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Chakraborty S, Venkataraman M, Infante V, Pfleger BF, Ané JM. Scripting a new dialogue between diazotrophs and crops. Trends Microbiol 2024; 32:577-589. [PMID: 37770375 PMCID: PMC10950843 DOI: 10.1016/j.tim.2023.08.007] [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: 05/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023]
Abstract
Diazotrophs are bacteria and archaea that can reduce atmospheric dinitrogen (N2) into ammonium. Plant-diazotroph interactions have been explored for over a century as a nitrogen (N) source for crops to improve agricultural productivity and sustainability. This scientific quest has generated much information about the molecular mechanisms underlying the function, assembly, and regulation of nitrogenase, ammonium assimilation, and plant-diazotroph interactions. This review presents various approaches to manipulating N fixation activity, ammonium release by diazotrophs, and plant-diazotroph interactions. We discuss the research avenues explored in this area, propose potential future routes, emphasizing engineering at the metabolic level via biorthogonal signaling, and conclude by highlighting the importance of biocontrol measures and public acceptance.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
| | - Maya Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Agronomy, University of Wisconsin - Madison, Madison, WI, USA.
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2
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Pal G, Saxena S, Kumar K, Verma A, Kumar D, Shukla P, Pandey A, White J, Verma SK. Seed endophytic bacterium Lysinibacillus sp. (ZM1) from maize (Zea mays L.) shapes its root architecture through modulation of auxin biosynthesis and nitrogen metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108731. [PMID: 38761545 DOI: 10.1016/j.plaphy.2024.108731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Seed endophytic bacteria have been shown to promote the growth and development of numerous plants. However, the underlying mechanism still needs to be better understood. The present study aims to investigate the role of a seed endophytic bacterium Lysinibacillus sp. (ZM1) in promoting plant growth and shaping the root architecture of maize seedlings. The study explores how bacteria-mediated auxin biosynthesis and nitrogen metabolism affect plant growth promotion and shape the root architecture of maize seedlings. The results demonstrate that ZM1 inoculation significantly enhances root length, root biomass, and the number of seminal roots in maize seedlings. Additionally, the treated seedlings exhibit increased shoot biomass and higher levels of photosynthetic pigments. Confocal laser scanning microscopy (CLSM) analysis revealed extensive colonization of ZM1 on root hairs, as well as in the cortical and stellar regions of the root. Furthermore, LC-MS analysis demonstrated elevated auxin content in the roots of the ZM1 treated maize seedlings compared to the uninoculated control. Inoculation with ZM1 significantly increased the levels of endogenous ammonium content, GS, and GOGAT enzyme activities in the roots of treated maize seedlings compared to the control, indicating enhanced nitrogen metabolism. Furthermore, inoculation of bacteria under nitrogen-deficient conditions enhanced plant growth, as evidenced by increased root shoot length, fresh and dry weights, average number of seminal roots, and content of photosynthetic pigments. Transcript analysis indicated upregulation of auxin biosynthetic genes, along with genes involved in nitrogen metabolism at different time points in roots of ZM1-treated maize seedlings. Collectively, our findings highlight the positive impact of Lysinibacillus sp. ZM1 inoculation on maize seeds by improving root architecture through modulation of auxin biosynthesis and affecting various nitrogen metabolism related parameters. These findings provide valuable insights into the potential utilization of seed endophytic bacteria as biofertilizers to enhance plant growth and yield in nutrient deficient soils.
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Affiliation(s)
- Gaurav Pal
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 276957612, USA.
| | - Samiksha Saxena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanchan Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Anand Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Deepak Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Pooja Shukla
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - James White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA
| | - Satish K Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Jin Y, Chen Z, White JF, Malik K, Li C. Interactions between Epichloë endophyte and the plant microbiome impact nitrogen responses in host Achnatherum inebrians plants. Microbiol Spectr 2024; 12:e0257423. [PMID: 38488391 PMCID: PMC10986526 DOI: 10.1128/spectrum.02574-23] [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: 06/20/2023] [Accepted: 01/24/2024] [Indexed: 04/06/2024] Open
Abstract
The clavicipitaceous fungus Epichloë gansuensis forms symbiotic associations with drunken horse grass (Achnatherum inebrians), providing biotic and abiotic stress protection to its host. However, it is unclear how E. gansuensis affects the assembly of host plant-associated bacterial communities after ammonium nitrogen (NH4+-N) treatment. We examined the shoot- and root-associated bacterial microbiota and root metabolites of A. inebrians when infected (I) or uninfected (F) with E. gansuensis endophyte. The results showed more pronounced NH4+-N-induced microbial and metabolic changes in the endophyte-infected plants compared to the endophyte-free plants. E. gansuensis significantly altered bacterial community composition and β-diversity in shoots and roots and increased bacterial α-diversity under NH4+-N treatment. The relative abundance of 117 and 157 root metabolites significantly changed with E. gansuensis infection under water and NH4+-N treatment compared to endophyte-free plants. Root bacterial community composition was significantly related to the abundance of the top 30 metabolites [variable importance in the projection (VIP) > 2 and VIP > 3] contributing to differences between I and F plants, especially alkaloids. The correlation network between root microbiome and metabolites was complex. Microorganisms in the Proteobacteria and Firmicutes phyla were significantly associated with the R00693 metabolic reaction of cysteine and methionine metabolism. Co-metabolism network analysis revealed common metabolites between host plants and microorganisms.IMPORTANCEOur results suggest that the effect of endophyte infection is sensitive to nitrogen availability. Endophyte symbiosis altered the composition of shoot and root bacterial communities, increasing bacterial diversity. There was also a change in the class and relative abundance of metabolites. We found a complex co-occurrence network between root microorganisms and metabolites, with some metabolites shared between the host plant and its microbiome. The precise ecological function of the metabolites produced in response to endophyte infection remains unknown. However, some of these compounds may facilitate plant-microbe symbiosis by increasing the uptake of beneficial soil bacteria into plant tissues. Overall, these findings advance our understanding of the interactions between the microbiome, metabolome, and endophyte symbiosis in grasses. The results provide critical insight into the mechanisms by which the plant microbiome responds to nutrient stress in the presence of fungal endophytes.
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Affiliation(s)
- Yuanyuan Jin
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhenjiang Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - James F. White
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, USA
| | - Kamran Malik
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chunjie Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Zhang X, Wu Y, Liu S, Li J, Jiang Z, Luo H, Huang X. Plant growth and development of tropical seagrass determined rhizodeposition and its related microbial community. MARINE POLLUTION BULLETIN 2024; 199:115940. [PMID: 38150979 DOI: 10.1016/j.marpolbul.2023.115940] [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: 10/07/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the South China Sea. We found that the quantity and quality of root exudates varied seasonally, with higher exudation rates and more bioavailable dissolved organic matter (DOM) during the seedling and vegetative stages in spring and summer. Using Illumina NovaSeq sequencing, we analyzed bacterial and fungal communities and discovered that microbial diversity and composition were influenced by root exudate characteristics s and seagrass biomass, which were strongly dependent on seagrass growth stages. Certain bacterial groups, such as Ruegeria, Sulfurovum, Photobacterium, and Ralstonia were closely associated with root exudation and may contribute to sulfur cycling, nitrogen fixation, and carbon remineralization, which were important for plant early development. Similarly, specific fungal taxa, including Astraeus, Alternaria, Rocella, and Tomentella, were enriched in spring and summer and showed growth-promoting abilities. Overall, our study suggests that seagrass secretes different compounds in its exudates at various developmental stages, shaping the rhizosphere microbial assemblages.
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Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinlong Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxue Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Wippel K. Plant and microbial features governing an endophytic lifestyle. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102483. [PMID: 37939457 DOI: 10.1016/j.pbi.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.
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Affiliation(s)
- Kathrin Wippel
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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6
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Karnwal A, Dohroo A, Malik T. Unveiling the Potential of Bioinoculants and Nanoparticles in Sustainable Agriculture for Enhanced Plant Growth and Food Security. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6911851. [PMID: 38075309 PMCID: PMC10699995 DOI: 10.1155/2023/6911851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023]
Abstract
The increasing public concern over the negative impacts of chemical fertilizers and pesticides on food security and sustainability has led to exploring innovative methods that offer both environmental and agricultural benefits. One such innovative approach is using plant-growth-promoting bioinoculants that involve bacteria, fungi, and algae. These living microorganisms are applied to soil, seeds, or plant surfaces and can enhance plant development by increasing nutrient availability and defense against plant pathogens. However, the application of biofertilizers in the field faced many challenges and required conjunction with innovative delivering approaches. Nanotechnology has gained significant attention in recent years due to its numerous applications in various fields, such as medicine, drug development, catalysis, energy, and materials. Nanoparticles with small sizes and large surface areas (1-100 nm) have numerous potential functions. In sustainable agriculture, the development of nanochemicals has shown promise as agents for plant growth, fertilizers, and pesticides. The use of nanomaterials is being considered as a solution to control plant pests, including insects, fungi, and weeds. In the food industry, nanoparticles are used as antimicrobial agents in food packaging, with silver nanomaterials being particularly interesting. However, many nanoparticles (Ag, Fe, Cu, Si, Al, Zn, ZnO, TiO2, CeO2, Al2O3, and carbon nanotubes) have been reported to negatively affect plant growth. This review focuses on the effects of nanoparticles on beneficial plant bacteria and their ability to promote plant growth. Implementing novel sustainable strategies in agriculture, biofertilizers, and nanoparticles could be a promising solution to achieve sustainable food production while reducing the negative environmental impacts.
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Affiliation(s)
- Arun Karnwal
- Department of Microbiology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Aradhana Dohroo
- Baddi University of Emerging Sciences and Technologies, Baddi, Himachal Pradesh 173405, India
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University, Ethiopia
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Pereira-Dias L, Oliveira-Pinto PR, Fernandes JO, Regalado L, Mendes R, Teixeira C, Mariz-Ponte N, Gomes P, Santos C. Peptaibiotics: Harnessing the potential of microbial secondary metabolites for mitigation of plant pathogens. Biotechnol Adv 2023; 68:108223. [PMID: 37536466 DOI: 10.1016/j.biotechadv.2023.108223] [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: 03/06/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Agricultural systems are in need of low-cost, safe antibiotics to protect crops from pests and diseases. Peptaibiotics, a family of linear, membrane-active, amphipathic polypeptides, have been shown to exhibit antibacterial, antifungal, and antiviral activity, and to be inducers of plant resistance against a wide range of phytopathogens. Peptaibiotics belong to the new generation of alternatives to agrochemicals, aligned with the United Nations Sustainable Development Goals and the One Health approach toward ensuring global food security and safety. Despite that, these fungi-derived, non-ribosomal peptides remain surprisingly understudied, especially in agriculture, where only a small number has been tested against a reduced number of phytopathogens. This lack of adoption stems from peptaibiotics' poor water solubility and the difficulty to synthesize and purify them in vitro, which compromises their delivery and inclusion in formulations. In this review, we offer a comprehensive analysis of peptaibiotics' classification, biosynthesis, relevance to plant protection, and mode of action against phytopathogens, along with the techniques enabling researchers to extract, purify, and elucidate their structure, and the databases holding such valuable data. It is also discussed how chemical synthesis and ionic liquids could increase their solubility, how genetic engineering and epigenetics could boost in vitro production, and how omics can reduce screenings' workload through in silico selection of the best candidates. These strategies could turn peptaibiotics into effective, ultra-specific, biodegradable tools for phytopathogen control.
