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Li Y, Narayanan M, Shi X, Chen X, Li Z, Ma Y. Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167774. [PMID: 37848152 DOI: 10.1016/j.scitotenv.2023.167774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.
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Affiliation(s)
- Yujia Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Mathiyazhagan Narayanan
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai 602105, Tamil Nadu, India
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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Klueken AM, Mahfoud Y, Rößler S, Ludwig-Müller J. Testing Effects of Seed Treatments against Clubroot Disease in Various Oilseed Rape Hybrids. Pathogens 2023; 12:1339. [PMID: 38003803 PMCID: PMC10675021 DOI: 10.3390/pathogens12111339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Clubroot disease, caused by the protist pathogen Plasmodiophora brassicae, is an emerging threat to cruciferous crops, including oilseed rape (Brassica napus L.). Most of the current commercial cultivars are highly susceptible, and efficient management tools are lacking practical implementation. Over three years and three experimental periods, we studied the effects of isotianil in comparison with Bacillus amyloliquefaciens QST713-HiCFU against clubroot disease under greenhouse experiments. Our results show control effects, which were strongly dependent on seasons, host plant genotype, and clubroot isolates: isotianil and B. amyloliquefaciens QST713-HiCFU reduced disease severity consistently at variable, but field-relevant spore concentrations of clubroot isolates; with seed treatments showing superior effects compared to drench applications. The co-application of isotianil with B. amyloliquefaciens QST713-HiCFU could, in some cases, increase the efficacy. Interestingly, all studied hybrids reacted to treatments, albeit to a somewhat different extent. When tested against a field isolate, the results obtained with the single spore isolate were partially confirmed but with greater variability. Overall, the generally positive effects of isotianil and B. amyloliquefaciens QST713-HiCFU on the reduction of clubroot were repeatedly observed. The inoculation of clubroot disease with different spore counts indicates a dose-response effect for tested products. This study highlights the importance of performing experiments holistically over multiple, consecutive seasons, with various isolates, application types, and different genetic resources of host plants.
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Affiliation(s)
- A. Michael Klueken
- Bayer AG, Crop Science Division, Disease Control Biology, 40789 Monheim am Rhein, Germany;
| | - Yamen Mahfoud
- Faculty of Biology, Technische Universität Dresden, 01217 Dresden, Germany; (Y.M.); (S.R.)
| | - Sabine Rößler
- Faculty of Biology, Technische Universität Dresden, 01217 Dresden, Germany; (Y.M.); (S.R.)
| | - Jutta Ludwig-Müller
- Faculty of Biology, Technische Universität Dresden, 01217 Dresden, Germany; (Y.M.); (S.R.)
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Hoosein S, Neuenkamp L, Trivedi P, Paschke MW. AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning? FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1141963. [PMID: 37746131 PMCID: PMC10512368 DOI: 10.3389/ffunb.2023.1141963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 09/26/2023]
Abstract
Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.
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Affiliation(s)
- Shabana Hoosein
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Lena Neuenkamp
- Institute of Landscape Ecology, Münster University, Münster, Germany
- Department of Ecology and Multidisciplinary Institute for Environment Studies “Ramon Margalef,” University of Alicante, Alicante, Spain
| | - Pankaj Trivedi
- Microbiome Network, Department of Agricultural Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Mark W. Paschke
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
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Lu X, Yan G, Fu L, Cui B, Wang J, Zhou D. A review of filamentous sludge bulking controls from conventional methods to emerging quorum quenching strategies. WATER RESEARCH 2023; 236:119922. [PMID: 37098319 DOI: 10.1016/j.watres.2023.119922] [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] [Received: 11/22/2022] [Revised: 03/16/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
Filamentous bulking, which results from the overgrowth of filamentous microorganisms, is a common issue that frequently disrupts the stable operation of activated sludge processes. Recent literature has paid attention to the relationship between quorum sensing (QS) and filamentous bulking highlighting that the morphological transformations of filamentous microbes are regulated by functional signal molecules in the bulking sludge system. In response to this, a novel quorum quenching (QQ) technology has been developed to control sludge bulking effectively and precisely by disturbing QS-mediated filamentation behaviors. This paper presents a critical review on the limitations of classical bulking hypotheses and traditional control methods, and provides an overview of recent QS/QQ studies that aim to elucidate and control filamentous bulking, including the characterization of molecule structures, the elaboration of QS pathways, and the precise design of QQ molecules to mitigate filamentous bulking. Finally, suggestions for further research and development of QQ strategies for precise bulking control are put forward.
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Affiliation(s)
- Xin Lu
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, PR China
| | - Ge Yan
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, PR China
| | - Liang Fu
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, PR China
| | - Bin Cui
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, PR China
| | - Dandan Zhou
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, PR China.
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Twizeyimana M, Hammer PE, Gachango E, Craig K, Espejo B, Biggs MB, Kremer J, Ingham DJ. Diverse environmental bacteria displaying activity against Phakopsora pachyrhizi, the cause of soybean rust. FRONTIERS IN PLANT SCIENCE 2023; 14:1080116. [PMID: 36818841 PMCID: PMC9932200 DOI: 10.3389/fpls.2023.1080116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
The management of soybean rust (SBR) caused by the obligate fungus Phakopsora pachyrhizi mostly relies on the use of synthetic fungicides, especially in areas where the disease inflicts serious yield losses. The reliance on synthetic fungicides to manage this disease has resulted in resistance of P. pachyrhizi populations to most fungicides. In this study, bacteria isolated from diverse environments were evaluated for their biocontrol potential against P. pachyrhizi using soybean detached-leaf method and on-plant in the growth chamber, greenhouse, and field. Among 998 bacterial isolates evaluated using the detached-leaf method; 58% were isolated from plant-related materials, 27% from soil, 10% from insects, and 5% from other environments. Of the isolates screened, 73 were active (they had ⪖ 75% rust reduction) with an active rate of 7.3%. From the active isolates, 65 isolates were re-tested on-plant in the growth chamber for activity confirmation. In the confirmation test, 49 bacteria isolated from plant-related materials maintained their activity with a confirmation rate of 75%. The majority of bacteria with confirmed activity belonged to the taxonomic classes Bacilli and Gammaproteobacteria (70%). Active isolates were prioritized for greenhouse and field testing based on activity in the initial screen and confirmation test. Six bacterial isolates AFS000009 (Pseudomonas_E chlororaphis), AFS032321 (Bacillus subtilis), AFS042929 (Bacillus_C megaterium), AFS065981 (Bacillus_X simplex_A), AFS090698 (Bacillus_A thuringiensis_S), and AFS097295 (Bacillus_A toyonensis) were selected from those bacteria that maintained activity in the confirmation test and were evaluated in the greenhouse, and five among them were evaluated in the field. From the Alabama field evaluation, all bacterial isolates reduced rust infection as well as azoxystrobin (Quadris® at 0.3 L/ha) used as the fungicide control (P > 0.05). Moreover, the scanning electron micrographs demonstrated evidence of antagonistic activity of AFS000009 and AFS032321 against P. pachyrhizi urediniospores. Bacterial isolates that consistently showed activity comparable to that of azoxystrobin can be improved through fermentation and formulation optimization, developed, and deployed. These bacteria strains would provide a valuable alternative to the synthetic fungicides and could play a useful role in integrated disease management programs for this disease.
