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Andreata MFL, Afonso L, Niekawa ETG, Salomão JM, Basso KR, Silva MCD, Alves LC, Alarcon SF, Parra MEA, Grzegorczyk KG, Chryssafidis AL, Andrade G. Microbial Fertilizers: A Study on the Current Scenario of Brazilian Inoculants and Future Perspectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:2246. [PMID: 39204682 PMCID: PMC11360115 DOI: 10.3390/plants13162246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
The increasing need for sustainable agricultural practices, combined with the demand for enhanced crop productivity, has led to a growing interest in utilizing microorganisms for biocontrol of diseases and pests, as well as for growth promotion. In Brazilian agriculture, the use of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF) has become increasingly prevalent, with a corresponding rise in the number of registered microbial inoculants each year. PGPR and PGPF occupy diverse niches within the rhizosphere, playing a crucial role in soil nutrient cycling and influencing a wide range of plant physiological processes. This review examines the primary mechanisms employed by these microbial agents to promote growth, as well as the strategy of co-inoculation to enhance product efficacy. Furthermore, we provide a comprehensive analysis of the microbial inoculants currently available in Brazil, detailing the microorganisms accessible for major crops, and discuss the market's prospects for the research and development of novel products in light of current challenges faced in the coming years.
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Affiliation(s)
- Matheus F. L. Andreata
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Leandro Afonso
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Erika T. G. Niekawa
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Julio M. Salomão
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Kawany Roque Basso
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Maria Clara D. Silva
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Leonardo Cruz Alves
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Stefani F. Alarcon
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Maria Eugenia A. Parra
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Kathlen Giovana Grzegorczyk
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | | | - Galdino Andrade
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
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2
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Li HH, Chen XW, Zhai FH, Li YT, Zhao HM, Mo CH, Luo Y, Xing B, Li H. Arbuscular Mycorrhizal Fungus Alleviates Charged Nanoplastic Stress in Host Plants via Enhanced Defense-Related Gene Expressions and Hyphal Capture. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6258-6273. [PMID: 38450439 DOI: 10.1021/acs.est.3c07850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Contamination of small-sized plastics is recognized as a factor of global change. Nanoplastics (NPs) can readily enter organisms and pose significant ecological risks. Arbuscular mycorrhizal (AM) fungi are the most ubiquitous and impactful plant symbiotic fungi, regulating essential ecological functions. Here, we first found that an AM fungus, Rhizophagus irregularis, increased lettuce shoot biomass by 25-100% when exposed to positively and negatively charged NPs vs control, although it did not increase that grown without NPs. The stress alleviation was attributed to the upregulation of gene expressions involving phytohormone signaling, cell wall metabolism, and oxidant scavenging. Using a root organ-fungus axenic growth system treated with fluorescence-labeled NPs, we subsequently revealed that the hyphae captured NPs and further delivered them to roots. NPs were observed at the hyphal cell walls, membranes, and spore walls. NPs mediated by the hyphae were localized at the root epidermis, cortex, and stele. Hyphal exudates aggregated positively charged NPs, thereby reducing their uptake due to NP aggregate formation (up to 5000 nm). This work demonstrates the critical roles of AM fungus in regulating NP behaviors and provides a potential strategy for NP risk mitigation in terrestrial ecosystems. Consequent NP-induced ecological impacts due to the affected AM fungi require further attention.