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Affiliation(s)
- Leandro Pereira-Dias
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Paulo R Oliveira-Pinto
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Juliana O Fernandes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Laura Regalado
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rafael Mendes
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Cátia Teixeira
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Nuno Mariz-Ponte
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Conceição Santos
- iB(2) Laboratory, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Sharifsadat SZ, Aghdasi M, Ghanati F, Arzanesh MH. Harmonized biochemical modification of cell walls to get permission for entrance of Azospirillum sp. to rice roots. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111823. [PMID: 37572965 DOI: 10.1016/j.plantsci.2023.111823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/16/2023] [Accepted: 08/08/2023] [Indexed: 08/14/2023]
Abstract
Biological nitrogen-fixation is important in increasing crop efficiency. Azospirillum is a nitrogen-fixing microorganism that naturally coexists with grasses roots. The present study was undertaken to clarify the role of rice root cell walls in the acceptance of two Azospirillum species, alone or in combination with indole-3-acetic acid (IAA) and gibberellic acid (GA3) treatments. Rice seedlings were grown in Yoshida solution for 21 days and then inoculated with A. brasilense and A. irakens in the presence of 0, 0.57, and 1.14 mM of IAA or 0, 0.29, and 0.58 mM GA3 or a combination of 1.14 mM of IAA and 0.58 mM of GA3. The results showed that the amount of hydrogen peroxide, lipid peroxidation, total nitrogen and activity of ferulic acid peroxidase, NADPH oxidase, nitrate reductase, pectin methyl esterase, cellulase, mannanase, xylanase and pectinase were significantly increased in inoculated samples treated with or without phytohormones. The highest activity of these enzymes was observed in A. brasilense- inoculated rice roots in auxin+gibberellin treatment. In the latter, the activity of phenylalanine ammonia lyase and wall ferulic acid peroxidase enzymes, the content of cell wall polysaccharide, lignin, and total phenolic compounds were the least, compared to controls and also with those samples which were inoculated with A. irakens. The results indicate an active role of the wall and its enzymes in allowing bacteria to enter the roots. Understanding this mechanism can improve the methods of inoculating bacteria into plants and increase crop efficiency, which will result in reduced use of chemical fertilizers and their destructive environmental effects.
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Affiliation(s)
| | - Mahnaz Aghdasi
- Laboratory of Plant Physiology, Department Biology, Golestan University, Gorgan, Iran.
| | - Faezeh Ghanati
- Department of Plant Biology, Faculty of Biological Scuience, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hossein Arzanesh
- Department of Soil and Water Research, Golestan's Agricultural and Natural Resources Research Center, Gorgan, Iran
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Bagci I, Suzuki K, Asiloglu R, Harada N. The Application of Organic Matter Temporarily Shifts Carrot Prokaryotic Communities in the Endosphere but Not in the Rhizosphere. Microorganisms 2023; 11:2377. [PMID: 37894035 PMCID: PMC10608867 DOI: 10.3390/microorganisms11102377] [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: 09/01/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Endophytic prokaryotes, bacteria, and archaea, are important microorganisms that benefit host plants by promoting plant growth and reducing stress. The objective of this study was to evaluate temporal shifts in the root endophytic prokaryotic communities associated with carrots (Daucus carota subsp. sativus) and the effect of organic matter application on them. Carrots were grown in a planter under five fertilizer treatments (weed compost, bark compost, cattle manure, chemical fertilizer, and no-fertilizer control) and the compositions of rhizosphere and root endosphere prokaryotic communities were determined via amplicon sequencing analysis targeting the 16S rRNA gene at 60 and 108 days after sowing. The results showed that the rhizosphere prokaryotic community compositions were stable despite different sampling times and fertilizer treatments; however, a greater temporal shift and an effect of the type of organic matter applied were observed in the endosphere prokaryotic communities. The differences in treatments resulted in significant differences in the abundance and Faith pyrogenetic diversity of the endosphere prokaryotic community. Genera, such as Burkholderia, Sphingomonas, and Rhodanobacter, that exhibit plant-growth-promoting and biocontrol activities, were detected regardless of the treatments, suggesting that they may play an important ecological role as the core endophytes in carrot roots.
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Affiliation(s)
- Irem Bagci
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kazuki Suzuki
- Institute of Science and Technology, Niigata University, Niigata 950-2181, Japan; (K.S.); (R.A.)
| | - Rasit Asiloglu
- Institute of Science and Technology, Niigata University, Niigata 950-2181, Japan; (K.S.); (R.A.)
| | - Naoki Harada
- Institute of Science and Technology, Niigata University, Niigata 950-2181, Japan; (K.S.); (R.A.)
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10
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Experimentally Induced Dieback Conditions Limit Phragmites australis Growth. Microorganisms 2023; 11:microorganisms11030639. [PMID: 36985213 PMCID: PMC10054352 DOI: 10.3390/microorganisms11030639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/20/2023] [Accepted: 02/04/2023] [Indexed: 03/06/2023] Open
Abstract
Phragmites australis is a cosmopolitan grass species common in wetland ecosystems across the world. In much of North America, the non-native subspecies of Phragmites threatens wetland biodiversity, hinders recreation, and is a persistent problem for natural resource managers. In other parts of the world, populations are in decline, as Reed Die-Back Syndrome (RDBS) plagues some Phragmites stands in its native range. RDBS is defined by a clumped growth form, stunted root and shoot growth, premature senescence, and shoot death. RDBS has been associated with a build-up of short-chain fatty acids (SCFAs) and altered bacterial and oomycete communities in soils, but the exact causes are unknown. To control invasive Phragmites populations, we sought to develop treatments that mimic the conditions of RDBS. We applied various SCFA treatments at various concentrations to mesocosm soils growing either Phragmites or native wetland plants. We found that the high-concentration SCFA treatments applied weekly induced strong significant declines in above- and belowground biomass of Phragmites. Declines were significant but slightly weaker in native species. In addition, soil bacterial abundance increased, diversity decreased, and bacterial community composition significantly differed following treatments, such that treated pots maintained a higher relative abundance of Pseudomonadaceae and fewer Acidobacteriaceae than untreated pots. Our results suggest that application of SCFAs to Phragmites can lead to stunted plants and altered soil bacterial communities similar to populations affected by RDBS. However, the lack of species-specificity and intensive application rate may not make this treatment ideal as a widespread management tool.
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Chiaranunt P, White JF. Plant Beneficial Bacteria and Their Potential Applications in Vertical Farming Systems. PLANTS (BASEL, SWITZERLAND) 2023; 12:400. [PMID: 36679113 PMCID: PMC9861093 DOI: 10.3390/plants12020400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
In this literature review, we discuss the various functions of beneficial plant bacteria in improving plant nutrition, the defense against biotic and abiotic stress, and hormonal regulation. We also review the recent research on rhizophagy, a nutrient scavenging mechanism in which bacteria enter and exit root cells on a cyclical basis. These concepts are covered in the contexts of soil agriculture and controlled environment agriculture, and they are also used in vertical farming systems. Vertical farming-its advantages and disadvantages over soil agriculture, and the various climatic factors in controlled environment agriculture-is also discussed in relation to plant-bacterial relationships. The different factors under grower control, such as choice of substrate, oxygenation rates, temperature, light, and CO2 supplementation, may influence plant-bacterial interactions in unintended ways. Understanding the specific effects of these environmental factors may inform the best cultural practices and further elucidate the mechanisms by which beneficial bacteria promote plant growth.
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Neelam A, Tabassum S. Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes. MICROMACHINES 2023; 14:195. [PMID: 36677256 PMCID: PMC9866067 DOI: 10.3390/mi14010195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Plant-microbe interactions are critical for ecosystem functioning and driving rhizosphere processes. To fully understand the communication pathways between plants and rhizosphere microbes, it is crucial to measure the numerous processes that occur in the plant and the rhizosphere. The present review first provides an overview of how plants interact with their surrounding microbial communities, and in turn, are affected by them. Next, different optical biosensing technologies that elucidate the plant-microbe interactions and provide pathogenic detection are summarized. Currently, most of the biosensors used for detecting plant parameters or microbial communities in soil are centered around genetically encoded optical and electrochemical biosensors that are often not suitable for field applications. Such sensors require substantial effort and cost to develop and have their limitations. With a particular focus on the detection of root exudates and phytohormones under biotic and abiotic stress conditions, novel low-cost and in-situ biosensors must become available to plant scientists.
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Symbiosis research in the anthropocene: science as usual in unusual times? Symbiosis 2022. [DOI: 10.1007/s13199-022-00892-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants. BIOLOGY 2022; 11:biology11121790. [PMID: 36552299 PMCID: PMC9775861 DOI: 10.3390/biology11121790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants have already been prospected for beneficial microbes, desert plants have been underrepresented in such studies. In this study, we show the growth-promoting potential of five strains of endophytic Pseudomonas sp. isolated from Agave palmeri, an agave from the Sonoran Desert. When inoculated onto Kentucky bluegrass, clover, carrot, coriander, and wheat, endophytic Pseudomonas sp. increased seedling root lengths in all hosts and seedling shoot lengths in Kentucky bluegrass, carrot, and wheat. Transformation of the Pseudomonas sp. strain P3AW to express the fluorescent protein mCherry revealed that Pseudomonas sp. becomes endophytic in non-native hosts and participates in parts of the rhizophagy cycle, a process by which endophytic bacteria cycle between the soil and roots, bringing in nutrients from the soil which are then extracted through reactive oxygen-mediated bacterial degradation in the roots. Tracking of the Pseudomonas sp. strain P3AW also provided evidence for a system of endophyte, or endophyte cell content, transport via the vascular bundle. These results provide further evidence of the rhizophagy cycle in plants and how it relates to growth promotion in plants by biostimulant bacteria.