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Wang L, Zhao M, Du X, Feng K, Gu S, Zhou Y, Yang X, Zhang Z, Wang Y, Zhang Z, Zhang Q, Xie B, Han G, Deng Y. Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions. Front Microbiol 2023; 13:1076610. [PMID: 36687630 PMCID: PMC9853292 DOI: 10.3389/fmicb.2022.1076610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
Wetlands are natural sources of methane (CH4) emissions, providing the largest contribution to the atmospheric CH4 pool. Changes in the ecohydrological environment of coastal salt marshes, especially the surface inundation level, cause instability in the CH4 emission levels of coastal ecosystems. Although soil methane-associated microorganisms play key roles in both CH4 generation and metabolism, how other microorganisms regulate methane emission and their responses to inundation has not been investigated. Here, we studied the responses of prokaryotic, fungal and cercozoan communities following 5 years of inundation treatments in a wetland experimental site, and molecular ecological networks analysis (MENs) was constructed to characterize the interdomain relationship. The result showed that the degree of inundation significantly altered the CH4 emissions, and the abundance of the pmoA gene for methanotrophs shifted more significantly than the mcrA gene for methanogens, and they both showed significant positive correlations to methane flux. Additionally, we found inundation significantly altered the diversity of the prokaryotic and fungal communities, as well as the composition of key species in interactions within prokaryotic, fungal, and cercozoan communities. Mantel tests indicated that the structure of the three communities showed significant correlations to methane emissions (p < 0.05), suggesting that all three microbial communities directly or indirectly contributed to the methane emissions of this ecosystem. Correspondingly, the interdomain networks among microbial communities revealed that methane-associated prokaryotic and cercozoan OTUs were all keystone taxa. Methane-associated OTUs were more likely to interact in pairs and correlated negatively with the fungal and cercozoan communities. In addition, the modules significantly positively correlated with methane flux were affected by environmental stress (i.e., pH) and soil nutrients (i.e., total nitrogen, total phosphorus and organic matter), suggesting that these factors tend to positively regulate methane flux by regulating microbial relationships under inundation. Our findings demonstrated that the inundation altered microbial communities in coastal wetlands, and the fungal and cercozoan communities played vital roles in regulating methane emission through microbial interactions with the methane-associated community.
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Affiliation(s)
- Linlin Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mingliang Zhao
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuqi Zhou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qi Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Baohua Xie
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China,Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Guangxuan Han
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China,Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China,CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Ye Deng,
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Anwar N, Jiang Y, Ma W, Yao Y, Li J, Ababaikeli G, Li G, Ma T. Culturable bacteria diversity in stem liquid and resina from Populus euphratica and screening of plant growth-promoting bacteria. BMC Microbiol 2022; 22:322. [PMID: 36581840 PMCID: PMC9798617 DOI: 10.1186/s12866-022-02731-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Populus euphratica Olivier is a kind of tree capable of growing in extremely arid desert and semi-desert environments. In this study, a culture-dependent method was used to analyze the bacterial diversity of stem liquid of P. euphratica and resina of P. euphratica, and to further evaluate plant growth promoting (PGP) activity. RESULTS A total of 434 bacteria were isolated from stem fluid and resina of P. euphratica in Ebinur Lake Wetland Nature Reserve and Mulei Primitive forest. The results of taxonomic composition analysis shows that Gammaproteobacteria, Firmicutes, and Actinobacteria_c are the three dominant groups in all the communities, and the representative genera are Bacillus, Nesterenkonia and Halomonas. The diversity analysis shows that the culturable bacterial community diversity of P. euphratica in Ebinur Lake Wetland Nature Reserve is higher than that in Mulei Primitive forest, and the bacterial community diversity of P. euphratica stem fluid is higher than that of resina. According to PGP activity evaluation, 158 functional bacteria with plant growth promoting potential were screened. Among them, 61 strains havephosphorus solubilizing abilities, 80 strains have potassium solubilizing abilities, 32 strains have nitrogen fixation abilities, and 151 strains have iron ammonia salt utilization abilities. The germination rate, plant height, and dry weight of the maize seedlings treated with strains BB33-1, TC10 and RC6 are significantly higher than those of the control group. CONCLUSION In this study, a large number of culturable bacteria were isolated from P. euphratica, which provides new functional bacteria sources for promoting plant growth.
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Affiliation(s)
- Nusratgul Anwar
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Yuhang Jiang
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Wenbo Ma
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Yuhao Yao
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Jue Li
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Gulibahaer Ababaikeli
- grid.464477.20000 0004 1761 2847College of Life Sciences, Xinjiang Normal University, Urumqi, 830054 China
| | - Guoqiang Li
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Ting Ma
- grid.216938.70000 0000 9878 7032Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071 China
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Ruan C, Ramoneda J, Gogia G, Wang G, Johnson DR. Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion. Curr Biol 2022; 32:5285-5294.e4. [PMID: 36455559 DOI: 10.1016/j.cub.2022.11.009] [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: 05/31/2022] [Revised: 09/20/2022] [Accepted: 11/03/2022] [Indexed: 12/05/2022]
Abstract
The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.
