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Park HE, Nebert L, King RM, Busby P, Myers JR. Influence of organic plant breeding on the rhizosphere microbiome of common bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1251919. [PMID: 37954997 PMCID: PMC10634438 DOI: 10.3389/fpls.2023.1251919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023]
Abstract
Introduction We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history. Methods Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set. Results Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens. Discussion The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.
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Affiliation(s)
- Hayley E. Park
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Lucas Nebert
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Ryan M. King
- National Clonal Germplasm Repository, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Posy Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - James R. Myers
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
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Lin Q, Xu Z, Li M, Wang Y, Li L. Spatial differences in Casuarina equisetifolia L. endophyte community structure. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01685-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Casuarina equisetifolia, a fast-growing, abundant tree species on the southeastern coast of China, plays an important role in protecting the coastal environment, but the ecological processes that govern microbiome assembly and within-plant microorganism transmission are poorly known.
Methods
In this paper, we used ITS and 16S amplification techniques to study the diversity of fungal and bacterial endophytes in critical plant parts of this species: seeds, branchlets, and roots. Additionally, we examined the litter of this species to understand the process of branchlets from birth to litter.
Result
We uncovered a non-random distribution of endophyte diversity in which branchlets had the greatest and seeds had the lowest endophytic fungal diversity. In contrast, litter endophytic bacteria had the highest diversity, and branchlets had the lowest diversity. As for fungi, a large part of the seed microbiome was transmitted to the phyllosphere, while a large part of the bacterial microbiome in the seed was transmitted to the root.
Conclusion
Our study provides comprehensive evidence on diversity, potential sources, and transmission pathways for non-crop microbiome assembly and has implications for the management and manipulation of the non-crop microbiome in the future.
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Pambuka GT, Kinge TR, Ghosh S, Cason ED, Nyaga MM, Gryzenhout M. Plant and Soil Core Mycobiomes in a Two-Year Sorghum-Legume Intercropping System of Underutilized Crops in South Africa. Microorganisms 2022; 10:2079. [PMID: 36296355 PMCID: PMC9611730 DOI: 10.3390/microorganisms10102079] [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: 08/24/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal communities form close beneficial (mutualists) or detrimental (pathogens) associations with their plant hosts. Their diversity and abundance can be affected by agricultural practices which include cropping systems such as rotations and intercropping. Despite the importance of cropping systems in increasing productivity, knowledge of the fungal mycobiome and the core inhabitants for under-utilised cereal and legume crops, particularly over a period, is still limited. The core mycobiomes in plant tissues and bulk soils of a cereal-legume intercrop were characterized over two years using high-throughput sequencing. The intercropping trial consisted of sorghum, Bambara groundnut, cowpea, dry bean, and soybean. A greater number of molecular operational taxonomic units (MOTUs) were found in plant tissues compared to those from the soils and between year one and year two. Principal coordinate analyses revealed that fungal communities for each year were relatively distinct, particularly for the soils. The core mycobiome was dominated by a Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Didymellaceae sp. 2 (Epicoccum), Fusarium sp. 2, Unidentified (Ascomycota), and Cryptococcus MOTUs that were present in all plant tissues and soils of year one and two. Other key MOTUs were only specific to a year, substrate, or crop. Although the mycobiome of sorghum were more distinct than the cores of the legumes, there were still MOTUs dominant across all of the crops. Characterization of this baseline core across two years provides insight into those fungi that are always present in these crops, and that could be utilized in improving crop performance and productivity.
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Affiliation(s)
- Gilmore T. Pambuka
- Department of Genetics, University of the Free State, Bloemfontein 9301, South Africa
| | | | - Soumya Ghosh
- Department of Genetics, University of the Free State, Bloemfontein 9301, South Africa
| | - Errol D. Cason
- Department of Animal Sciences, University of the Free State, Bloemfontein 9301, South Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit, Department of Biological Sciences, Division of Virology, University of the Free State, Bloemfontein 9301, South Africa
| | - Marieka Gryzenhout
- Department of Genetics, University of the Free State, Bloemfontein 9301, South Africa
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Pang B, Yin D, Zhai Y, He A, Qiu L, Liu Q, Ma N, Shen H, Jia Q, Liang Z, Wang D. Diversity of endophytic fungal community in Huperzia serrata from different ecological areas and their correlation with Hup A content. BMC Microbiol 2022; 22:191. [PMID: 35931950 PMCID: PMC9354316 DOI: 10.1186/s12866-022-02605-y] [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: 03/24/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Huperzine A (Hup A) has attracted considerable attention as an effective therapeutic candidate drug used to treat Alzheimer’s disease. Whereas, the production of Hup A from wild plants faced a major challenge, which is the wild Huperzia Serrata harbor a low Hup A content, has a long-life cycle, and has a small yield. At present, several reports showed that Hup A is produced by various endophytic fungal strains isolated from H. serrata, thereby providing an alternative method to produce the compound and reduce the consumption of this rare and endangered plant. However, till now, very few comprehensive studies are available on the biological diversity and structural composition of endophytic fungi and the effects of endophytic fungi on the Hup A accumulation in H. serrata. Results In this research, the composition and diversity of fungal communities in H. serrata were deciphered based on high-throughput sequencing technology of fungal internal transcribed spacer regions2 (ITS2). The correlation between endophytic fungal community and Hup A content was also investigated. Results revealed that the richness and the diversity of endophytic fungi in H. serrata was various according to different tissues and different ecological areas. The endophytic fungal communities of H. serrata exhibit species-specific, ecological-specific, and tissue-specific characteristics. There are 6 genera (Ascomycota_unclassified, Cyphellophora, Fungi_unclassified, Sporobolomyces, and Trichomeriaceae_unclassified) were significantly positively correlated with Hup A content in all two areas, whereas, there are 6 genera (Auricularia, Cladophialophora, Cryptococcus, Mortierella, and Mycena) were significantly negatively correlated with Hup A content of in all two areas. Conclusions This study indicated a different composition and diverse endophytic fungal communities in H. serrata from different organs and ecological areas. The current study will provide the realistic basis and theoretical significance for understanding the biological diversity and structural composition of endophytic fungal communities in H. serrata, as well as providing novel insights into the interaction between endophytic fungi and Hup A content.