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Affiliation(s)
- Han Hao Li
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xun Wen Chen
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Feng Hua Zhai
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yong Tao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Hai Ming Zhao
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce Hui Mo
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yongming Luo
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Hui Li
- Guangdong Provincial Research Centre for Environment Pollution Control and Remediation Materials, Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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Li P, Tedersoo L, Crowther TW, Wang B, Shi Y, Kuang L, Li T, Wu M, Liu M, Luan L, Liu J, Li D, Li Y, Wang S, Saleem M, Dumbrell AJ, Li Z, Jiang J. Global diversity and biogeography of potential phytopathogenic fungi in a changing world. Nat Commun 2023; 14:6482. [PMID: 37838711 PMCID: PMC10576792 DOI: 10.1038/s41467-023-42142-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Phytopathogenic fungi threaten global food security but the ecological drivers of their global diversity and biogeography remain unknown. Here, we construct and analyse a global atlas of potential phytopathogenic fungi from 20,312 samples across all continents and major oceanic island regions, eleven land cover types, and twelve habitat types. We show a peak in the diversity of phytopathogenic fungi in mid-latitude regions, in contrast to the latitudinal diversity gradients observed in aboveground organisms. Our study identifies climate as an important driver of the global distribution of phytopathogenic fungi, and our models suggest that their diversity and invasion potential will increase globally by 2100. Importantly, phytopathogen diversity will increase largely in forest (37.27-79.12%) and cropland (34.93-82.51%) ecosystems, and this becomes more pronounced under fossil-fuelled industry dependent future scenarios. Thus, we recommend improved biomonitoring in forests and croplands, and optimised sustainable development approaches to reduce potential threats from phytopathogenic fungi.
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Affiliation(s)
- Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Thomas W Crowther
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China.
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lu Kuang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
| | - Ting Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Ming Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Dongzhen Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, 100091, Beijing, China
| | - Yongxia Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, 100091, Beijing, China
| | - Songhan Wang
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Colchester, Essex, UK.
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China.
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Sun X, Sharon O, Sharon A. Distinct Features Based on Partitioning of the Endophytic Fungi of Cereals and Other Grasses. Microbiol Spectr 2023; 11:e0061123. [PMID: 37166321 PMCID: PMC10269846 DOI: 10.1128/spectrum.00611-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
Endophytic fungi form a significant part of the plant mycobiome. Defining core members is crucial to understanding the assembly mechanism of fungal endophytic communities (FECs) and identifying functionally important community members. We conducted a meta-analysis of FECs in stems of wheat and five wild cereal species and generated a landscape of the fungal endophytic assemblages in this group of plants. The analysis revealed that several Ascomycota members and basidiomycetous yeasts formed an important compartment of the FECs in these plants. We observed a weak spatial autocorrelation at the regional scale and high intrahost variations in the FECs, suggesting a space-related heterogeneity. Accordingly, we propose that the heterogeneity among subcommunities should be a criterion to define the core endophytic members. Analysis of the subcommunities and meta-communities showed that the core and noncore members had distinct roles in various assembly processes, such as stochasticity, universal dynamics, and network characteristics, within each host. The distinct features identified between the community partitions of endophytes aid in understanding the principles that govern the assembly and function of natural communities. These findings can assist in designing synthetic microbiomes. IMPORTANCE This study proposes a novel method for diagnosing core microbiotas based on prevalence of community members in a meta-community, which could be determined and supported statistically. Using this approach, the study found stratification in community assembly processes within fungal endophyte communities (FECs) in the stems of wheat and cereal-related wild species. The core and noncore partitions of the FECs exhibited certain degrees of determinism from different aspects. Further analysis revealed abundant and consistent interactions between rare taxa, which might contribute to the determinism process in noncore partitions. Despite minor differences in FEC compositions, wheat FECs showed distinct patterns in community assembly processes compared to wild species, suggesting the effects of domestication on FECs. Overall, our study provided a new approach for identifying core microbiota and provides insights into the community assembly processes within FECs in wheat and related wild species.