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Affiliation(s)
- Chujin Ruan
- College of Land Science and Technology, China Agricultural University, 100193 Beijing, China; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Josep Ramoneda
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland; Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
| | - Guram Gogia
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland; Department of Environmental Systems Science, Swiss Federal Institute of Technology, 8092 Zürich, Switzerland
| | - Gang Wang
- College of Land Science and Technology, China Agricultural University, 100193 Beijing, China; National Black Soil & Agriculture Research, China Agricultural University, 100193 Beijing, China.
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
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Zhang W, Luo X, Mei YZ, Yang Q, Zhang AY, Chen M, Mei Y, Ma CY, Du YC, Li M, Zhu Q, Sun K, Xu FJ, Dai CC. Priming of rhizobial nodulation signaling in the mycosphere accelerates nodulation of legume hosts. THE NEW PHYTOLOGIST 2022; 235:1212-1230. [PMID: 35488499 DOI: 10.1111/nph.18192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
The simultaneous symbiosis of leguminous plants with two root mutualists, endophytic fungi and rhizobia is common in nature, yet how two mutualists interact and co-exist before infecting plants and the concomitant effects on nodulation are less understood. Using a combination of metabolic analysis, fungal deletion mutants and comparative transcriptomics, we demonstrated that Bradyrhizobium and a facultatively biotrophic fungus, Phomopsis liquidambaris, interacted to stimulate fungal flavonoid production, and thereby primed Bradyrhizobial nodulation signaling, enhancing Bradyrhizobial responses to root exudates and leading to early nodulation of peanut (Arachis hypogaea), and such effects were compromised when disturbing fungal flavonoid biosynthesis. Stress sensitivity assays and reactive oxygen species (ROS) determination revealed that flavonoid production acted as a strategy to alleviate hyphal oxidative stress during P. liquidambaris-Bradyrhizobial interactions. By investigating the interactions between P. liquidambaris and a collection of 38 rhizobacteria, from distinct bacterial genera, we additionally showed that the flavonoid-ROS module contributed to the maintenance of fungal and bacterial co-existence, and fungal niche colonization under soil conditions. Our results demonstrate for the first time that rhizobial nodulation signaling can be primed by fungi before symbiosis with host plants and highlight the importance of flavonoid in tripartite interactions between legumes, beneficial fungi and rhizobia.
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Affiliation(s)
- Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Xue Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan-Zhen Mei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Qian Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Man Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan Mei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Ying-Chun Du
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Min Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Qiang Zhu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Fang-Ji Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, 250100, Shandong, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
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10
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de Oliveira AA, Ramalho MDO, Moreau CS, Campos AEDC, Harakava R, Bueno OC. Exploring the diversity and potential interactions of bacterial and fungal endophytes associated with different cultivars of olive (Olea europaea) in Brazil. Microbiol Res 2022; 263:127128. [PMID: 35868260 DOI: 10.1016/j.micres.2022.127128] [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: 05/26/2021] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 10/17/2022]
Abstract
The olive crop has expanded in the southeastern region of South America, particularly in Brazil. Thus, the objectives of this study were to identify the diversity of endophytic microorganisms associated with olive leaves with culture-dependent and culture-independent methods, to explore which factors influence the composition and abundance of this microbial community, to identify the trophic mode of these fungi by FunGuild and, to verify type associations between bacterial and fungal communities. Leaf samples were collected from 93 plants in nine locations in the Brazilian states of São Paulo and Minas Gerais. Leaves were first superficially disinfected before fungal isolation and next-generation metabarcoding sequencing was completed targeting the 16S rRNA regions for bacteria and ITS1 for fungi. In total, 800 isolates were obtained, which were grouped into 191 morphotypes and molecularly identified, resulting in 38 genera, 32 of which were recorded for the first time in cultivated olive trees in Brazil. For the isolated fungi, the most abundant trophic level was pathotrophic and for the culture-independent method was unidentified followed by symbiotrophic. The metabarcoding results revealed that factors such as plant age, altitudinal gradient, and geographic location can influence the microbial community of commercial olive plants, while the specific cultivar did not.
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Affiliation(s)
- Amanda Aparecida de Oliveira
- São Paulo State University (UNESP) - Institute of Biosciences - Campus Rio Claro, Department of General and Applied Biology. Center for Social Insect Studies, Rio Claro, SP 13506-900, Brazil; Biological Institute of São Paulo - Vila Mariana, São Paulo, SP 04014-002, Brazil.
| | | | - Corrie Saux Moreau
- Cornell University, Department of Entomology, Ithaca, NY 14853, USA; Cornell University, Department of Ecology and Evolutionary Biology, Ithaca, NY 14853, USA
| | | | - Ricardo Harakava
- Biological Institute of São Paulo - Vila Mariana, São Paulo, SP 04014-002, Brazil
| | - Odair Correa Bueno
- São Paulo State University (UNESP) - Institute of Biosciences - Campus Rio Claro, Department of General and Applied Biology. Center for Social Insect Studies, Rio Claro, SP 13506-900, Brazil
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11
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Bandyopadhyay P, Yadav BG, Kumar SG, Kumar R, Kogel KH, Kumar S. Piriformospora indica and Azotobacter chroococcum Consortium Facilitates Higher Acquisition of N, P with Improved Carbon Allocation and Enhanced Plant Growth in Oryza sativa. J Fungi (Basel) 2022; 8:jof8050453. [PMID: 35628709 PMCID: PMC9146537 DOI: 10.3390/jof8050453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 12/21/2022] Open
Abstract
The soil microbiome contributes to nutrient acquisition and plant adaptation to numerous biotic and abiotic stresses. Numerous studies have been conducted over the past decade showing that plants take up nutrients better when associated with fungi and additional beneficial bacteria that promote plant growth, but the mechanisms by which the plant host benefits from this tripartite association are not yet fully understood. In this article, we report on a synergistic interaction between rice (Oryza sativa), Piriformospora indica (an endophytic fungus colonizing the rice roots), and Azotobacter chroococcum strain W5, a free-living nitrogen-fixing bacterium. On the basis of mRNA expression analysis and enzymatic activity, we found that co-inoculation of plant roots with the fungus and the rhizobacterium leads to enhanced plant growth and improved nutrient uptake compared to inoculation with either of the two microbes individually. Proteome analysis of O. sativa further revealed that proteins involved in nitrogen and phosphorus metabolism are upregulated and improve nitrogen and phosphate uptake. Our results also show that A. chroococcum supports colonization of rice roots by P. indica, and consequentially, the plants are more resistant to biotic stress upon co-colonization. Our research provides detailed insights into the mechanisms by which microbial partners synergistically promote each other in the interaction while being associated with the host plant.