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Affiliation(s)
- Bo Pang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Dengpan Yin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Yufeng Zhai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Anguo He
- Administration of Zhejiang Dapanshan National Nature Reserve, Pan'an, Zhejiang, 322300, China
| | - Linlin Qiu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Qiao Liu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Nan Ma
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Hongjun Shen
- Ningbo Delai Medicinal Material Planting Co, Zhejiang, 315444, Ltd Ningbo, China
| | - Qiaojun Jia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Zongsuo Liang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Dekai Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China.
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Ma W, Yang Z, Liang L, Ma Q, Wang G, Zhao T. Characteristics of the Fungal Communities and Co-occurrence Networks in Hazelnut Tree Root Endospheres and Rhizosphere Soil. FRONTIERS IN PLANT SCIENCE 2021; 12:749871. [PMID: 34956257 PMCID: PMC8692873 DOI: 10.3389/fpls.2021.749871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Hazelnut has gained economic value in China in recent years, but its large-scale planting and research started later than other countries. Conducting basic research on hazelnut trees requires studying their related microorganisms. Here, we used high-throughput DNA sequencing to quantify the fungal communities in the root endospheres and rhizosphere soil of four hazelnut species. Fungal diversity in the rhizosphere soil was significantly higher than that in the root endospheres. Rhizosphere soil had more Mortierellomycota, and the fungal community compositions differed among the four hazelnut species. The root endospheres, especially those of the Ping'ou (Corylus heterophylla × Corylus avellana) trees, contained more ectomycorrhizal fungi. The co-occurrence networks in the rhizosphere soil were more sophisticated and stable than those in the root endospheres, even when the root endospheres had higher modularity, because the structural differentiation of the root endospheres differed from that of the rhizosphere soil. Two-factor correlation network analysis and linear regression analysis showed that the total organic carbon was the main environmental factor affecting the fungal communities. Our study revealed the community compositions, functional predictions, and co-occurrence network structural characteristics of fungi in hazelnut root endospheres and rhizosphere soil. We also examined the potential keystone taxa, and analyzed the environmental factors of the dominant fungal community compositions. This study provides guidance for the growth of hazelnut and the management of hazelnut garden, and provides an insight for future development of fungal inoculants to be used in hazelnut root.
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Affiliation(s)
- Wenxu Ma
- Key Laboratory Tree Breeding and Cultivation of the National Forestry and Grassland Administration/Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Beijing, China
- National Hazelnut Industry Innovation Alliance of National Forestry and Grassland Administration, Beijing, China
- Hazelnut Engineering and Technical Research Center of National Forestry and Grassland Administration, Beijing, China
| | - Zhen Yang
- Key Laboratory Tree Breeding and Cultivation of the National Forestry and Grassland Administration/Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Beijing, China
- National Hazelnut Industry Innovation Alliance of National Forestry and Grassland Administration, Beijing, China
- Hazelnut Engineering and Technical Research Center of National Forestry and Grassland Administration, Beijing, China
| | - Lisong Liang
- Key Laboratory Tree Breeding and Cultivation of the National Forestry and Grassland Administration/Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Beijing, China
- National Hazelnut Industry Innovation Alliance of National Forestry and Grassland Administration, Beijing, China
- Hazelnut Engineering and Technical Research Center of National Forestry and Grassland Administration, Beijing, China
| | - Qinghua Ma
- Key Laboratory Tree Breeding and Cultivation of the National Forestry and Grassland Administration/Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Beijing, China
- National Hazelnut Industry Innovation Alliance of National Forestry and Grassland Administration, Beijing, China
- Hazelnut Engineering and Technical Research Center of National Forestry and Grassland Administration, Beijing, China
| | - Guixi Wang
- Key Laboratory Tree Breeding and Cultivation of the National Forestry and Grassland Administration/Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Beijing, China
- National Hazelnut Industry Innovation Alliance of National Forestry and Grassland Administration, Beijing, China
- Hazelnut Engineering and Technical Research Center of National Forestry and Grassland Administration, Beijing, China
| | - Tiantian Zhao
- Key Laboratory Tree Breeding and Cultivation of the National Forestry and Grassland Administration/Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Beijing, China
- National Hazelnut Industry Innovation Alliance of National Forestry and Grassland Administration, Beijing, China
- Hazelnut Engineering and Technical Research Center of National Forestry and Grassland Administration, Beijing, China
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Baseline Data of the Fungal Phytobiome of Three Sorghum ( Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing. J Fungi (Basel) 2021; 7:jof7110978. [PMID: 34829265 PMCID: PMC8622221 DOI: 10.3390/jof7110978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.
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Adeleke BS, Babalola OO. The endosphere microbial communities, a great promise in agriculture. Int Microbiol 2020; 24:1-17. [PMID: 32737846 DOI: 10.1007/s10123-020-00140-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022]
Abstract
Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security. Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes. The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota live interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue. Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress. Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising. Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.
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Affiliation(s)
- Bartholomew Saanu Adeleke
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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