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Affiliation(s)
- Xiang Sun
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Or Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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Yu J, Tang SN, Lee PKH. Universal Dynamics of Microbial Communities in Full-Scale Textile Wastewater Treatment Plants and System Prediction by Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3345-3356. [PMID: 36795777 DOI: 10.1021/acs.est.2c08116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The performance of full-scale biological wastewater treatment plants (WWTPs) depends on the operational and environmental conditions of treatment systems. However, we do not know how much these conditions affect microbial community structures and dynamics across systems over time and predictability of the treatment performance. For over a year, the microbial communities of four full-scale WWTPs processing textile wastewater were monitored. During temporal succession, the environmental conditions and system treatment performance were the main drivers, which explained up to 51% of community variations within and between all plants based on the multiple regression models. We identified the universality of community dynamics in all systems using the dissimilarity-overlap curve method, with the significant negative slopes suggesting that the communities containing the same taxa from different plants over time exhibited a similar composition dynamic. The Hubbell neutral theory and the covariance neutrality test indicated that all systems had a dominant niche-based assembly mechanism, supporting that the communities had a similar composition dynamic. Phylogenetically diverse biomarkers for the system conditions and treatment performance were identified by machine learning. Most of the biomarkers (83%) were classified as generalist taxa, and the phylogenetically related biomarkers responded similarly to the system conditions. Many biomarkers for treatment performance perform functions that are crucial for wastewater treatment processes (e.g., carbon and nutrient removal). This study clarifies the relationships between community composition and environmental conditions in full-scale WWTPs over time.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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6
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Zhimo VY, Kumar A, Biasi A, Abdelfattah A, Sharma VK, Salim S, Feygenberg O, Bartuv R, Freilich S, Whitehead SR, Wisniewski M, Droby S. Assembly and dynamics of the apple carposphere microbiome during fruit development and storage. Front Microbiol 2022; 13:928888. [PMID: 36016781 PMCID: PMC9395710 DOI: 10.3389/fmicb.2022.928888] [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: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at different developmental stages and storage. There was a significant effect (Adonis, p ≤ 0.001) of fruit genotype and its developmental stages and storage times on the fruit surface microbial assemblage and a strong temporal microbial community succession was detected (Mantel test: R ≤ 0.5, p = 0.001) in both bacterial and fungal communities. A set of 15 bacterial and 35 fungal core successional taxa and members exhibiting differential abundances at different fruit stages were identified. For the first time, we show the existence of underlying universal dynamics in the assembly of fruit-associated microbiomes. We also provide evidence of strong microbial cross-domain associations and uncover potential microbe-microbe correlations in the apple carposphere. Together our findings shed light on how the fruit carposphere assemble and change over time, and provide new insights into fruit microbial ecology.
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Affiliation(s)
- V. Yeka Zhimo
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ajay Kumar
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Antonio Biasi
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee, Potsdam, Germany
| | - Vijay Kumar Sharma
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Shoshana Salim
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Rotem Bartuv
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishay, Israel
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishay, Israel
| | - Susan R. Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Samir Droby
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
- *Correspondence: Samir Droby,
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7
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Zhang G, Wei F, Chen Z, Wang Y, Jiao S, Yang J, Chen Y, Liu C, Huang Z, Dong L, Chen S. Evidence for saponin diversity-mycobiome links and conservatism of plant-fungi interaction patterns across Holarctic disjunct Panax species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154583. [PMID: 35304141 DOI: 10.1016/j.scitotenv.2022.154583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.
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Affiliation(s)
- Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co, Ltd., Wenshan 663000, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling 712100, China.
| | - JiaYing Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yongzhong Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Congsheng Liu
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Zhixin Huang
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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8
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Lino IAN, Silva DKADA, Martins LMV, Maia LC, Yano-Melo AM. Microbial inoculation and fertilizer application on growth of cowpea and spore-based assemblages of arbuscular mycorrhizal fungi in its rhizophere. AN ACAD BRAS CIENC 2022; 94:e20201243. [PMID: 35830070 DOI: 10.1590/0001-3765202220201243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/11/2020] [Indexed: 11/22/2022] Open
Abstract
In this study, the effect of microbial inoculants and fertilizer application on cowpea (BRS Pujante) growth and on the structure and composition of arbuscular mycorrhizal fungi (AMF) assemblages were evaluated. A completely randomized experiment was set up involving 17 treatments: four with AMF, three with nodulating bacteria, six with AMF + nodulating bacteria, two with phosphorus, one with nitrogen and one control (reference) in five replicates. Plant growth and nutritional content, mycorrhizal colonization, glomerospores number, spore-based AMF assemblages and ecological indices were evaluated. Mycorrhizal inoculants associated with Bradyrhizobium BR3267 strain were more effective than the Microvirga BR3296 strain. Multidimensional scaling analysis showed that Acaulospora longula treatments were more similar among themselves, and distinct from the other treatments. A difference was observed in the structure of AMF community assemblage between treatments with G. albida + Bradyrhizobium BR 3267 and A. longula, with greater Shannon diversity and Pielou equitability indices in the first treatment and greater dominance in the treatment with A. longula only. Long-term studies are required to determine if the successful establishment of A. longula among indigenous species persists over time and if its dominant behavior is not deleterious to the AMF native community.