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Affiliation(s)
- Prasun Bandyopadhyay
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (P.B.); (B.G.Y.); (S.G.K.); (R.K.)
| | - Bal Govind Yadav
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (P.B.); (B.G.Y.); (S.G.K.); (R.K.)
| | - Srinivasan Ganesh Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (P.B.); (B.G.Y.); (S.G.K.); (R.K.)
| | - Rahul Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (P.B.); (B.G.Y.); (S.G.K.); (R.K.)
| | - Karl-Heinz Kogel
- Institute for Phytopathology, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392 Giessen, Germany;
| | - Shashi Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; (P.B.); (B.G.Y.); (S.G.K.); (R.K.)
- Correspondence:
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12
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Lu X, Wang Y, Chen C, Feng Z, Huo Y, Zhou D. C12-HSL is an across-boundary signal molecule that could alleviate fungi Galactomyces's filamentation: A new mechanism on activated sludge bulking. ENVIRONMENTAL RESEARCH 2022; 204:111823. [PMID: 34400160 DOI: 10.1016/j.envres.2021.111823] [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: 05/07/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Fungal bulking is caused by fungi excessive growth and morphological changes, resulting from the evolution toward fungi dominant activated sludge. Communication across fungi and bacteria boundary that mediated by bacterial signal molecules (SMs) probably is the central induce caused fungal bulking occurrence. In this work, it intended to identify the bacterial SM that affected fungal bulking, and verified its roles in regulate the spore germination and hyphal growth. We found C12-HSL concentration decreased significantly from 12.36 to 3.38 ng/g-VSS (P < 0.05) when fungal sludge bulking happened, and filamentous Galactomyces's relatively abundant was correlatively enriched. To test the effects of this SM, trace commercial C12-HSL was added to pure cultured Galactomyces, in which spore germination rates decreased by 20 % and hyphal extension inhibited by 15 %. Ras1-cAMP-PKA and mitogen-activated protein kinase (MAPK) pathways of Galactomyces were responsible for signal C12-HSL transduction, which inhibited peroxisome biosynthesis, suppressed the biological activity of the actin cytoskeleton, and disrupted intercellular organelle transport. All these results showed C12-HSL was the functional SM that could suppress the development of fungal filamentous. This study provided a new insight into the sludge bulking mechanism from view of cross-kingdom communication.
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Affiliation(s)
- Xin Lu
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun, 130117, China
| | - Yue Wang
- Quality, Safety & Environmental Protection Department, Shanxi Road & Bridge Construction Group Co., Ltd, Taiyuan, 030000, China
| | - Congli Chen
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun, 130117, China
| | - Zhixuan Feng
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun, 130117, China
| | - Yang Huo
- School of Physics, Northeast Normal University, Changchun, 130117, China.
| | - Dandan Zhou
- Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun, 130117, China.
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13
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Laihonen M, Saikkonen K, Helander M, Vázquez de Aldana BR, Zabalgogeazcoa I, Fuchs B. Epichloë Endophyte-Promoted Seed Pathogen Increases Host Grass Resistance Against Insect Herbivory. Front Microbiol 2022; 12:786619. [PMID: 35087489 PMCID: PMC8787217 DOI: 10.3389/fmicb.2021.786619] [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: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Plants host taxonomically and functionally complex communities of microbes. However, ecological studies on plant-microbe interactions rarely address the role of multiple co-occurring plant-associated microbes. Here, we contend that plant-associated microbes interact with each other and can have joint consequences for higher trophic levels. In this study we recorded the occurrence of the plant seed pathogenic fungus Claviceps purpurea and aphids (Sitobion sp.) on an established field experiment with red fescue (Festuca rubra) plants symbiotic to a seed transmitted endophytic fungus Epichloë festucae (E+) or non-symbiotic (E-). Both fungi are known to produce animal-toxic alkaloids. The study was conducted in a semi-natural setting, where E+ and E- plants from different origins (Spain and Northern Finland) were planted in a randomized design in a fenced common garden at Kevo Subarctic Research Station in Northern Finland. The results reveal that 45% of E+ plants were infected with Claviceps compared to 31% of E- plants. Uninfected plants had 4.5 times more aphids than Claviceps infected plants. By contrast, aphid infestation was unaffected by Epichloë symbiosis. Claviceps alkaloid concentrations correlated with a decrease in aphid numbers, which indicates their insect deterring features. These results show that plant mutualistic fungi can increase the infection probability of a pathogenic fungus, which then becomes beneficial to the plant by controlling herbivorous insects. Our study highlights the complexity and context dependency of species-species and multi-trophic interactions, thus challenging the labeling of species as plant mutualists or pathogens.
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Affiliation(s)
| | | | - Marjo Helander
- Department of Biology, University of Turku, Turku, Finland
| | | | - Iñigo Zabalgogeazcoa
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
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14
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Roychoudhury T, Ray B, Seal A. Metabolically dependent consortia in biofilm: A new horizon for green agriculture. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Bahram M, Netherway T. Fungi as mediators linking organisms and ecosystems. FEMS Microbiol Rev 2021; 46:6468741. [PMID: 34919672 PMCID: PMC8892540 DOI: 10.1093/femsre/fuab058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.