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Liang D, Bowatte S. Seed endophytic ammonia oxidizing bacteria in Elymus nutans transmit to offspring plants and contribute to nitrification in the root zone. Front Microbiol 2022; 13:1036897. [PMID: 36523826 PMCID: PMC9744808 DOI: 10.3389/fmicb.2022.1036897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Ammonia oxidizing bacteria (AOB) in soil are of great biological importance as they regulate the cycling of N in agroecosystems. Plants are known to harbor AOB but how they occupy the plant is an unresolved question. METHODS Metabarcoding studies were carried out using Illumina MiSeq sequencing to test the potential of seed vectored AOB exchange between plants and soil. RESULTS AND DISCUSSION We found 27 sequences associated with AOB strains belonging to the genera Nitrosospira, Nitrosovibrio, and Nitrosomonas inhabiting Elymus nutans seeds collected from four geographically distanced alpine meadows. Nitrosospira multiformis was the most dominant across the four locations. The AOB community in E. nutans seeds was compared with that of the leaves, roots and soil in one location. Soil and seeds harbored a rich but dissimilar AOB community, and Nitrosospira sp. PJA1, Nitrosospira sp. Nsp17 and Nitrosovibrio sp. RY3C were present in all plant parts and soils. When E. nutans seeds were germinated in sterilized growth medium under greenhouse conditions, the AOB in seeds later appeared in leaves, roots and growth medium, and contributed to nitrification. Testing the AOB community of the second-generation seeds confirmed vertical transmission, but low richness was observed. CONCLUSION These results suggest seed vectored AOB may play a critical role in N cycle.
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Affiliation(s)
- Danni Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Saman Bowatte
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Das PP, Singh KR, Nagpure G, Mansoori A, Singh RP, Ghazi IA, Kumar A, Singh J. Plant-soil-microbes: A tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices. ENVIRONMENTAL RESEARCH 2022; 214:113821. [PMID: 35810815 DOI: 10.1016/j.envres.2022.113821] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/24/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Plants can achieve their proper growth and development with the help of microorganisms associated with them. Plant-associated microbes convert the unavailable nutrients to available form and make them useful for plants. Besides nutrient acquisition, soil microbes also inhibit the pathogens that cause harm to plant growth and induces defense response. Due to the beneficial activities of soil nutrient-microbe-plant interactions, it is necessary to study more on this topic and develop microbial inoculant technology in the agricultural field for better crop improvement. The soil microbes can be engineered, and plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting bacteria (PGPB) technology can be developed as well, as its application can be improved for utilization as biofertilizer, biopesticides, etc., instead of using harmful chemical biofertilizers. Moreover, plant growth-promoting microbe inoculants can enhance crop productivity. Although, scientists have discussed several tools and techniques by omics and gene editing approaches for crop improvement to avoid biotic and abiotic stress and make the plant healthier and more nutritive. However, beneficial soil microbes that help plants with the nutrient acquisition, development, and stress resistance were ignored, and farmers started utilizing chemical fertilizers. Thus, this review attempts to summarize the interaction system of plant microbes, the role of beneficiary soil microbes in the rhizosphere zone, and their role in plant health promotion, particularly in the nutrition acquisition of the plant. The review will also provide a better understanding of soil microbes that can be exploited as biofertilizers and plant growth promoters in the field to create environmentally friendly, sustainable agriculture systems.
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Affiliation(s)
- Prajna Priyadarshini Das
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Kshitij Rb Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 211005, India
| | - Gunjan Nagpure
- Department of Biotechnology, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India
| | - Aadil Mansoori
- Department of Botany, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India
| | - Ravindra Pratap Singh
- Department of Biotechnology, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Anirudh Kumar
- Department of Botany, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, 484887, India.
| | - Jay Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 211005, India.
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Procter M, Kundu B, Sudalaimuthuasari N, AlMaskari RS, Saeed EE, Hazzouri KM, Amiri KMA. Microbiome of Citrullus colocynthis (L.) Schrad. Reveals a Potential Association with Non-Photosynthetic Cyanobacteria. Microorganisms 2022; 10:microorganisms10102083. [PMID: 36296358 PMCID: PMC9607294 DOI: 10.3390/microorganisms10102083] [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: 09/22/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Citrullus colocynthis grows in the sandy desert soil of the Arabian Peninsula with limited access to water, aside from occasional precipitation or dew. Understanding its ability to produce water-filled fruit and nutrient-rich seeds despite the harsh environment, can be useful for agricultural applications. However, information regarding the microbiome of C. colocynthis is lacking. We hypothesized that C. colocynthis associates with bacteria that aid its survival, like what has been observed in other desert plants. Here, we used 16S rRNA gene data to gain insight into the microbiome of C. colocynthis to identify its associated bacteria. In total, 9818 and 6983 OTUs were generated from root, soil, and leaf samples combined. Overall, bulk soils had the highest alpha diversity, followed by rhizosphere and root zone soils. Furthermore, C. colocynthis is associated with known plant-growth-promoting bacteria (including Acidobacteria, Bacterioidetes, and Actinobacteria), and interestingly a class of non-photosynthetic Cyanobacteria (Melainabacteria) that is more abundant on the inside and outside of the root surface than control samples, suggesting its involvement in the rhizophagy process. This study will provide a foundation for functional studies to further understand how C. colocynthis-microbes interactions help them grow in the desert, paving the path for possible agricultural applications.
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Affiliation(s)
- Miranda Procter
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Biduth Kundu
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Raja S. AlMaskari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Esam E. Saeed
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
| | - Khaled M. A. Amiri
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
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Znój A, Gawor J, Gromadka R, Chwedorzewska KJ, Grzesiak J. Root-Associated Bacteria Community Characteristics of Antarctic Plants: Deschampsia antarctica and Colobanthus quitensis-a Comparison. MICROBIAL ECOLOGY 2022; 84:808-820. [PMID: 34661728 PMCID: PMC9622554 DOI: 10.1007/s00248-021-01891-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/30/2021] [Indexed: 05/11/2023]
Abstract
Colobanthus quitensis (Kunth) Bartl. and Deschampsia antarctica Desv. are the only Magnoliophyta to naturally colonize the Antarctic region. The reason for their sole presence in Antarctica is still debated as there is no definitive consensus on how only two unrelated flowering plants managed to establish breeding populations in this part of the world. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of C. quitensis and D. antarctica specimens sampled in maritime Antarctica from sites displaying contrasting edaphic characteristics. Bacterial phylogenetic diversity (high-throughput 16S rRNA gene fragment targeted sequencing) and microbial metabolic activity (Biolog EcoPlates) with a geochemical soil background were assessed. Gathered data showed that the microbiome of C. quitensis root system was mostly site-dependent, displaying different characteristics in each of the examined locations. This plant tolerated an active bacterial community only in severe conditions (salt stress and nutrient deprivation), while in other more favorable circumstances, it restricted microbial activity, with a possibility of microbivory-based nutrient acquisition. The microbial communities of D. antarctica showed a high degree of similarity between samples within a particular rhizocompartment. The grass' endosphere was significantly enriched in plant beneficial taxa of the family Rhizobiaceae, which displayed obligatory endophyte characteristics, suggesting that at least part of this community is transmitted vertically. Ultimately, the ecological success of C. quitensis and D. antarctica in Antarctica might be largely attributed to their associations and management of root-associated microbiota.
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Affiliation(s)
- Anna Znój
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
- Botanical Garden-Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973, Warsaw, Poland
| | - Jan Gawor
- Environmental Laboratory of DNA Sequencing and Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Robert Gromadka
- Environmental Laboratory of DNA Sequencing and Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Katarzyna J Chwedorzewska
- Department of Botany, Warsaw, University of Life Sciences-SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
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Martinez-Rodriguez A, Beltran-Garcia C, Valdez-Salas B, Santacruz-Ruvalcaba F, Di Mascio P, Beltran-Garcia MJ. Micropropagation of Seed-Derived Clonal Lines of the Endangered Agave marmorata Roezl and Their Compatibility with Endophytes. BIOLOGY 2022; 11:biology11101423. [PMID: 36290326 PMCID: PMC9598202 DOI: 10.3390/biology11101423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/03/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary The wild Agave marmorata Roezl has been classified as an endangered species. Extracting these plants from the forest for commercial purposes and long maturation periods of close to 30 years have contributed to their loss. A. marmorata interacts with pollinators and other Agaves species to maintain genetic variability. Thus, the conservation and restoration of the agave ecosystem is an ecological challenge. Typically, agave micropropagation use meristem or leaves as explants to rapidly produce uniform agave plants in age and size on a large scale leading to homogeneous plantations. However, introducing these clones to the field reduces genetic variability. This study evaluated in vitro micropropagation of A. marmorata from seeds to generate clonal lines. The selected seedlings exhibited variations in multiplication capacity and stable tissue formation. Variations in clonal lines could be exploited to produce high-quality plants with different capacities, such as faster propagation, enhanced stress adaptation, and continued growth under nutrient limitation conditions, consequently maintaining genetic variability. Furthermore, some clonal lines were inoculated with four endophytic bacteria to identify other differences among these plants, including endophyte-host compatibility. Variable responses to inoculation were observed among clonal lines. We found that Achromobacter xylosoxidans was compatible, unlike Enterobacter cloacae which caused plant death. Abstract A. marmorata is the raw material used for tepextate mescal production but is classified as an endangered species. In the present study, we obtain and multiply clonal lines of Agave marmorata Roezl by selecting seedlings derived from seeds. Ten seedlings from two lots of 400 germinated seeds were selected for axillary bud proliferation induced by BAP 5 mg/L in vitamin-free Murashige and Skoog’s medium. Differences in shoot numbers, heights and senescent tissue formation were observed. Notably, the AM32 line formed 84 shoots and presented low senescent tissue after 60 d of culture. We also selected the AM31 and AM33 clonal lines. Four-month shoots were extracted with 80% methanol in water to determine the total content of saponins, flavonoids, and phenolic acids and compare the three clonal lines. Some bioactive molecules were identified using HPLC techniques and MALDI-TOF mass spectrometry none showed significant differences in content. Additionally, plants derived from the clonal lines were inoculated with four endophytic bacteria. Among these, Achromobacter xylosoxidans supported plant growth of AM32. A notable effect of plant death was observed after inoculation with Enterobacter cloacae, an endophyte of A. tequilana. Additionally, Pseudomonas aeruginosa, an endophyte from A. marmorata, reduced biomass. Our results demonstrate the incompatibility of A. marmorata to E. cloacae and specialization between the host plant and its endophytes. The compatibility of the plant-endophyte could be exploited to boost the establishment and stability of mutualisms to benefit plant development, stress tolerance and pathogen resistance. The differences in multiplication capacity, stable tissue formation, and endophyte biotization responses may indicate genetic variability. Clonal selection and micropropagation from seed-derived plants could contribute to conserving the endangered A. marmorata plant for reforestation in their natural habitats, thus, assuring mass propagation for sustainable industrial production of mescal, bioactive compounds, and prebiotics.
