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Yang J, Ding D, Zhang X, Gu H. A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain. Microbiol Spectr 2024; 12:e0368323. [PMID: 38376351 DOI: 10.1128/spectrum.03683-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality. IMPORTANCE The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.
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Affiliation(s)
- Jia Yang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Dang Ding
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Xiuru Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Huiyan Gu
- School of Forestry, Northeast Forestry University, Harbin, China
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Dubey S, Bhattacharjee A, Pradhan S, Kumar A, Sharma S. Composition of fungal communities upon multiple passaging of rhizosphere microbiome for salinity stress mitigation in Vigna radiata. FEMS Microbiol Ecol 2023; 99:fiad132. [PMID: 37838474 DOI: 10.1093/femsec/fiad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/27/2023] [Accepted: 10/13/2023] [Indexed: 10/16/2023] Open
Abstract
The top-down approach of microbiome-mediated rhizosphere engineering has emerged as an eco-friendly approach for mitigating stress and enhancing crop productivity. It has been established to mitigate salinity stress in Vigna radiata using multi-passaging approach. During the process of acclimatization under increasing levels of salinity stress, the structure of rhizospheric microbial community undergoes dynamic changes, while facilitating stress mitigation in plants. In this study, using ITS-based amplicon sequencing, the dynamics of rhizosphere fungal community was unravelled over successive passages under salinity stress in V. radiata. Clear shifts were evident among the fungal community members under stress and non-stress conditions, upon application of acclimatized rhizosphere microbiome in V. radiata across successive passages. These shifts correlated with enhanced plant biometrics and reduced stress marker levels in plant. Significant changes in the fungal community structure were witnessed in the rhizosphere across specific passaging cycles under salinity stress, which possibly facilitated stress mitigation in V. radiata.
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Affiliation(s)
- Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Salila Pradhan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Abhay Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
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Ramirez-Villacis DX, Erazo-Garcia P, Quijia-Pillajo J, Llerena-Llerena S, Barriga-Medina N, Jones CD, Leon-Reyes A. Influence of Grafting on Rootstock Rhizosphere Microbiome Assembly in Rosa sp. 'Natal Brier'. Biology (Basel) 2023; 12:biology12050663. [PMID: 37237477 DOI: 10.3390/biology12050663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/28/2023]
Abstract
The root microbiome is vital in plant development and health and is highly influenced by crop cultural practices. Rose (Rosa sp.) is the most popular cut flower worldwide. Grafting in rose production is a standard practice to increase yield, improve flower quality, or reduce root-associated pests and diseases. 'Natal Brier' is a standard rootstock used in most commercial operations in Ecuador and Colombia, leading countries in producing and exporting ornamentals. It is known that the rose scion genotype affects root biomass and the root exudate profile of grafted plants. However, little is known about the influence of the rose scion genotype on the rhizosphere microbiome. We examined the influence of grafting and scion genotype on the rhizosphere microbiome of the rootstock 'Natal Brier'. The microbiomes of the non-grafted rootstock and the rootstock grafted with two red rose cultivars were assessed using 16S rRNA and ITS sequencing. Grafting changed microbial community structure and function. Further, analysis of grafted plant samples revealed that the scion genotype highly influences the rootstock microbiome. Under the presented experimental conditions, the rootstock 'Natal Brier' core microbiome consisted of 16 bacterial and 40 fungal taxa. Our results highlight that the scion genotype influences root microbe's recruitment, which might also influence the functionality of assembled microbiomes.
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Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Pablo Erazo-Garcia
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Juan Quijia-Pillajo
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 43210, USA
| | - Sol Llerena-Llerena
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Noelia Barriga-Medina
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Corbin D Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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Zhang H, Yang Z, Jiang Z, Zhang X, Nizamani MM, Wu Y, Wei S, Wang Y, Xie X. Diversity of Fungi Isolated from Potato Nematode Cysts in Guizhou Province, China. J Fungi (Basel) 2023; 9:247. [PMID: 36836361 PMCID: PMC9965506 DOI: 10.3390/jof9020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Potatoes rank third in terms of human consumption after rice and wheat. Globodera spp. are significant pests of potato crop worldwide. Globodera rostochiensis was found in Weining County, Guizhou Province, China, in 2019. We collected soil from the rhizosphere zone from infected potato plants and separated mature cysts through simple floatation and sieving methods. The selected cysts were surface-sterilized, and the colonized fungi were isolated and purified. At the same time, the preliminary identification of fungi and fungi parasites on the cysts of nematodes was carried out. This study aimed to define the species and frequency of fungi-colonizing cysts of G. rostochiensis collected from Weining County, Guizhou Province, China, and provide a basis for the control of G. rostochiensis. As a result, 139 strains of colonized fungi were successfully isolated. Multigene analyses showed that these isolates included 11 orders, 17 families, and 23 genera. The genera Fusarium (with a separation frequency of 59%), Penicillium (11%), Edenia (3.6%), and Paraphaeosphaeria (3.6%) were the most frequently occurring. Among the 44 strains, 27 had a colonization rate of 100% on the cysts of G. rostochiensis. Meanwhile, the functional annotation of 23 genera indicated that some fungi have multitrophic lifestyles combining endophytic, pathogenic, and saprophytic behavior. In conclusion, this study showed the species composition and lifestyle diversity of colonized fungi from G. rostochiensis and demonstrated these isolates as potential sources of biocontrol agents. Colonized fungi were isolated from G. rostochiensis for the first time in China, and the taxonomic diversity of fungi from G. rostochiensis was clarified.