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Affiliation(s)
- Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 40 Lai St. Estonia
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden
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16
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Dixit AR, Khodadad CLM, Hummerick ME, Spern CJ, Spencer LE, Fischer JA, Curry AB, Gooden JL, Maldonado Vazquez GJ, Wheeler RM, Massa GD, Romeyn MW. Persistence of Escherichia coli in the microbiomes of red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) - does seed sanitization matter? BMC Microbiol 2021; 21:289. [PMID: 34686151 PMCID: PMC8532290 DOI: 10.1186/s12866-021-02345-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants' health or productivity. To determine the impact of seed sanitization on the plants' microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli. RESULT E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment. CONCLUSION Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.
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Affiliation(s)
- Anirudha R Dixit
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | | | - Mary E Hummerick
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Cory J Spern
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - LaShelle E Spencer
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Jason A Fischer
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Aaron B Curry
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Jennifer L Gooden
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | | | | | - Gioia D Massa
- NASA UB, Kennedy Space Center, Merritt Island, FL, USA
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17
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Zhou Z, Hu R, Ni Y, Zhuang W, Luo Z, Huang W, Yan Q, He Z, Zhong Q, Wang C. Genetic Elucidation of Quorum Sensing and Cobamide Biosynthesis in Divergent Bacterial-Fungal Associations Across the Soil-Mangrove Root Interface. Front Microbiol 2021; 12:698385. [PMID: 34675891 PMCID: PMC8524053 DOI: 10.3389/fmicb.2021.698385] [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: 04/21/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
Plant roots in soil host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, the potential microbial interactions and underlying mechanisms remain largely unknown across the soil-mangrove root interface. We herein analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere, and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment harboring more dense co-occurrences with a higher average connectivity in bacterial-fungal network (2.986) than in bacterial (2.628) or fungal network (2.419), which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae, and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. In support of this finding, we also found that the genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH, and lasR) and aerobic cobamide biosynthesis (cobG, cobF, and cobA) were highly enriched in the endosphere, whereas anaerobic cobamide biosynthesis (encoded by cbiT and cbiE) was dominant in three peripheral compartments. Our results provide genetic evidence for the intensified bacterial-fungal associations of root endophytes, highlighting the critical role of the soil-root interface in structuring the microbial inter-domain associations.
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Affiliation(s)
- Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yanmei Ni
- Guangdong Agribusiness Tropical Agriculture Institute, Guangzhou, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Weiming Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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18
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Bhalla K, Qu X, Kretschmer M, Kronstad JW. The phosphate language of fungi. Trends Microbiol 2021; 30:338-349. [PMID: 34479774 DOI: 10.1016/j.tim.2021.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022]
Abstract
Phosphate is an essential macronutrient for fungal proliferation as well as a key mediator of antagonistic, beneficial, and pathogenic interactions between fungi and other organisms. In this review, we summarize recent insights into the integration of phosphate metabolism with mechanisms of fungal adaptation that support growth and survival. In particular, we highlight aspects of phosphate sensing important for responses to stress and regulation of cell-surface changes with an impact on fungal pathogenesis, host immune responses, and disease outcomes. Additionally, new studies provide insights into the influence of phosphate availability on cooperative or antagonistic interactions between fungi and other microbes, the associations of mycorrhizal and endophytic fungi with plants, and connections with plant immunity. Overall, phosphate homeostasis is emerging as an integral part of fungal metabolism and communication to support diverse lifestyles.
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Affiliation(s)
- Kabir Bhalla
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Xianya Qu
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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19
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Harrison XA, McDevitt AD, Dunn JC, Griffiths SM, Benvenuto C, Birtles R, Boubli JP, Bown K, Bridson C, Brooks DR, Browett SS, Carden RF, Chantrey J, Clever F, Coscia I, Edwards KL, Ferry N, Goodhead I, Highlands A, Hopper J, Jackson J, Jehle R, da Cruz Kaizer M, King T, Lea JMD, Lenka JL, McCubbin A, McKenzie J, de Moraes BLC, O'Meara DB, Pescod P, Preziosi RF, Rowntree JK, Shultz S, Silk MJ, Stockdale JE, Symondson WOC, de la Pena MV, Walker SL, Wood MD, Antwis RE. Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proc Biol Sci 2021; 288:20210552. [PMID: 34403636 PMCID: PMC8370808 DOI: 10.1098/rspb.2021.0552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.
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Affiliation(s)
| | - Allan D. McDevitt
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenny C. Dunn
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, UK
| | - Sarah M. Griffiths
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Chiara Benvenuto
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard Birtles
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jean P. Boubli
- School of Science, Engineering and Environment, University of Salford, UK
| | - Kevin Bown
- School of Science, Engineering and Environment, University of Salford, UK
| | - Calum Bridson
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Darren R. Brooks
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S. Browett
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ruth F. Carden
- School of Archaeology, University College Dublin, Ireland
- Wildlife Ecological and Osteological Consultancy, Wicklow, Ireland
| | - Julian Chantrey
- Institute of Veterinary Science, University of Liverpool, UK
| | - Friederike Clever
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, UK
| | - Katie L. Edwards
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, UK
| | - Andrew Highlands
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jane Hopper
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
| | - Joseph Jackson
- School of Science, Engineering and Environment, University of Salford, UK
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Tony King
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
- School of Anthropology and Conservation, University of Kent, UK
| | - Jessica M. D. Lea
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Jessica L. Lenka
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Jack McKenzie
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Denise B. O'Meara
- School of Science and Computing, Waterford Institute of Technology, Ireland
| | - Poppy Pescod
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard F. Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Jennifer K. Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | | | - Jennifer E. Stockdale
- School of Biosciences, University of Cardiff, UK
- School of Life Sciences, University of Nottingham, UK
| | | | | | - Susan L. Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Michael D. Wood
- School of Science, Engineering and Environment, University of Salford, UK
| | - Rachael E. Antwis
- School of Science, Engineering and Environment, University of Salford, UK
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20
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Leino L, Tall T, Helander M, Saloniemi I, Saikkonen K, Ruuskanen S, Puigbò P. Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase) for assessing sensitivity of organisms to the herbicide. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124556. [PMID: 33243645 DOI: 10.1016/j.jhazmat.2020.124556] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/01/2020] [Accepted: 11/10/2020] [Indexed: 06/11/2023]
Abstract
Glyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the widespread use of glyphosate may have unsuspected impacts on the diversity and composition of microbial communities, including the human gut microbiome. Here, we introduce the first bioinformatics method to assess the potential sensitivity of organisms to glyphosate based on the type of EPSPS enzyme. We have precomputed a dataset of EPSPS sequences from thousands of species that will be an invaluable resource to advancing the research field. This novel methodology can classify sequences from nearly 90% of eukaryotes and >80% of prokaryotes. A conservative estimate from our results shows that 54% of species in the core human gut microbiome are sensitive to glyphosate.