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Affiliation(s)
- Ingrid A N Lino
- Programa de Pós-Graduação em Biologia de Fungos, Universidade Federal de Pernambuco, Departamento de Micologia, Av. Prof. Moraes Rego, s/n, Cidade Universitária, 50740-600 Recife, PE, Brazil
| | - Danielle K A DA Silva
- Programa de Pós-Graduação em Ecologia e Monitoramento Ambiental, Universidade Federal da Paraíba, Centro de Ciências Aplicadas e Educação, Departamento de Engenharia e Meio Ambiente, Campus IV, Conj. Pres. Castelo Branco III, 58297-000 Rio Tinto, PB, Brazil
| | - Lindete M V Martins
- Universidade do Estado da Bahia/UNEB, Departamento de Tecnologia e Ciências Sociais-DTCS, Campus III, Rua Edgar Chastinet, s/n, São Geraldo, 48900-000 Juazeiro, BA, Brazil
| | - Leonor C Maia
- Programa de Pós-Graduação em Biologia de Fungos, Universidade Federal de Pernambuco, Departamento de Micologia, Av. Prof. Moraes Rego, s/n, Cidade Universitária, 50740-600 Recife, PE, Brazil
| | - Adriana M Yano-Melo
- Programa de Pós-Graduação em Biologia de Fungos, Universidade Federal de Pernambuco, Departamento de Micologia, Av. Prof. Moraes Rego, s/n, Cidade Universitária, 50740-600 Recife, PE, Brazil
- Universidade Federal do Vale do São Francisco, Colegiado de Zootecnia, Campus de Ciências Agrárias, Rodovia BR-407, Km 12, Lote 543, s/n, 56300-990 Petrolina, PE, Brazil
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Estrela S, Sánchez Á, Rebolleda-Gómez M. Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology. Front Microbiol 2021; 12:657467. [PMID: 33897672 PMCID: PMC8062719 DOI: 10.3389/fmicb.2021.657467] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.
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Affiliation(s)
- Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
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Vila JCC, Liu YY, Sanchez A. Dissimilarity-Overlap analysis of replicate enrichment communities. THE ISME JOURNAL 2020; 14:2505-2513. [PMID: 32555503 PMCID: PMC7490387 DOI: 10.1038/s41396-020-0702-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/29/2020] [Accepted: 06/09/2020] [Indexed: 11/09/2022]
Abstract
The taxonomic composition of microbial communities can vary substantially across habitats and within the same habitat over time. Efforts to build quantitative and predictive models of microbial population dynamics are underway, but fundamental questions remain. How different are population dynamics in different environments? Do communities that share the same taxa also exhibit identical dynamics? In vitro communities can help establish baseline expectations that are critical towards resolving these questions in natural communities. Here, we applied a recently developed tool, Dissimilarity-Overlap Analysis (DOA), to a set of experimental in vitro communities that differed in nutrient composition. The Dissimilarity and Overlap of these communities are negatively correlated in replicate habitats, as one would expect if microbial population dynamics were on average strongly convergent (or "universal") across these replicate habitats. However, the existence of such a negative correlation does not necessarily imply that population dynamics are always universal in all communities. Even in replicate, identical habitats, two different communities may contain the same set of taxa at different abundances in equilibrium. The formation of alternative states in community assembly is strongly associated with the presence of specific taxa in the communities. Our results benchmark DOA, providing support for some of its core assumptions, and suggest that communities sharing the same taxa and external abiotic factors generally (but not necessarily) have a negative correlation between Dissimilarity and Overlap.