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Affiliation(s)
- Hui Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Zaifu Yang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
- Vegetable Research Academy, Guizhou University, Guiyang, 550025, China
| | - Zhaochun Jiang
- Guizhou Station of Plant Protection and Quarantine, Guiyang, 550001, China
| | - Xinyue Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Yan Wu
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Shan Wei
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Yong Wang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xin Xie
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
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Pires D, Vicente CSL, Menéndez E, Faria JMS, Rusinque L, Camacho MJ, Inácio ML. The Fight against Plant-Parasitic Nematodes: Current Status of Bacterial and Fungal Biocontrol Agents. Pathogens 2022; 11:1178. [PMID: 36297235 PMCID: PMC9606992 DOI: 10.3390/pathogens11101178] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/24/2022] Open
Abstract
Plant-parasitic nematodes (PPNs) are among the most notorious and underrated threats to food security and plant health worldwide, compromising crop yields and causing billions of dollars of losses annually. Chemical control strategies rely heavily on synthetic chemical nematicides to reduce PPN population densities, but their use is being progressively restricted due to environmental and human health concerns, so alternative control methods are urgently needed. Here, we review the potential of bacterial and fungal agents to suppress the most important PPNs, namely Aphelenchoides besseyi, Bursaphelenchus xylophilus, Ditylenchus dipsaci, Globodera spp., Heterodera spp., Meloidogyne spp., Nacobbus aberrans, Pratylenchus spp., Radopholus similis, Rotylenchulus reniformis, and Xiphinema index.
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Pulavarty A, Singh A, Smyth D, Mehta JP, Horgan K, Kakouli-Duarte T. Sustainable management of the potato cyst nematode, Globodera rostochiensis, with two microbial fermentation products. Front Plant Sci 2022; 13:987059. [PMID: 36275579 PMCID: PMC9580274 DOI: 10.3389/fpls.2022.987059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Potato cyst nematodes (PCN) cause an overall 9% yield loss of total potato production worldwide. Research on sustainable management of PCN is still under progress. Two microbial fermentation products (MFPs) from Alltech, a proprietary blend formulated with a bacterial fermentation media and a Cu component (MFP5075), and a microbial based product (MFP3048), were evaluated against the PCN Globodera rostochiensis. In laboratory tests, effectiveness of the MFPs was recorded in terms of PCN juveniles (J2) hatching from cysts, J2 mortality and their attraction toward potato roots using pluronic gel. Greenhouse trials were conducted to study the effect of the products on PCN infestation in potato plants and a pilot scale experiment was conducted to study the impact of these MFPs on nematode biodiversity in garden soil. All treatments were performed within a concentration range of 0, 0.5, 1, and 2% (v/v) MFP5075 and 2, 6, 10, and 20 g/10 ml (w/v) MFP3048. The attraction assay, juvenile hatching and the PCN infestation in plants results were compared with those in an untreated control and a commercial nematicide (Nemguard™) treatment. After 24 h of treatment with 0.5 and 1% MFP5075, a 13-fold and 43-fold reduction, respectively, relative to J2 survival was recorded compared to that of untreated control. However, no J2 survived at 2% and above concentration of the MFP5075 treatment. Treatment with MFP3048 was effective in causing mortality of J2 only after 48-h. In the attraction assay, a 20-fold and 8-fold reduction in number of J2 attracted toward potato roots was observed, when treated with MFP5075, compared to the untreated and the Nemguard™ treatment, respectively. Subsequently, 30-35 PCN cysts were treated with both products dissolved in potato root diffusate and the results were recorded in terms of number of J2 hatched in each treatment after 10 days. No J2 hatched in the MFP5075 treatment, whereas mean numbers (±SE) of 243 ± 11.5, 30 ± 2.5, and 1.3 ± 0.6 J2 were noted in the untreated control, MFP3048, and the Nemguard™ treatment, respectively. The treatment with the MFPs compromised the integrity of the unhatched J2, which looked granular, whereas the internal organs of the unhatched J2 could be clearly identified in the untreated control. In plant infestation studies, treatment with MFP3048 and MFP5075 caused 90.6 and 84.9 percent reduction in PCN infestation, respectively, in terms of cysts developed on roots compared to untreated control. Overall, results indicate that the MFPs could potentially provide a promising alternative for sustainable PCN management.
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Affiliation(s)
- Anusha Pulavarty
- Molecular Ecology and Nematode Research Group, enviroCORE, Department of Applied Science, South East Technological University (SETU), Carlow, Ireland
| | - Ankit Singh
- Molecular Ecology and Nematode Research Group, enviroCORE, Department of Applied Science, South East Technological University (SETU), Carlow, Ireland
| | - David Smyth
- Molecular Ecology and Nematode Research Group, enviroCORE, Department of Applied Science, South East Technological University (SETU), Carlow, Ireland
| | - Jai Prakash Mehta
- Molecular Ecology and Nematode Research Group, enviroCORE, Department of Applied Science, South East Technological University (SETU), Carlow, Ireland
| | - Karina Horgan
- Alltech Bioscience Centre, Dunboyne, County Meath, Ireland
| | - Thomais Kakouli-Duarte
- Molecular Ecology and Nematode Research Group, enviroCORE, Department of Applied Science, South East Technological University (SETU), Carlow, Ireland
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