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Affiliation(s)
- Lyydia Leino
- Department of Biology, University of Turku, Turku, Finland
| | - Tuomas Tall
- Department of Biology, University of Turku, Turku, Finland
| | - Marjo Helander
- Department of Biology, University of Turku, Turku, Finland
| | - Irma Saloniemi
- Department of Biology, University of Turku, Turku, Finland
| | | | - Suvi Ruuskanen
- Department of Biology, University of Turku, Turku, Finland
| | - Pere Puigbò
- Department of Biology, University of Turku, Turku, Finland; Nutrition and Health Unit, Eurecat Technology Centre of Catalonia, Reus, Catalonia, Spain; Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Catalonia, Spain.
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21
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Faddetta T, Abbate L, Alibrandi P, Arancio W, Siino D, Strati F, De Filippo C, Fatta Del Bosco S, Carimi F, Puglia AM, Cardinale M, Gallo G, Mercati F. The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures. Sci Rep 2021; 11:7078. [PMID: 33782436 PMCID: PMC8007603 DOI: 10.1038/s41598-021-86399-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 03/10/2021] [Indexed: 11/28/2022] Open
Abstract
Citrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi—belonging to Aspergillus, Quambalaria and Bjerkandera genera—and bacteria—belonging to Staphylococcus genus—were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions from in vitro growing seedlings regenerated from surface-sterilized seeds. This analysis highlighted that Cutibacterium and Acinetobacter were the most abundant bacterial genera in both seeds and shoots, while Cladosporium and Debaryomyces were the most abundant fungal genera in seeds and shoots, respectively. The localization of bacterial endophytes in seed and shoot tissues was revealed by Fluorescence In Situ Hybridization coupled with Confocal Laser Scanning Microscopy revealing vascular bundle colonization. Thus, these results highlighted for the first time the structures of endophytic microbiota of C. limon seeds and the transmission to shoots, corroborating the idea of a vertical transmission of plant microbiota and suggesting its crucial role in seed germination and plant development.
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Affiliation(s)
- Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Loredana Abbate
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Pasquale Alibrandi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Walter Arancio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.,Ri.MED Foundation, Palermo, Italy
| | - Davide Siino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Francesco Strati
- Laboratory of Mucosal Immunology, Department of Experimental Oncology, European Institute of Oncology, Milano, Italy
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council, Pisa, Italy
| | - Sergio Fatta Del Bosco
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Francesco Carimi
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany.,Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.
| | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
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22
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Liang Y, Li B, Zhang Q, Zhang S, He X, Jiang L, Jin Y. Interaction analyses based on growth parameters of GWAS between Escherichia coli and Staphylococcus aureus. AMB Express 2021; 11:34. [PMID: 33646434 PMCID: PMC7921238 DOI: 10.1186/s13568-021-01192-x] [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: 11/28/2020] [Accepted: 02/09/2021] [Indexed: 01/02/2023] Open
Abstract
To accurately explore the interaction mechanism between Escherichia coli and Staphylococcus aureus, we designed an ecological experiment to monoculture and co-culture E. coli and S. aureus. We co-cultured 45 strains of E. coli and S. aureus, as well as each species individually to measure growth over 36 h. We implemented a genome wide association study (GWAS) based on growth parameters (λ, R, A and s) to identify significant single nucleotide polymorphisms (SNPs) of the bacteria. Three commonly used growth regression equations, Logistic, Gompertz, and Richards, were used to fit the bacteria growth data of each strain. Then each equation's Akaike's information criterion (AIC) value was calculated as a commonly used information criterion. We used the optimal growth equation to estimate the four parameters above for strains in co-culture. By plotting the estimates for each parameter across two strains, we can visualize how growth parameters respond ecologically to environment stimuli. We verified that different genotypes of bacteria had different growth trajectories, although they were the same species. We reported 85 and 52 significant SNPs that were associated with interaction in E. coli and S. aureus, respectively. Many significant genes might play key roles in interaction, such as yjjW, dnaK, aceE, tatD, ftsA, rclR, ftsK, fepA in E. coli, and scdA, trpD, sdrD, SAOUHSC_01219 in S. aureus. Our study illustrated that there were multiple genes working together to affect bacterial interaction, and laid a solid foundation for the later study of more complex inter-bacterial interaction mechanisms.
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23
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Wanke A, Malisic M, Wawra S, Zuccaro A. Unraveling the sugar code: the role of microbial extracellular glycans in plant-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:15-35. [PMID: 32929496 PMCID: PMC7816849 DOI: 10.1093/jxb/eraa414] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/14/2020] [Indexed: 05/14/2023]
Abstract
To defend against microbial invaders but also to establish symbiotic programs, plants need to detect the presence of microbes through the perception of molecular signatures characteristic of a whole class of microbes. Among these molecular signatures, extracellular glycans represent a structurally complex and diverse group of biomolecules that has a pivotal role in the molecular dialog between plants and microbes. Secreted glycans and glycoconjugates such as symbiotic lipochitooligosaccharides or immunosuppressive cyclic β-glucans act as microbial messengers that prepare the ground for host colonization. On the other hand, microbial cell surface glycans are important indicators of microbial presence. They are conserved structures normally exposed and thus accessible for plant hydrolytic enzymes and cell surface receptor proteins. While the immunogenic potential of bacterial cell surface glycoconjugates such as lipopolysaccharides and peptidoglycan has been intensively studied in the past years, perception of cell surface glycans from filamentous microbes such as fungi or oomycetes is still largely unexplored. To date, only few studies have focused on the role of fungal-derived cell surface glycans other than chitin, highlighting a knowledge gap that needs to be addressed. The objective of this review is to give an overview on the biological functions and perception of microbial extracellular glycans, primarily focusing on their recognition and their contribution to plant-microbe interactions.