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Affiliation(s)
- America Martinez-Rodriguez
- Engineering Institute, Universidad Autónoma de Baja California, Mexicali 21280, Baja California, Mexico
- Lab 309-E Building, Chemistry Department, Universidad Autónoma de Guadalajara, Zapopan 45129, Jalisco, Mexico
| | - Celia Beltran-Garcia
- Lab 309-E Building, Chemistry Department, Universidad Autónoma de Guadalajara, Zapopan 45129, Jalisco, Mexico
| | - Benjamin Valdez-Salas
- Engineering Institute, Universidad Autónoma de Baja California, Mexicali 21280, Baja California, Mexico
| | - Fernando Santacruz-Ruvalcaba
- Departamento de Producción Agrícola, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan 45110, Jalisco, Mexico
| | - Paolo Di Mascio
- Departament of Biochemistry, Institute of Chemistry, University of São Paulo, Sao Paulo 05508-000, Brazil
- Correspondence: (P.D.M.); (M.J.B.-G.)
| | - Miguel J. Beltran-Garcia
- Lab 309-E Building, Chemistry Department, Universidad Autónoma de Guadalajara, Zapopan 45129, Jalisco, Mexico
- Departamento de Biotecnologicas y Ambientales, Universidad Autónoma de Guadalajara, Zapopan 45129, Jalisco, Mexico
- Correspondence: (P.D.M.); (M.J.B.-G.)
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Johnston-Monje D, Gutiérrez JP, Becerra Lopez-Lavalle LA. Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants. Life (Basel) 2022; 12:life12091372. [PMID: 36143410 PMCID: PMC9506401 DOI: 10.3390/life12091372] [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: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant–microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.
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Affiliation(s)
- David Johnston-Monje
- Max Planck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali 76001, Colombia
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Correspondence: ; Tel.: +57-315-545-6227
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Verma SK, Chen Q, White JF. Evaluation of colonization and mutualistic endophytic symbiosis of Escherichia coli with tomato and Bermuda grass seedlings. PeerJ 2022; 10:e13879. [PMID: 35971430 PMCID: PMC9375544 DOI: 10.7717/peerj.13879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli is generally considered a bacterium associated with animal microbiomes. However, we present evidence that E. coli may also mutualistically colonize roots of plant species, even to the extent that it may become endophytic in plants. In this study we used GFP tagged E. coli to observe its colonization and effects on tomato (Solanum lycopersicum) and Bermuda grass (Cynodon dactylon) seedling development and growth. Inoculation with the bacterium significantly improved root development of both seedlings tested. Treatment also increased the photosynthetic pigments in Bermuda grass seedlings. However, effects on shoot length in both seedlings were not significant. This bacterium was found to produce indole acetic acid (IAA) up to 8.68 ± 0.43 µg ml-1 in the broth medium amended with tryptophan. Effects on seedling root growth could, in part, be explained by IAA production. Bacteria successfully colonized the root surfaces and interiors of both seedlings. Tagged bacteria expressing the GFP were observed in the vascular tissues of Bermuda grass seedling roots. Seedlings with bacteria showed greater survival and were healthier than seedlings without bacteria, indicating that E. coli set up a successful mutualistic symbiosis with seedlings. E. coli is not commonly considered to be a plant endophyte but is more generally considered to be a crop contaminant. In this study we show that E. coli may also be an endophyte in plant tissues.
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Affiliation(s)
- Satish K. Verma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Qiang Chen
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - James Francis White
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, United States of America
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Ranade YH, Saha S, Chandrashekar M, Sawant IS, Shinde RC, Pathak PD. Functionality of fructosphere bacteria Kocuria sediminis strain AC3 in plant growth promotion and biodegradation of the acephate in grape berries. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01171-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rashed R, Valcheva R, Dieleman LA. Manipulation of Gut Microbiota as a Key Target for Crohn's Disease. Front Med (Lausanne) 2022; 9:887044. [PMID: 35783604 PMCID: PMC9244564 DOI: 10.3389/fmed.2022.887044] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) sub-type characterized by transmural chronic inflammation of the gastrointestinal tract. Research indicates a complex CD etiology involving genetic predisposition and immune dysregulation in response to environmental triggers. The chronic mucosal inflammation has been associated with a dysregulated state, or dysbiosis, of the gut microbiome (bacteria), mycobiome (fungi), virome (bacteriophages and viruses), and archeaome (archaea) further affecting the interkingdom syntrophic relationships and host metabolism. Microbiota dysbiosis in CD is largely described by an increase in facultative anaerobic pathobionts at the expense of strict anaerobic Firmicutes, such as Faecalibacterium prausnitzii. In the mycobiome, reduced fungal diversity and fungal-bacteria interactions, along with a significantly increased abundance of Candida spp. and a decrease in Saccharomyces cerevisiae are well documented. Virome analysis also indicates a significant decrease in phage diversity, but an overall increase in phages infecting bacterial groups associated with intestinal inflammation. Finally, an increase in methanogenic archaea such as Methanosphaera stadtmanae exhibits high immunogenic potential and is associated with CD etiology. Common anti-inflammatory medications used in CD management (amino-salicylates, immunomodulators, and biologics) could also directly or indirectly affect the gut microbiome in CD. Other medications often used concomitantly in IBD, such as antibiotics, antidepressants, oral contraceptives, opioids, and proton pump inhibitors, have shown to alter the gut microbiota and account for increased susceptibility to disease onset or worsening of disease progression. In contrast, some environmental modifications through alternative therapies including fecal microbiota transplant (FMT), diet and dietary supplements with prebiotics, probiotics, and synbiotics have shown potential protective effects by reversing microbiota dysbiosis or by directly promoting beneficial microbes, together with minimal long-term adverse effects. In this review, we discuss the different approaches to modulating the global consortium of bacteria, fungi, viruses, and archaea in patients with CD through therapies that include antibiotics, probiotics, prebiotics, synbiotics, personalized diets, and FMT. We hope to provide evidence to encourage clinicians and researchers to incorporate these therapies into CD treatment options, along with making them aware of the limitations of these therapies, and indicate where more research is needed.
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Micci A, Zhang Q, Chang X, Kingsley K, Park L, Chiaranunt P, Strickland R, Velazquez F, Lindert S, Elmore M, Vines PL, Crane S, Irizarry I, Kowalski KP, Johnston-Monje D, White JF. Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms. BIOLOGY 2022; 11:biology11060876. [PMID: 35741397 PMCID: PMC9220352 DOI: 10.3390/biology11060876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/15/2022] [Accepted: 06/01/2022] [Indexed: 12/13/2022]
Abstract
Simple Summary We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. We detected chemical exchanges between intracellular bacteria and plant cells. We found that endophytic bacteria that show evidence of the transfer of nitrogen to plants are present in non-photosynthetic cells of leaves and bracts of diverse plant species. Nitrogen transfer from bacteria was observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. The most efficient of the nitrogen-transfer endosymbioses were seen to involve glandular trichomes, as seen in hops (Humulus lupulus) and hemp (Cannabis sativa). Trichome chemistry is hypothesized to function to scavenge oxygen around bacteria to facilitate nitrogen fixation. Abstract We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.
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Affiliation(s)
- April Micci
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
- Correspondence: (A.M.); (J.F.W.); Tel.: +848-932-6286 (J.F.W.)
| | - Qiuwei Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Xiaoqian Chang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Kathryn Kingsley
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Linsey Park
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Peerapol Chiaranunt
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Raquele Strickland
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Fernando Velazquez
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Sean Lindert
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Matthew Elmore
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Philip L. Vines
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Sharron Crane
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA;
| | - Ivelisse Irizarry
- School of Health and Sciences, Universidad del Sagrado Corazón, San Juan 00914, Puerto Rico;
| | - Kurt P. Kowalski
- US Geological Survey Great Lakes Science Center, Ann Arbor, MI 48105, USA;
| | - David Johnston-Monje
- Max Planck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali 760043, Colombia;
| | - James F. White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
- Correspondence: (A.M.); (J.F.W.); Tel.: +848-932-6286 (J.F.W.)
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25
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Angulo V, Beriot N, Garcia-Hernandez E, Li E, Masteling R, Lau JA. Plant-microbe eco-evolutionary dynamics in a changing world. THE NEW PHYTOLOGIST 2022; 234:1919-1928. [PMID: 35114015 DOI: 10.1111/nph.18015] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Both plants and their associated microbiomes can respond strongly to anthropogenic environmental changes. These responses can be both ecological (e.g. a global change affecting plant demography or microbial community composition) and evolutionary (e.g. a global change altering natural selection on plant or microbial populations). As a result, global changes can catalyse eco-evolutionary feedbacks. Here, we take a plant-focused perspective to discuss how microbes mediate plant ecological responses to global change and how these ecological effects can influence plant evolutionary response to global change. We argue that the strong and functionally important relationships between plants and their associated microbes are particularly likely to result in eco-evolutionary feedbacks when perturbed by global changes and discuss how improved understanding of plant-microbe eco-evolutionary dynamics could inform conservation or even agriculture.
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Affiliation(s)
- Violeta Angulo
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Nicolas Beriot
- Soil Physics and Land Management Group, Wageningen University & Research, PO Box 47, Wageningen, 6700AA, the Netherlands
- Sustainable Use, Management and Reclamation of Soil and Water Research Group, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, Cartagena, 30203, Spain
| | - Edisa Garcia-Hernandez
- Microbial Community Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9700 CC, the Netherlands
| | - Erqin Li
- Plant-Microbe Interactions Group, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Institut für Biologie, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Raul Masteling
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, Wageningen, 6708 PB, the Netherlands
- Institute of Biology, Leiden University, Leiden, 2333 BE, the Netherlands
| | - Jennifer A Lau
- Biology Department and the Environmental Resilience Institute, Indiana University, 1001 East 3rd St., Bloomington, IN, 47405, USA
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26
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Qiu Z, Paungfoo-Lonhienne C, Ye J, Garcia AG, Petersen I, Di Bella L, Hobbs R, Ibanez M, Heenan M, Wang W, Reeves S, Schmidt S. Biofertilizers can enhance nitrogen use efficiency of sugarcane. Environ Microbiol 2022; 24:3655-3671. [PMID: 35506306 PMCID: PMC9544788 DOI: 10.1111/1462-2920.16027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/21/2022] [Indexed: 12/01/2022]
Abstract
Fertilizers are costly inputs into crop systems. To compensate for inefficiencies and losses from soil, farmers apply on average double the amount of nitrogen (N) fertilizer acquired by crops. We explored if N efficiency improves with biofertilizers formulated with organic waste, mineral N or plant growth-promoting rhizobacteria (PGPR). We compared treatments receiving mineral N fertilizer or biofertilizers at industry-recommended (100%) or lower (60%) N rates at two commercial sugarcane farms. Biofertilizer at the 60% N-rate generated promising results at one farm with significantly higher biomass and sugar yield than the no-N control, which matched the 100% mineral N treatment. This yield difference was accompanied by a shift in microbial diversity and composition. Correlation analysis confirmed that shifts in microbial communities were strongly linked to soil mineral N levels, as well as crop productivity and yield. Microbial co-occurrence networks further revealed that biofertilizer, including treatments with an added PGPR, can enhance bacterial associations, especially in the context of complex fungal networks. Collectively, the results confirm that biofertilizers have quantifiable effects on soil microbial communities in a crop system setting, which underscores the opportunities for biofertilizers to promote N use efficiency and the circular N economy.
