rare microbial communities, interactions and driving factors respond differently to secondary forest succession.
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Affiliation(s)
- Xiaoying Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenqiang Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yongping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Kai Fang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yanjiao Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Heliang He
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Zhao X, Zhu D, Tan J, Wang R, Qi G. Cooperative Action of Fulvic Acid and Bacillus paralicheniformis Ferment in Regulating Soil Microbiota and Improving Soil Fertility and Plant Resistance to Bacterial Wilt Disease. Microbiol Spectr 2023; 11:e0407922. [PMID: 36861975 PMCID: PMC10100657 DOI: 10.1128/spectrum.04079-22] [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: 10/06/2022] [Accepted: 01/28/2023] [Indexed: 03/03/2023] Open
Abstract
Excessive continuous cropping and soil degradation, such as acidification, hardening, fertility decline, and the degradation of microbial community, lead to the epidemic of soilborne diseases and cause great loss in agriculture production. Application of fulvic acid can improve the growth and yield of various crops and effectively suppress soilborne plant diseases. Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid is used to remove the organic acid that can cause soil acidification and increase the fertilizer effect of fulvic acid and the effect of improving soil quality and inhibiting soilborne disease. In field experiments, the application of fulvic acid and Bacillus paralicheniformis ferment effectively reduced the incidence of bacterial wilt disease and improved soil fertility. Both fulvic acid powder and B. paralicheniformis ferment improved soil microbial diversity and increased the complexity and stability of the microbial network. For B. paralicheniformis ferment, the molecular weight of poly-gamma-glutamic acid became smaller after heating, which could better improve the soil microbial community and network structure. In fulvic acid and B. paralicheniformis ferment-treated soils, the synergistic interaction between microorganisms increased and the number of keystone microorganisms increased, which included antagonistic bacteria and plant growth-promoting bacteria. Changes in the microbial community and network structure were the main reason for the reduced incidence of bacterial wilt disease. Application of fulvic acid and Bacillus paralicheniformis ferment improved soil physicochemical properties and effectively controlled bacterial wilt disease by changing microbial community and network structure and enriching antagonistic and beneficial bacteria. IMPORTANCE Continuous cropping tobacco has led to soil degradation and caused soilborne bacterial wilt disease. Fulvic acid as a biostimulator was applied to restore soil and control bacterial wilt disease. For improving its effect, fulvic acid was fermented with Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid. Fulvic acid and B. paralicheniformis ferment inhibited bacterial wilt disease, improved soil quality, enriched beneficial bacteria, and increased microbial diversity and microbial network complexity. Some keystone microorganisms in fulvic acid and B. paralicheniformis ferment-treated soils had potential antimicrobial activity and plant growth-promoting attributes. Fulvic acid and B. paralicheniformis 285-3 ferment could be used to restore soil quality and microbiota and control bacterial wilt disease. This study found new biomaterial to control soilborne bacterial disease by combining fulvic acid and poly-gamma-glutamic acid application.
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Affiliation(s)
- Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Di Zhu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jun Tan
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Rui Wang
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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10
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Berrios L. Examining the genomic features of human and plant-associated Burkholderia strains. Arch Microbiol 2022; 204:335. [PMID: 35587294 DOI: 10.1007/s00203-022-02953-3] [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: 06/14/2021] [Revised: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 11/28/2022]
Abstract
Humans and plants have evolved in the near omnipresence of a microbial milieu, and the factors that govern host-microbe interactions continue to require scientific exploration. To better understand if and to what degree patterns between microbial genomic features and host association (i.e., human and plant) exist, I analyzed the genomes of select Burkholderia strains-a bacterial genus comprised of both human and plant-associated strains-that were isolated from either humans or plants. To this end, I uncovered host-specific, genomic patterns related to metabolic pathway potentials in addition to convergent features that may be related to pathogenic overlap between hosts. Together, these findings detail the genomic associations of human and plant-associated Burkholderia strains and provide a framework for future investigations that seek to link host-host transmission potentials.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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Berrios L, Rentsch JD. Linking Reactive Oxygen Species (ROS) to Abiotic and Biotic Feedbacks in Plant Microbiomes: The Dose Makes the Poison. Int J Mol Sci 2022; 23:ijms23084402. [PMID: 35457220 PMCID: PMC9030523 DOI: 10.3390/ijms23084402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
In nature, plants develop in complex, adaptive environments. Plants must therefore respond efficiently to environmental stressors to maintain homeostasis and enhance their fitness. Although many coordinated processes remain integral for achieving homeostasis and driving plant development, reactive oxygen species (ROS) function as critical, fast-acting orchestrators that link abiotic and biotic responses to plant homeostasis and development. In addition to the suite of enzymatic and non-enzymatic ROS processing pathways that plants possess, they also rely on their microbiota to buffer and maintain the oxidative window needed to balance anabolic and catabolic processes. Strong evidence has been communicated recently that links ROS regulation to the aggregated function(s) of commensal microbiota and plant-growth-promoting microbes. To date, many reports have put forth insightful syntheses that either detail ROS regulation across plant development (independent of plant microbiota) or examine abiotic–biotic feedbacks in plant microbiomes (independent of clear emphases on ROS regulation). Here we provide a novel synthesis that incorporates recent findings regarding ROS and plant development in the context of both microbiota regulation and plant-associated microbes. Specifically, we discuss various roles of ROS across plant development to strengthen the links between plant microbiome functioning and ROS regulation for both basic and applied research aims.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence:
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC 29502, USA;
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Dysbiosis in the Rhizosphere Microbiome of Standing Dead Korean Fir (Abies koreana). PLANTS 2022; 11:plants11070990. [PMID: 35406970 PMCID: PMC9002731 DOI: 10.3390/plants11070990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 11/25/2022]
Abstract
The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work.
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