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Affiliation(s)
- Alan Wanke
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Milena Malisic
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, Cologne, Germany
| | - Stephan Wawra
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, Cologne, Germany
| | - Alga Zuccaro
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, Cologne, Germany
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24
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Becker R, Ulrich K, Behrendt U, Kube M, Ulrich A. Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus. Front Microbiol 2020; 11:590944. [PMID: 33193255 PMCID: PMC7649789 DOI: 10.3389/fmicb.2020.590944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/02/2020] [Indexed: 01/17/2023] Open
Abstract
The invasive ascomycete Hymenoscyphus fraxineus has been threatening Fraxinus excelsior populations throughout Europe for over two decades. Since the infection and first colonization by the pathogen occurs in leaves, leaf-colonizing microorganisms have been discussed as a barrier and as possible biocontrol agents against the disease. To identify fungal groups with health-supporting potential, we compared the fungal microbiota of compound leaves from susceptible and tolerant ash trees in four ash stands with high H. fraxineus exposure. The fungal communities were analyzed both culture-independently by ITS2 amplicon sequencing and by the taxonomic classification of 1,704 isolates using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) or sequencing of the entire ITS region. The fungal community structure did not show significant differences depending on the health status. However, for several OTUs and a MALDI group, a significantly higher abundance was found in tolerant ash trees. Thus, the yeast Papiliotrema flavescens was significantly increased and accounted for 12.3% of the mycobiome of tolerant ashes (OTU0003), and it had also a distinctly higher abundance among the isolates. The filamentous ascomycete Sarocladium strictum was increased 24-fold among the isolates of tolerant trees, but its abundance was comparably low. An in vitro screening for the growth inhibition of the pathogen via cocultivation resulted in 28 yeast-like isolates and 79 filamentous fungi with antagonistic activity. A statistical cocultivation test on two H. fraxineus strains confirmed six of the yeast-like isolates that suppressed H. fraxineus significantly, from 39-50%, two of them through a fungicidal effect. The highest inhibition rates among the yeasts were found for three isolates belonging to Aureobasidium pullulans and P. flavescens. The cocultivation test of the filamentous isolates revealed higher effects compared to the yeasts. Four isolates showed significant inhibition of both H. fraxineus strains with a rate of 72-100%, and five further isolates inhibited only one H. fraxineus strain significantly. The most effective isolates were members of the genus Cladosporium. During the next step, in planta tests will be necessary to verify the efficacy of the antagonistic isolates and to assess their suitability as biocontrol agents.
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Affiliation(s)
- Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Michael Kube
- Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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25
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Floral fungal-bacterial community structure and co-occurrence patterns in four sympatric island plant species. Fungal Biol 2020; 125:49-61. [PMID: 33317776 DOI: 10.1016/j.funbio.2020.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 01/30/2023]
Abstract
Flowers' fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success-both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada, Ipomoea cairica, Ipomoea pes-caprae, and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities.
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26
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Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
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Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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27
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28
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Bastías DA, Johnson LJ, Card SD. Symbiotic bacteria of plant-associated fungi: friends or foes? CURRENT OPINION IN PLANT BIOLOGY 2020; 56:1-8. [PMID: 31786411 DOI: 10.1016/j.pbi.2019.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Many bacteria form symbiotic associations with plant-associated fungi. The effects of these symbionts on host fitness usually depend on symbiont or host genotypes and environmental conditions. However, bacterial endosymbionts, that is those living within fungal cells, may positively regulate host performance as their survival is often heavily dependent on host fitness. Contrary to this, bacteria that establish ectosymbiotic associations with fungi, that is those located on the hyphal surface or in close vicinity to fungal mycelia, may not have an apparent net effect on fungal performance due to the low level of fitness dependency on their host. Our analysis supports the hypothesis that endosymbiotic bacteria of fungi are beneficial symbionts, and that effects of ectosymbiotic bacteria on fungal performance depends on the bacterial type involved in the interaction (e.g. helper versus pathogen of fungi). Ecological scenarios, where the presence of beneficial bacterial endosymbionts of fungi could be compromised, are also discussed.
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Affiliation(s)
- Daniel A Bastías
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
| | - Linda J Johnson
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Stuart D Card
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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29
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Exploring Rice Root Microbiome; The Variation, Specialization and Interaction of Bacteria and Fungi In Six Tropic Savanna Regions in Ghana. SUSTAINABILITY 2020. [DOI: 10.3390/su12145835] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We investigated the root microbiomes of rice sampled from six major rice-producing regions in Ghana using Illumina MiSeq high-throughput amplicon sequencing analysis. The result showed that both bacterial and fungal community compositions were significantly varied across the regions. Bacterial communities were shaped predominantly by biotic factors, including root fungal diversity and abundance. In contrast, fungal communities were influenced by abiotic factors such as soil nitrate, total carbon and soil pH. A negative correlation between the diversity and abundance of root fungi with soil nitrate (NO3-) level was observed. It suggested that there were direct and indirect effects of NO3- on the root-associated bacterial and fungal community composition. The gradient of soil nitrate from North to South parts of Ghana may influence the composition of rice root microbiome. Bacterial community composition was shaped by fungal diversity and abundance; whereas fungal community composition was shaped by bacterial abundance. It suggested the mutualistic interaction of bacteria and fungi at the community level in the rice root microbiome. Specific bacterial and fungal taxa were detected abundantly in the ‘Northern’ regions of Ghana, which were very low or absent from the samples of other regions. The analysis of indicator species suggested that an ‘ecological specialization’ may have occurred which enabled specific microbial taxa to adapt to the local environment, such as the low-nitrate condition in the Northern regions.
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30
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Ulrich K, Becker R, Behrendt U, Kube M, Ulrich A. A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus. Front Microbiol 2020; 11:966. [PMID: 32547506 PMCID: PMC7273808 DOI: 10.3389/fmicb.2020.00966] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.