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Affiliation(s)
- Zhiguang Qiu
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Qld, 4072, Australia.,School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | | | - Jun Ye
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Axa Gonzalez Garcia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ian Petersen
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Qld, 4072, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Lawrence Di Bella
- Herbert Cane Productivity Services Ltd., Ingham, Qld, 4850, Australia
| | - Richard Hobbs
- Herbert Cane Productivity Services Ltd., Ingham, Qld, 4850, Australia
| | - Minka Ibanez
- Herbert Cane Productivity Services Ltd., Ingham, Qld, 4850, Australia
| | - Marijke Heenan
- Department of Environment and Science, Brisbane, Qld, 4001, Australia
| | - Weijin Wang
- Department of Environment and Science, Brisbane, Qld, 4001, Australia
| | - Steven Reeves
- Department of Environment and Science, Brisbane, Qld, 4001, Australia
| | - Susanne Schmidt
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Qld, 4072, Australia
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27
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Hafiz FB, Moradtalab N, Goertz S, Rietz S, Dietel K, Rozhon W, Humbeck K, Geistlinger J, Neumann G, Schellenberg I. Synergistic Effects of a Root-Endophytic Trichoderma Fungus and Bacillus on Early Root Colonization and Defense Activation Against Verticillium longisporum in Rapeseed. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:380-392. [PMID: 35147443 DOI: 10.1094/mpmi-11-21-0274-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rhizosphere-competent microbes often interact with plant roots and exhibit beneficial effects on plant performance. Numerous bacterial and fungal isolates are able to prime host plants for fast adaptive responses against pathogen attacks. Combined action of fungi and bacteria may lead to synergisms exceeding effects of single strains. Individual beneficial fungi and bacteria have been extensively studied in Arabidopsis thaliana, but little is known about their concerted actions in the Brassicaceae. Here, an in-vitro system with oilseed rape (Brassica napus) was established. Roots of two different cultivars were inoculated with well-characterized fungal (Trichoderma harzianum OMG16) and bacterial (Bacillus velezensis FZB42) isolates alone or in combination. Microscopic analysis confirmed that OMG16 hyphae entered root hairs through root hair tips and formed distinct intracellular structures. Quantitative PCR revealed that root colonization of OMG16 increased up to 10-fold in the presence of FZB42. Relative transcript levels of the ethylene- and jasmonic acid-responsive genes PDF1.2, ERF2, and AOC3 were recorded in leaves by quantitative reverse transcription PCR to measure induced systemic resistance in tissues distant from the roots. Combined action of OMG16 and FZB42 induced transcript abundances more efficiently than single inoculation. Importantly, microbial priming reduced Verticillium longisporum root infection in rapeseed by approximately 100-fold compared with nonprimed plants. Priming also led to faster and stronger systemic responses of the defense genes PDF1.2, ERF2, AOC3, and VSP2.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Fatema Binte Hafiz
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
| | - Narges Moradtalab
- Institute of Crop Sciences, University of Hohenheim, 70593 Stuttgart, Baden-Württemberg, Germany
| | - Simon Goertz
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Schleswig-Holstein, Germany
| | - Steffen Rietz
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Schleswig-Holstein, Germany
| | | | - Wilfried Rozhon
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
| | - Klaus Humbeck
- Institute of Biology, Plant Physiology Department, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Saxony-Anhalt, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
| | - Günter Neumann
- Institute of Crop Sciences, University of Hohenheim, 70593 Stuttgart, Baden-Württemberg, Germany
| | - Ingo Schellenberg
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
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28
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Thomas P, Rajendran TP, Franco CMM. Cytobacts: Abundant and Diverse Vertically Seed-Transmitted Cultivation-Recalcitrant Intracellular Bacteria Ubiquitous to Vascular Plants. Front Microbiol 2022; 13:806222. [PMID: 35369514 PMCID: PMC8967353 DOI: 10.3389/fmicb.2022.806222] [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: 10/31/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
We have recently described ‘Cytobacts’ as abundant intracellular endophytic bacteria inhabiting live plant cells based on the observations with callus and cell suspension cultures of grapevine and other plant species with the origin ascribable to field explants. In this study, we investigated the prevalence of such cytoplasmic bacterial associations in field plants across different taxa, their cultivability, and the extent of taxonomic diversity and explored the possibility of their embryo-mediated vertical transmission. Over 100 genera of field plants were surveyed for ‘Cytobacts’ through bright-field live-cell imaging as per our previous experience using fresh tissue sections from surface-sterilized shoot-tissues with parallel cultivation-based assessments. This revealed widespread cellular bacterial associations visualized as copious motile micro-particles in the cytoplasm with no or sparse colony forming units (CFU) from the tissue-homogenates indicating their general non-cultivability. Based on the ease of detection and the abundance of ‘Cytobacts’ in fresh tissue sections, the surveyed plants were empirically classified into three groups: (i) motile bacteria detected instantly in most cells; (ii) motility not so widely observed, but seen in some cells; and (iii) only occasional motile units observed, but abundant non-motile bacterial cells present. Microscopy versus 16S-rRNA V3–V4 amplicon profiling on shoot-tip tissues of four representative plants—tomato, watermelon, periwinkle, and maize—showed high bacterial abundance and taxonomic diversity (11–15 phyla) with the dominance of Proteobacteria followed by Firmicutes/Actinobacteria, and several other phyla in minor shares. The low CFU/absence of bacterial CFU from the tissue homogenates on standard bacteriological media endorsed their cultivation-recalcitrance. Intracellular bacterial colonization implied that the associated organisms are able to transmit vertically to the next generation through the seed-embryos. Microscopy and 16S-rRNA V3–V4 amplicon/metagenome profiling of mature embryos excised from fresh watermelon seeds revealed heavy embryo colonization by diverse bacteria with sparse or no CFU. Observations with grapevine fresh fruit-derived seeds and seed-embryos endorsed the vertical transmission by diverse cultivation-recalcitrant endophytic bacteria (CREB). By and large, Proteobacteria formed the major phylum in fresh seed-embryos with varying shares of diverse phyla. Thus, we document ‘Cytobacts’ comprising diverse and vertically transmissible CREBs as a ubiquitous phenomenon in vascular plants.
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Affiliation(s)
- Pious Thomas
- Thomas Biotech & Cytobacts Centre for Biosciences, Bengaluru, India.,Division of Biotechnology, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Thekepat P Rajendran
- Research Information System for Developing Countries, India Habitat Centre, New Delhi, India
| | - Christopher M M Franco
- Department of Medical Biotechnology, College of Medicine & Public Health, Flinders University, Bedford Park, Adelaide, SA, Australia
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29
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Rodrigo S, García-Latorre C, Santamaria O. Metabolites Produced by Fungi against Fungal Phytopathogens: Review, Implementation and Perspectives. PLANTS (BASEL, SWITZERLAND) 2021; 11:81. [PMID: 35009084 PMCID: PMC8747711 DOI: 10.3390/plants11010081] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 01/06/2023]
Abstract
Many fungi, especially endophytes, have been found to produce multiple benefits in their plant hosts, with many of these benefits associated with the protection of plants against fungal diseases. This fact could be used in the development of new bio-products that could gradually reduce the need for chemical fungicides, which have been associated with multiple health and environmental problems. However, the utilization of the living organism may present several issues, such as an inconsistency in the results obtained and more complicated management and application, as fungal species are highly influenced by environmental conditions, the type of relationship with the plant host and interaction with other microorganisms. These issues could be addressed by using the bioactive compounds produced by the fungus, in cases where they were responsible for positive effects, instead of the living organism. Multiple bioactive compounds produced by fungal species, especially endophytes, with antifungal properties have been previously reported in the literature. However, despite the large amount of these metabolites and their potential, extensive in-field application on a large scale has not yet been implemented. In the present review, the main aspects explaining this limited implementation are analyzed, and the present and future perspectives for its development are discussed.
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Affiliation(s)
- Sara Rodrigo
- Department of Agronomy and Forest Environment Engineering, University of Extremadura, Avda, Adolfo Suárez s/n, 06007 Badajoz, Spain; (S.R.); (C.G.-L.)
| | - Carlos García-Latorre
- Department of Agronomy and Forest Environment Engineering, University of Extremadura, Avda, Adolfo Suárez s/n, 06007 Badajoz, Spain; (S.R.); (C.G.-L.)
| | - Oscar Santamaria
- Department of Construction and Agronomy, University of Salamanca, Avda, Cardenal Cisneros 34, 49029 Zamora, Spain
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30
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Kumar K, Verma A, Pal G, Anubha, White JF, Verma SK. Seed Endophytic Bacteria of Pearl Millet ( Pennisetum glaucum L.) Promote Seedling Development and Defend Against a Fungal Phytopathogen. Front Microbiol 2021; 12:774293. [PMID: 34956137 PMCID: PMC8696672 DOI: 10.3389/fmicb.2021.774293] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
Seed endophytic bacteria (SEB) are primary symbionts that play crucial roles in plant growth and development. The present study reports the isolation of seven culturable SEB including Kosakonia cowanii (KAS1), Bacillus subtilis (KAS2), Bacillus tequilensis (KAS3), Pantoea stewartii (KAS4), Paenibacillus dendritiformis (KAS5), Pseudomonas aeruginosa (KAS6), and Bacillus velezensis (KAS7) in pearl millet seeds. All the isolates were characterized for their plant growth promoting activities. Most of the SEB also inhibited the growth of tested fungal phytopathogens in dual plate culture. Removal of these SEB from seeds compromised the growth and development of seedlings, however, re-inoculation with the SEB (Kosakonia cowanii, Pantoea stewartii, and Pseudomonas aeruginosa) restored the growth and development of seedlings significantly. Fluorescence microscopy showed inter and intracellular colonization of SEB in root parenchyma and root hair cells. Lipopeptides were extracted from all three Bacillus spp. which showed strong antifungal activity against tested fungal pathogens. Antifungal lipopeptide genes were also screened in Bacillus spp. After lipopeptide treatment, live-dead staining with fluorescence microscopy along with bright-field and scanning electron microscopy (SEM) revealed structural deformation and cell death in Fusarium mycelia and spores. Furthermore, the development of pores in the membrane and leakages of protoplasmic substances from cells and ultimately death of hyphae and spores were also confirmed. In microcosm assays, treatment of seeds with Bacillus subtilis or application of its lipopeptide alone significantly protected seedlings from Fusarium sp. infection.