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Affiliation(s)
- Jean C C Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA.
- Microbial Sciences Institute, Yale University West Campus, West Haven, CT, 06516, USA.
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
| | - Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA.
- Microbial Sciences Institute, Yale University West Campus, West Haven, CT, 06516, USA.
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11
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Radujković D, van Diggelen R, Bobbink R, Weijters M, Harris J, Pawlett M, Vicca S, Verbruggen E. Initial soil community drives heathland fungal community trajectory over multiple years through altered plant-soil interactions. THE NEW PHYTOLOGIST 2020; 225:2140-2151. [PMID: 31569277 DOI: 10.1111/nph.16226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Dispersal limitation, biotic interactions, and environmental filters interact to drive plant and fungal community assembly, but their combined effects are rarely investigated. This study examines how different heathland plant and fungal colonization scenarios realized via three biotic treatments - addition of mature heathland-derived sod, addition of hay, and no additions - affect soil fungal community development over 6 yr along a manipulated pH gradient in a large-scale experiment starting from an agricultural, topsoil removed state. Our results show that both biotic and abiotic (pH) treatments had a persistent influence on the development of fungal communities, but that sod additions diminished the effect of abiotic treatments through time. Analysis of correlation networks between soil fungi and plants suggests that the reduced effect of pH in the sod treatment, where both soil and plant propagules were added, might be due to plant-fungal interactions since the sod additions caused stronger, more specific, and more consistent connections compared with the no addition treatment. Based on these results, we suggest that the initial availability of heathland fungal and plant taxa, which reinforce each other, can significantly steer further fungal community development to an alternative configuration, overriding the otherwise prominent effect of abiotic (pH) conditions.
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Affiliation(s)
- Dajana Radujković
- Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
| | - Rudy van Diggelen
- Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
| | - Roland Bobbink
- B-WARE Research Centre, Radboud University, PO Box 6558, 6503 GB, Nijmegen, the Netherlands
| | - Maaike Weijters
- B-WARE Research Centre, Radboud University, PO Box 6558, 6503 GB, Nijmegen, the Netherlands
| | - Jim Harris
- School of Water, Energy, and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Mark Pawlett
- School of Water, Energy, and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Sara Vicca
- Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
| | - Erik Verbruggen
- Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, Antwerp, 2610, Belgium
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Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics. Nat Commun 2020; 11:34. [PMID: 31911594 PMCID: PMC6946711 DOI: 10.1038/s41467-019-13913-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/28/2019] [Indexed: 11/16/2022] Open
Abstract
Community assembly of crop-associated fungi is thought to be strongly influenced by deterministic selection exerted by the plant host, rather than stochastic processes. Here we use a simple, sorghum system with abundant sampling to show that stochastic forces (drift or stochastic dispersal) act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed, conditions when mycobiomes are small. Unexpectedly, we find no signal for stochasticity when drought stress is relieved, likely due to renewed selection by the host. In our experimental system, the host compartment exerts the strongest effects on mycobiome assembly, followed by the timing of plant development and lastly by plant genotype. Using a dissimilarity-overlap approach, we find a universality in the forces of community assembly of the mycobiomes of the different sorghum compartments and in functional guilds of fungi. Fungal community assembly on crop plants is thought to be driven by deterministic selection exerted by the host. Here Gao et al. use a sorghum system to show that stochastic forces act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed.
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Zhao J, Gao Q, Zhou J, Wang M, Liang Y, Sun B, Chu H, Yang Y. The scale dependence of fungal community distribution in paddy soil driven by stochastic and deterministic processes. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.07.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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