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Affiliation(s)
- Kanchan Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Verma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Gaurav Pal
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anubha
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - James F White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
| | - Satish K Verma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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31
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Pinheiro Machado Filho LC, Seó HLS, Daros RR, Enriquez-Hidalgo D, Wendling AV, Pinheiro Machado LC. Voisin Rational Grazing as a Sustainable Alternative for Livestock Production. Animals (Basel) 2021; 11:3494. [PMID: 34944271 PMCID: PMC8698051 DOI: 10.3390/ani11123494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
Current livestock practices do not meet current real-world social and environmental requirements, pushing farmers away from rural areas and only sustaining high productivity through the overuse of fossil fuels, causing numerous environmental side effects. In this narrative review, we explore how the Voisin Rational Grazing (VRG) system responds to this problem. VRG is an agroecological system based on four principles that maximise pasture growth and ruminant intake, while, at the same time, maintaining system sustainability. It applies a wide range of regenerative agricultural practices, such as the use of multispecies swards combined with agroforestry. Planning allows grazing to take place when pastures reach their optimal resting period, thus promoting vigorous pasture regrowth. Moreover, paddocks are designed in a way that allow animals to have free access to water and shade, improving overall animal welfare. In combination, these practices result in increased soil C uptake and soil health, boost water retention, and protect water quality. VRG may be used to provide ecosystem services that mitigate some of the current global challenges and create opportunities for farmers to apply greener practices and become more resilient. It can be said that VRG practitioners are part of the initiatives that are rethinking modern livestock agriculture. Its main challenges, however, arise from social constraints. More specifically, local incentives and initiatives that encourage farmers to take an interest in the ecological processes involved in livestock farming are still lacking. Little research has been conducted to validate the empirical evidence of VRG benefits on animal performance or to overcome VRG limitations.
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Affiliation(s)
- Luiz C. Pinheiro Machado Filho
- LETA, Laboratory of Applied Ethology, Department of Zootechny and Rural Development, Federal University of Santa Catarina, Florianópolis 88034-001, Brazil; (H.L.S.S.); (L.C.P.M.)
| | - Hizumi L. S. Seó
- LETA, Laboratory of Applied Ethology, Department of Zootechny and Rural Development, Federal University of Santa Catarina, Florianópolis 88034-001, Brazil; (H.L.S.S.); (L.C.P.M.)
| | - Ruan R. Daros
- Graduate Program in Animal Science, School of Life Science, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil;
| | - Daniel Enriquez-Hidalgo
- Bristol Veterinary School, University of Bristol, North Somerset, Langford BS40 5DU, Somerset, UK;
- Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Okehampton EX20 2SB, Devon, UK
| | | | - Luiz C. Pinheiro Machado
- LETA, Laboratory of Applied Ethology, Department of Zootechny and Rural Development, Federal University of Santa Catarina, Florianópolis 88034-001, Brazil; (H.L.S.S.); (L.C.P.M.)
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Pal G, Kumar K, Verma A, Verma SK. Seed inhabiting bacterial endophytes of maize promote seedling establishment and provide protection against fungal disease. Microbiol Res 2021; 255:126926. [PMID: 34856481 DOI: 10.1016/j.micres.2021.126926] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/27/2022]
Abstract
Bacteria from different crops and plant varieties have been shown to possess enormous growth promotional attributes. The study aimed to investigate the role of the endophytic microbiome of seeds of corn in improving the growth of seedlings of two different varieties of maize crops (K-25 and baby corn). Furthermore, the study also assessed the role of these bacteria in the protection of seedlings from fungal pathogens. Total twenty-three endophytic bacterial strains were isolated from maize seeds and identified using 16S rDNA sequencing. Most of the isolates had the ability to synthesize auxin (70 %) and solubilize phosphate (74 %), while all the isolates showed nitrogen fixation ability. Some isolates also showed antagonistic activity against phytopathogenic fungi including Rhizoctonia solani and Fusarium sp. suggesting their biocontrol potential. The presence of different lipopeptide genes including bacillomycin D, fengycin, iturin A and surfactin was confirmed in some of the isolates. We observed that treating seeds with an antibiotic compromised the seedlings' growth; however, re-inoculation with endophytic isolates (ZM1/Lysinibacillus sp. and ZM2/Paenibacillus dendritiformis) restored the growth of the seedlings in terms of improved root and shoot development in comparison to non-inoculated controls. The colonization of inoculated bacteria on the root surface was visualized using fluorescent microscopy. Seedling protection assay showed that treated seeds (with ZMW8/ Bacillus velezensis) were protected from fungal infestation (Fusarium verticillioides) even after 12 days of inoculation in comparison to the uninoculated control. The study concludes that indigenous seed-associated bacteria of maize play a major role during seed germination, seedling formation and protect them from phytopathogens.
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Affiliation(s)
- Gaurav Pal
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, 221005, India
| | - Kanchan Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, 221005, India
| | - Anand Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, 221005, India
| | - Satish Kumar Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, UP, 221005, India.
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Johnston-Monje D, Gutiérrez JP, Lopez-Lavalle LAB. Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes. Front Microbiol 2021; 12:737616. [PMID: 34745040 PMCID: PMC8569520 DOI: 10.3389/fmicb.2021.737616] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.
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Affiliation(s)
- David Johnston-Monje
- MaxPlanck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali, Colombia.,International Center for Tropical Agriculture, Palmira, Colombia.,Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Bioprospecting Desert Plants for Endophytic and Biostimulant Microbes: A Strategy for Enhancing Agricultural Production in a Hotter, Drier Future. BIOLOGY 2021; 10:biology10100961. [PMID: 34681060 PMCID: PMC8533330 DOI: 10.3390/biology10100961] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023]
Abstract
Simple Summary Endophytes are microbes that live inside plants without causing negative effects in their hosts. All land plants are known to have endophytes, and these endophytes have the capacity to be transferred between plants. Taking endophytes from desert plants, which grow in low-nutrient, high-stress environments, and transferring them to crop plants may alleviate some of the challenges being faced by the agricultural industry, such as increasing drought frequency and rising opposition to chemical use in agriculture. Studies have shown that desert endophytes have the capacity to increase nutrient uptake and increase plant resistance to drought and heat stress, salt stress, and pathogen attack. Currently, the agricultural industry focuses on using irrigation, chemical fertilizers, and chemical pesticides to solve such issues, which can be extremely damaging to the environment. While there is still a lot that is unknown about endophytes, particularly desert plant endophytes, current research provides evidence that desert plant endophytes could be an environmentally friendly alternative to the conventional solutions being applied today. Abstract Deserts are challenging places for plants to survive in due to low nutrient availability, drought and heat stress, water stress, and herbivory. Endophytes—microbes that colonize and infect plant tissues without causing apparent disease—may contribute to plant success in such harsh environments. Current knowledge of desert plant endophytes is limited, but studies performed so far reveal that they can improve host nutrient acquisition, increase host tolerance to abiotic stresses, and increase host resistance to biotic stresses. When considered in combination with their broad host range and high colonization rate, there is great potential for desert endophytes to be used in a commercial agricultural setting, especially as croplands face more frequent and severe droughts due to climate change and as the agricultural industry faces mounting pressure to break away from agrochemicals towards more environmentally friendly alternatives. Much is still unknown about desert endophytes, but future studies may prove fruitful for the discovery of new endophyte-based biofertilizers, biocontrol agents, and abiotic stress relievers of crops.
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Re-vitalizing of endophytic microbes for soil health management and plant protection. 3 Biotech 2021; 11:399. [PMID: 34422540 DOI: 10.1007/s13205-021-02931-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022] Open
Abstract
Soil health management and increase crop productivity are challenging issues for researchers and scientists. Many research publications have given multiple technological solutions for improving soil health and crop productivity but main problem is sustainability of those technologies under field condition and different agro-climatic zone. Due to the random industrialization, deforestation, mining and other environmental factor reduce soil fertility and human health. Many alternative options e.g., crop rotation, green manuring, integrated farming, biofertilizer (plant-growth-promoting microorganism, microbial consortium of rhizosphere soils), and vermicomposting are available for adapting and improving the soil heath and crop productivity by farmers. Recent trends of new research dimension for sustainable agriculture, endophytic microbes and its consortium is one of the better alternative for increasing crop productivity, soil health and fertility management. However, current trends are focuses on the endophytic microbes, which are present mostly in all plant species. Endophytic microbes are isolated from plant parts-root, shoot, leaf, flower and seeds which have very potential ability of plant growth promotion and bio-controlling agent for enhancing plant growth and development. Mostly plant endophytes showed multi-dimensional (synergistic, mutualistic, symbiotic etc.) interactions within the host plants. It promotes the plant growth, protects from pathogen, and induces resistance against biotic and abiotic environmental stresses, and improves the soil fertility. Till date, most of the scientific research has been done on assuming that interaction of plant endophytes with the host is similar like the plant-growth-promoting microorganism (PGPM). It would be very interesting to explore the functional properties of plant endophytes to modulate the essential gene expression during biotic and abiotic stresses. Endophytes have the ability to induce the soil fertility by improving soil essential nutrient, enzymatic activity and influence the other physiochemical property. In this study, we have discussed details about functional properties of plant endophytes and their mechanism for enhancing plant productivity and soil health and fertility management under climate-resilient agricultural practices. Our main objective is to promote and explore the beneficial plant endophytes for enhancing sustainable agricultural productivity.
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Probiotic Endophytes for More Sustainable Banana Production. Microorganisms 2021; 9:microorganisms9091805. [PMID: 34576701 PMCID: PMC8469954 DOI: 10.3390/microorganisms9091805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022] Open
Abstract
Climatic factors and pathogenic fungi threaten global banana production. Moreover, bananas are being cultivated using excessive amendments of nitrogen and pesticides, which shift the microbial diversity in plants and soil. Advances in high-throughput sequencing (HTS) technologies and culture-dependent methods have provided valuable information about microbial diversity and functionality of plant-associated endophytic communities. Under stressful (biotic or abiotic) conditions, plants can recruit sets of microorganisms to alleviate specific potentially detrimental effects, a phenomenon known as “cry for help”. This mechanism is likely initiated in banana plants infected by Fusarium wilt pathogen. Recently, reports demonstrated the synergistic and cumulative effects of synthetic microbial communities (SynComs) on naturally occurring plant microbiomes. Indeed, probiotic SynComs have been shown to increase plant resilience against biotic and abiotic stresses and promote growth. This review focuses on endophytic bacterial diversity and keystone taxa of banana plants. We also discuss the prospects of creating SynComs composed of endophytic bacteria that could enhance the production and sustainability of Cavendish bananas (Musa acuminata AAA), the fourth most important crop for maintaining global food security.
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Lang M, Zhou J, Chen T, Chen Z, Malik K, Li C. Influence of Interactions between Nitrogen, Phosphorus Supply and Epichloёbromicola on Growth of Wild Barley ( Hordeum brevisubulatum). J Fungi (Basel) 2021; 7:jof7080615. [PMID: 34436154 PMCID: PMC8397062 DOI: 10.3390/jof7080615] [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: 07/12/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 02/03/2023] Open
Abstract
Epichloë endophytes are biotrophic fungi that establish mutualistic symbiotic relationship with grasses and affect performance of the host under different environments. Wild barley (Hordeum brevisubulatum) is an important forage grass and often infected by Epichloë bromicola, thus showing tolerances to stresses. Since the plant growth correlates with both microbial infection and nutrient stoichiometry, this study was performed to investigate whether the function of Epichloë bromicola endophyte to improve host growth depend upon the nitrogen (N), phosphorus (P) fertilization. Epichloë-infected (E+) and Epichloë-free (E-) wild barley plants were subjected to nine types of mixed N (0.2 mM, 3 mM, 15 mM) and P (0.01 mM, 0.1 mM, 1.5 mM) levels treatments for 90 d to collect plant samples and determine multiple related indexes. We found that E. bromicola and N, P additions positively affected seed germination. Further, E. bromicola significantly enhanced chlorophyll content and root metabolic activity under N-deficiency, and meanwhile, might alter allocation of photosynthate under different conditions. The contents of N, P and stoichiometry of C:N:P of E+ plants were significantly higher than that of E- under nutrient deficiency, but contrary results were observed under adequate nutrients. Therefore, we propose that the growth-promoting ability of E. bromicola is closely correlated with N and P additional levels. Under low N, P additions, positive roles of endophyte are significant as opposed to negative roles under high N, P additions.
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Yung L, Sirguey C, Azou-Barré A, Blaudez D. Natural Fungal Endophytes From Noccaea caerulescens Mediate Neutral to Positive Effects on Plant Biomass, Mineral Nutrition and Zn Phytoextraction. Front Microbiol 2021; 12:689367. [PMID: 34295322 PMCID: PMC8290495 DOI: 10.3389/fmicb.2021.689367] [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: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/14/2022] Open
Abstract
Phytoextraction using hyperaccumulating plants is a method for the remediation of soils contaminated with trace elements (TEs). As a strategy for improvement, the concept of fungal-assisted phytoextraction has emerged in the last decade. However, the role played by fungal endophytes of hyperaccumulating plants in phytoextraction is poorly studied. Here, fungal endophytes isolated from calamine or non-metalliferous populations of the Cd/Zn hyperaccumulator Noccaea caerulescens were tested for their growth promotion abilities affecting the host plant. Plants were inoculated with seven different isolates and grown for 2 months in trace element (TE)-contaminated soil. The outcomes of the interactions between N. caerulescens and its native strains ranged from neutral to beneficial. Among the strains, Alternaria thlaspis and Metapochonia rubescens, respectively, isolated from the roots of a non-metallicolous and a calamine population of N. caerulescens, respectively, exhibited the most promising abilities to enhance the Zn phytoextraction potential of N. caerulescens related to a significant increase of the plant biomass. These strains significantly increased the root elemental composition, particularly in the case of K, P, and S, suggesting an improvement of the plant nutrition. Results obtained in this study provide new insights into the relevance of microbial-assisted phytoextraction approaches in the case of hyperaccumulating plants.
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Affiliation(s)
- Loïc Yung
- Université de Lorraine, CNRS, LIEC, Nancy, France
| | | | - Antonin Azou-Barré
- Université de Lorraine, CNRS, LIEC, Nancy, France
- Université de Lorraine, INRAE, LSE, Nancy, France
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de Moraes ACP, Ribeiro LDS, de Camargo ER, Lacava PT. The potential of nanomaterials associated with plant growth-promoting bacteria in agriculture. 3 Biotech 2021; 11:318. [PMID: 34194902 PMCID: PMC8190246 DOI: 10.1007/s13205-021-02870-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 05/31/2021] [Indexed: 01/18/2023] Open
Abstract
The impacts of chemical fertilizers and pesticides have raised public concerns regarding the sustainability and security of food supplies, prompting the investigation of alternative methods that have combinations of both agricultural and environmental benefits, such as the use of biofertilizers involving microbes. These types of microbial inoculants are living microorganisms that colonize the soil or plant tissues when applied to the soil, seeds, or plant surfaces, facilitating plant nutrient acquisition. They can enhance plant growth by transforming nutrients into a form assimilable by plants and by acting as biological control agents, known as plant growth-promoting bacteria. The potential use of bacteria as biofertilizers in agriculture constitutes an economical and eco-friendly way to reduce the use of chemical fertilizers and pesticides. In this context, nanotechnology has emerged as a new source of quality enrichment for the agricultural sector. The use of nanoparticles can be an effective method to meet the challenges regarding the effectiveness of biofertilizers in natural environments. Given the novel sustainable strategies applied in agricultural systems, this review addresses the effects of nanoparticles on beneficial plant bacteria for promoting plant growth.
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Affiliation(s)
- Amanda Carolina Prado de Moraes
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
- Biotechnology Graduation Program (PPG-Biotec), Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
| | - Lucas da Silva Ribeiro
- Interdisciplinary Laboratory of Electrochemistry and Ceramics, Department of Chemistry, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
| | - Emerson Rodrigues de Camargo
- Interdisciplinary Laboratory of Electrochemistry and Ceramics, Department of Chemistry, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
| | - Paulo Teixeira Lacava
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
- Biotechnology Graduation Program (PPG-Biotec), Federal University of São Carlos (UFSCar), Rod. Washington Luiz, s/n, São Carlos, 13565-905 Brazil
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Lobanov VP, Combot D, Pelissier P, Labbé L, Joyce A. Improving Plant Health Through Nutrient Remineralization in Aquaponic Systems. FRONTIERS IN PLANT SCIENCE 2021; 12:683690. [PMID: 34194456 PMCID: PMC8236952 DOI: 10.3389/fpls.2021.683690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
The exploitation of readily bioavailable fish excreta as a source of plant nutrients lies at the cornerstone of aquaponics farming. Research on nutrient cycling in aquaponic systems has devoted considerable attention to the plant uptake of dissolved nutrients in fish excreta, however, the integration of particulate-bound nutrients into downstream hydroponic farming has remained elusive. The high amount of organic carbon present in fish sludge may lead to biofouling if directly incorporated into hydroponic circulation systems, reducing the utility of incorporating fish solids on a large scale. In this study, we implemented a novel treatment system capable of reducing the carbon and nitrogen load of fish solids to produce a liquid fertilizer for a downstream hydroponics unit. Lettuce (Lactuca sativa) fertilized with exclusively a commercial nutrient solution, the biofilter effluent (coupled aquaponic system), effluent from the solids treatment system, or the latter two combined were grown in nutrient flow technique gutters downstream of a recirculating aquaculture system stocked with rainbow trout (Oncorhynchus mykiss). While crop yields were lower for the aquaponic treatments compared to lettuce grown in a commercial nutrient solution, plant sap analysis demonstrated a contrasting picture with respect to internal nutrient concentrations. Lettuce grown in the commercial hydroponic solution were deficient in several mineral nutrients (Mg, Ca, Na, and Si) nor did they have higher iron concentrations despite the significantly higher EDTA-chelated aqueous iron (460 × greater than other treatments) in the nutrient solution. Nutrient uptake in the rhizosphere was not investigated on a molecular level, although stunted rhizosphere growth in the commercial nutrient solution control suggests a weakened capacity for nutrient uptake in comparison to other treatments. Alongside the remineralization of micronutrients, the solids treatment system addressed the common issue of excess carbon leading to biofouling via a total suspended solids reduction of 87.27% ± 9.95 during the coupled aquaponics cultivation period. Ultimately, these data lead to two important conclusions. Firstly, optimizing nutrient bioavailability is not synonymous to increasing the presence of a nutrient in the water column. Secondly, estimating ideal nutrient solution concentrations involves both preventing nutrient blocking and improving bioavailability.
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Affiliation(s)
- Victor P. Lobanov
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Doriane Combot
- PEIMA-INRAe, UE0937, Fish Farming Systems Experimental Facility, Sizun, France
| | - Pablo Pelissier
- PEIMA-INRAe, UE0937, Fish Farming Systems Experimental Facility, Sizun, France
| | - Laurent Labbé
- PEIMA-INRAe, UE0937, Fish Farming Systems Experimental Facility, Sizun, France
| | - Alyssa Joyce
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
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Chang X, Kingsley KL, White JF. Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular Bacteria. Microorganisms 2021; 9:1041. [PMID: 34066008 PMCID: PMC8150332 DOI: 10.3390/microorganisms9051041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
In this research, we conducted histochemical, inhibitor and other experiments to evaluate the chemical interactions between intracellular bacteria and plant cells. As a result of these experiments, we hypothesize two chemical interactions between bacteria and plant cells. The first chemical interaction between endophyte and plant is initiated by microbe-produced ethylene that triggers plant cells to grow, release nutrients and produce superoxide. The superoxide combines with ethylene to form products hydrogen peroxide and carbon dioxide. In the second interaction between microbe and plant the microbe responds to plant-produced superoxide by secretion of nitric oxide to neutralize superoxide. Nitric oxide and superoxide combine to form peroxynitrite that is catalyzed by carbon dioxide to form nitrate. The two chemical interactions underlie hypothesized nutrient exchanges in which plant cells provide intracellular bacteria with fixed carbon, and bacteria provide plant cells with fixed nitrogen. As a consequence of these two interactions between endophytes and plants, plants grow and acquire nutrients from endophytes, and plants acquire enhanced oxidative stress tolerance, becoming more tolerant to abiotic and biotic stresses.
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Affiliation(s)
| | | | - James F. White
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA; (X.C.); (K.L.K.)
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Verma SK, Sahu PK, Kumar K, Pal G, Gond SK, Kharwar RN, White JF. Endophyte roles in nutrient acquisition, root system architecture development and oxidative stress tolerance. J Appl Microbiol 2021; 131:2161-2177. [PMID: 33893707 DOI: 10.1111/jam.15111] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/06/2021] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
Plants associate with communities of microbes (bacteria and fungi) that play critical roles in plant development, nutrient acquisition and oxidative stress tolerance. The major share of plant microbiota is endophytes which inhabit plant tissues and help them in various capacities. In this article, we have reviewed what is presently known with regard to how endophytic microbes interact with plants to modulate root development, branching, root hair formation and their implications in overall plant development. Endophytic microbes link the interactions of plants, rhizospheric microbes and soil to promote nutrient solubilization and further vectoring these nutrients to the plant roots making the soil-plant-microbe continuum. Further, plant roots internalize microbes and oxidatively extract nutrients from microbes in the rhizophagy cycle. The oxidative interactions between endophytes and plants result in the acquisition of nutrients by plants and are also instrumental in oxidative stress tolerance of plants. It is evident that plants actively cultivate microbes internally, on surfaces and in soils to acquire nutrients, modulate development and improve health. Understanding this continuum could be of greater significance in connecting endophytes with the hidden half of the plant that can also be harnessed in applied terms to enhance nutrient acquisition through the development of favourable root system architecture for sustainable production under stress conditions.
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Affiliation(s)
- S K Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - P K Sahu
- National Bureau of Agriculturally Important Microorganism, Mau, Uttar Pradesh, India
| | - K Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - G Pal
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - S K Gond
- Botany Section, MMV, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - R N Kharwar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - J F White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA
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Dudeja SS, Suneja-Madan P, Paul M, Maheswari R, Kothe E. Bacterial endophytes: Molecular interactions with their hosts. J Basic Microbiol 2021; 61:475-505. [PMID: 33834549 DOI: 10.1002/jobm.202000657] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 01/19/2023]
Abstract
Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.
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Affiliation(s)
- Surjit S Dudeja
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Pooja Suneja-Madan
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Minakshi Paul
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Rajat Maheswari
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Faculty for Biosciences, Friedrich Schiller University of Jena, Jena, Germany
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Adamczyk B. Root-Derived Proteases as a Plant Tool to Access Soil Organic Nitrogen; Current Stage of Knowledge and Controversies. PLANTS 2021; 10:plants10040731. [PMID: 33918076 PMCID: PMC8069566 DOI: 10.3390/plants10040731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
Anthropogenic deterioration of the global nitrogen (N) cycle emerges mainly from overuse of inorganic N fertilizers in nutrient-limited cropping systems. To counteract a further dysregulation of the N cycle, we need to improve plant nitrogen use efficiency. This aim may be reached via unravelling all plant mechanisms to access soil N, with special attention to the dominating high-molecular-mass N pool. Traditionally, we believe that inorganic N is the only plant-available N pool, however, more recent studies point to acquisition of organic N compounds, i.e., amino acids, short peptides, and proteins. The least known mechanism of plants to increase the N uptake is a direct increase of soil proteolysis via root-derived proteases. This paper provides a review of the knowledge about root-derived proteases and also controversies behind this phenomenon.
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Affiliation(s)
- Bartosz Adamczyk
- The Natural Resources Institute, Luonnonvarakeskus, Viikinkaari 4, 00790 Helsinki, Finland
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Xia Q, Rufty T, Shi W. Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp. Front Microbiol 2021; 12:643904. [PMID: 33833744 PMCID: PMC8021697 DOI: 10.3389/fmicb.2021.643904] [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: 12/19/2020] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
Microbes can colonize plant roots to modulate plant health and environmental fitness. Thus, using microbes to improve plant adaptation to biotic and abiotic stresses will be promising to abate the heavy reliance of management systems on synthetic chemicals and limited resource. This is particularly important for turfgrass systems because intensive management for plant available nutrients (e.g., nitrogen), water, and pest control is necessary to maintain a healthy and aesthetic landscape. However, little is known on microbial species and host compatibility in turfgrass root endosphere and rhizosphere. Here, by using marker gene high throughput sequencing approaches we demonstrated that a few bacterial and fungal species prevailed the root endosphere and rhizosphere and were of a broad host spectrum. Irrespective of turfgrass species (bermudagrass, ultradwarf bermudagrass, creeping bentgrass, and tall fescue), defoliation intensities (i.e., mowing height and frequency), turfgrass sites, and sampling time, Pseudomonas veronii was predominant in the root endosphere, constituting ∼38% of the total bacterial community, which was much higher than its presence in the bulk soil (∼0.5%) and rhizosphere (∼4.6%). By contrast, Janthinobacterium lividum and fungal species of the genus Pseudogymnoascus were more abundant in the rhizosphere, constituting ∼15 and ∼ 39% of the total bacterial and fungal community, respectively, compared to their respective presence in the bulk soil (∼ 0.1 and 5%) and root endosphere (∼ 0.8 and 0.3%). Such stark contrasts in the microbiome composition between the root endosphere, rhizosphere, and bulk soil were little influenced by turfgrass species, suggesting the broad turfgrass host compatibility of these bacterial and fungal species. Further, their dominance in respective niches were mutually unaffected, implying the possibility of developing a multiple species formula for coping turfgrass with environmental stresses. These species were likely involved in controlling pests, such as infectious nematodes and fungi, decomposing root debris, and helping turfgrass water and nutrient uptake; yet these possibilities need to be further examined.
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Affiliation(s)
| | | | - Wei Shi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
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Al Dayel MF, El Sherif F. Evaluation of the effects of Chlorella vulgaris, Nannochloropsis salina, and Enterobacter cloacae on growth, yield and active compound compositions of Moringa oleifera under salinity stress. Saudi J Biol Sci 2021; 28:1687-1696. [PMID: 33732054 PMCID: PMC7938152 DOI: 10.1016/j.sjbs.2020.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/05/2020] [Accepted: 12/06/2020] [Indexed: 10/31/2022] Open
Abstract
Application of Chlorella vulgaris, Nannochloropsis salina and Enterobacter cloacae has been reported to improve the growth of multiple plant species. Moringa oleifera is a medicinal plant found in Saudi Arabia. Its leaves, flowers and fruit have been used as food. Moringa oleifera is rich in rutin and gallic acid and many other bioactive compounds, which collectively contribute to its demonstrated range of pharmacological activities. In Saudi Arabia, the semi-arid and arid weather presents a significant challenge to agriculture. High salinity in cultivated land is a particular threat. We applied Chlorella vulgaris, Nannochloropsis salina, and Enterobacter cloacae at multiple salinities to Moringa oleifera to investigate their effects on the growth, yield, and photosynthetic pigment content. We also examined possible changes in the phytochemical composition. The application of Chlorella vulgaris, Nannochloropsis salina and Enterobacter cloacae enhanced plant growth and yield, while inhibition was observed at high (6000 ppm) salinity. The presence of Chlorella vulgaris and Nannochloropsis salina altered plant growth and yield and rutin and gallic acid content of Moringa oleifera plants grown in saline conditions. Microalgae species were recommended for use as a bio-fertiliser alternative to mainstream synthetic fertilisers.
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Affiliation(s)
- Munirah F Al Dayel
- Department of Biological Sciences, Faculty of Science, King Faisal University, Saudi Arabia
| | - Fadia El Sherif
- Department of Biological Sciences, Faculty of Science, King Faisal University, Saudi Arabia
- Department of Horticulture, Faculty of Agriculture, Suez Canal University, Egypt
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Guo DJ, Singh RK, Singh P, Li DP, Sharma A, Xing YX, Song XP, Yang LT, Li YR. Complete Genome Sequence of Enterobacter roggenkampii ED5, a Nitrogen Fixing Plant Growth Promoting Endophytic Bacterium With Biocontrol and Stress Tolerance Properties, Isolated From Sugarcane Root. Front Microbiol 2020; 11:580081. [PMID: 33072048 PMCID: PMC7536287 DOI: 10.3389/fmicb.2020.580081] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022] Open
Abstract
Sugarcane is the leading economic crop in China, requires huge quantities of nitrogen in the preliminary plant growth stages. However, the use of an enormous amount of nitrogen fertilizer increases the production price, and have detrimental results on the environment, causes severe soil and water pollution. In this study, a total of 175 endophytic strains were obtained from the sugarcane roots, belonging to five different species, i.e., Saccharum officinarum, Saccharum barberi, Saccharum robustum, Saccharum spontaneum, and Saccharum sinense. Among these, only 23 Enterobacter strains were chosen based on nitrogen fixation, PGP traits, hydrolytic enzymes production, and antifungal activities. Also, all selected strains were showed diverse growth range under different stress conditions, i.e., pH (5–10), temperature (20–45°C), and NaCl (7–12%) and 14 strains confirmed positive nifH, and 12 strains for acdS gene amplification, suggested that these strains could fix nitrogen along with stress tolerance properties. Out of 23 selected strains, Enterobacter roggenkampii ED5 was the most potent strain. Hence, this strain was further selected for comprehensive genome analysis, which includes a genome size of 4,702,851 bp and 56.05% of the average G + C content. Genome annotations estimated 4349 protein-coding with 83 tRNA and 25 rRNA genes. The CDSs number allocated to the KEGG, COG, and GO database were 2839, 4028, and 2949. We recognized a total set of genes that are possibly concerned with ACC deaminase activity, siderophores and plant hormones production, nitrogen and phosphate metabolism, symbiosis, root colonization, biofilm formation, sulfur assimilation and metabolism, along with resistance response toward a range of biotic and abiotic stresses. E. roggenkampii ED5 strain was also a proficient colonizer in sugarcane (variety GT11) and enhanced growth of sugarcane under the greenhouse. To the best of our knowledge, this is the first information on the whole-genome sequence study of endophytic E. roggenkampii ED5 bacterium associated with sugarcane root. And, our findings proposed that identification of predicted genes and metabolic pathways might describe this strain an eco-friendly bioresource to promote sugarcane growth by several mechanisms of actions under multi-stresses.
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Affiliation(s)
- Dao-Jun Guo
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Yong-Xiu Xing
- College of Agriculture, Guangxi University, Nanning, China
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Li-Tao Yang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- College of Agriculture, Guangxi University, Nanning, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
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Xie F, Ma A, Zhou H, Liang Y, Yin J, Ma K, Zhuang X, Zhuang G. Revealing Fungal Communities in Alpine Wetlands Through Species Diversity, Functional Diversity and Ecological Network Diversity. Microorganisms 2020; 8:E632. [PMID: 32349397 PMCID: PMC7284966 DOI: 10.3390/microorganisms8050632] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Accepted: 04/22/2020] [Indexed: 11/16/2022] Open
Abstract
The biodiversity of fungi, which are extremely important in maintaining the ecosystem balance in alpine lakeside wetlands, has not been fully studied. In this study, we investigated the fungal communities of three lakeside wetlands from different altitudes in the Qinghai-Tibet Plateau and its edge. The results showed that the fungi of the alpine lakeside wetland had higher species diversity. Functional annotation of fungi by FUNGild software showed that saprophytic fungi were the most abundant type in all three wetlands. Further analysis of the microbial phylogenetic molecular ecological network (pMEN) showed that saprophytic fungi are important species in the three wetland fungal networks, while symbiotic fungi and pathotrophic fungi have different roles in the fungal networks in different wetlands. Community diversity was high in all three lakeside wetlands, but there were significant differences in the composition, function and network structure of the fungal communities. Contemporary environmental conditions (soil properties) and historical contingencies (geographic sampling location) jointly determine fungi community diversity in this study. These results expand our knowledge of fungal biodiversity in the alpine lakeside wetlands.
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Affiliation(s)
- Fei Xie
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anzhou Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanchang Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101400, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (F.X.); (H.Z.); (Y.L.); (J.Y.); (K.M.); (X.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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