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Affiliation(s)
- Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | - Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Michael Kube
- Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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31
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Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nat Commun 2020; 11:2577. [PMID: 32444671 PMCID: PMC7244730 DOI: 10.1038/s41467-020-16431-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
The gut microbiome consists of a multi-kingdom microbial community. Whilst the role of bacteria as causal contributors governing host physiological development is well established, the role of fungi remains to be determined. Here, we use germ-free mice colonized with defined species of bacteria, fungi, or both to differentiate the causal role of fungi on microbiome assembly, immune development, susceptibility to colitis, and airway inflammation. Fungal colonization promotes major shifts in bacterial microbiome ecology, and has an independent effect on innate and adaptive immune development in young mice. While exclusive fungal colonization is insufficient to elicit overt dextran sulfate sodium-induced colitis, bacterial and fungal co-colonization increase colonic inflammation. Ovalbumin-induced airway inflammation reveals that bacterial, but not fungal colonization is necessary to decrease airway inflammation, yet fungi selectively promotes macrophage infiltration in the airway. Together, our findings demonstrate a causal role for fungi in microbial ecology and host immune functionality, and therefore prompt the inclusion of fungi in therapeutic approaches aimed at modulating early life microbiomes. The immunomodulatory role of commensal gut fungi and interactions with bacteria remain unclear. Here, using germ-free mice colonized with defined species of bacteria and fungi, the authors find that fungal colonization induces changes in bacterial microbiome ecology while having an independent effect on innate and adaptive immunity in mice.
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32
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Li H, Yan C, Tang Y, Ma X, Chen Y, Chen S, Lin M, Liu Z. Endophytic bacterial and fungal microbiota in different cultivars of cassava (Manihot esculenta Crantz). J Microbiol 2020; 58:614-623. [PMID: 32424579 DOI: 10.1007/s12275-020-9565-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 01/01/2023]
Abstract
Endophytes colonize tissues of healthy host plants and play a crucial role in plant growth and development. However, little attention has been paid to the endophytes of tuber crops such as cassava, which is used as a staple food by approximately 800 million people worldwide. This study aimed to elucidate the diversity and composition of endophytic bacterial and fungal communities in different cassava cultivars using high-throughput sequencing. Although no significant differences in richness or diversity were observed among the different cassava cultivars, the community compositions were diverse. Two cultivars (SC124 and SC205) tolerant to root rot exhibited similar community compositions, while two other cultivars (SC10 and SC5), which are moderately and highly susceptible to root rot, respectively, harboured similar community compositions. Proteobacteria, Firmicutes, and Ascomycota dominated the endophyte assemblages, with Weissella, Serratia, Lasiodiplodia, Fusarium, and Diaporthe being the predominant genera. The differentially abundant taxonomic clades between the tolerant and susceptible cultivars were mainly rare taxa, such as Lachnoclostridium_5, Rhizobium, Lampropedia, and Stenotrophomonas. These seemed to be key genera that affected the susceptibility of cassava to root rot. Moreover, the comparison of KEGG functional profiles revealed that 'Environmental adaptation' category was significantly enriched in the tolerant cultivars, while 'Infectious diseases: Parasitic' category was significantly enriched in the susceptible cultivars. The present findings open opportunities for further studies on the roles of endophytes in the susceptibility of plants to diseases.
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Affiliation(s)
- Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, P. R. China
| | - Chengliang Yan
- School of Tropical Crops, Hainan University, Haikou, 570228, P. R. China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, P. R. China
| | - Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, P. R. China
| | - Yinhua Chen
- School of Tropical Crops, Hainan University, Haikou, 570228, P. R. China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, P. R. China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, P. R. China.
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Hamzah N, Kasmuri N, Tao W, Singhal N, Padhye L, Swift S. Effect of rhamnolipid on the physicochemical properties and interaction of bacteria and fungi. Braz J Microbiol 2020; 51:1317-1326. [PMID: 32399689 DOI: 10.1007/s42770-020-00295-0] [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: 08/25/2019] [Accepted: 05/07/2020] [Indexed: 10/24/2022] Open
Abstract
Bacterial adhesion on surfaces is an essential initial step in promoting bacterial mobilization for soil bioremediation process. Modification of the cell surface is required to improve the adhesion of bacteria. The modification of physicochemical properties by rhamnolipid to Pseudomonas putida KT2442, Rhodococcus erythropolis 3586 and Aspergillus brasiliensis ATCC 16404 strains was analysed using contact angle measurements. The surface energy and total free energy of adhesion were calculated to predict the adhesion of both bacteria strains on the A. brasiliensis surface. The study of bacterial adhesion was carried out to evaluate experimental value with the theoretical results. Bacteria and fungi physicochemical properties were modified significantly when treated with rhamnolipid. The adhesion rate of P. putida improved by 16% with the addition of rhamnolipid (below 1 CMC), while the increase of rhamnolipid concentration beyond 1 CMC did not further enhance the bacterial adhesion. The addition of rhamnolipid did not affect the adhesion of R. erythropolis. A good relationship has been obtained in which water contact angle and surface energy of fungal surfaces are the major factors contributing to the bacterial adhesion. The adhesion is mainly driven by acid-base interaction. This finding provides insight to the role of physicochemical properties in controlling the bacterial adhesion on the fungal surface to enhance bacteria transport in soil bioremediation.
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Affiliation(s)
- Nurhidayah Hamzah
- Department of Water Resources and Environmental Systems, Faculty of Civil Engineering, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia
| | - Norhafezah Kasmuri
- Department of Water Resources and Environmental Systems, Faculty of Civil Engineering, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia.
| | - Wei Tao
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, People's Republic of China
| | - Naresh Singhal
- Department of Environmental Engineering, Faculty of Civil and Environmental Engineering, University of Auckland, Auckland, New Zealand
| | - Lokesh Padhye
- Department of Environmental Engineering, Faculty of Civil and Environmental Engineering, University of Auckland, Auckland, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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Saikkonen K, Nissinen R, Helander M. Toward Comprehensive Plant Microbiome Research. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00061] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Mycelial network-mediated rhizobial dispersal enhances legume nodulation. ISME JOURNAL 2020; 14:1015-1029. [PMID: 31974462 DOI: 10.1038/s41396-020-0587-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/07/2020] [Accepted: 01/14/2020] [Indexed: 12/14/2022]
Abstract
The access of rhizobia to legume host is a prerequisite for nodulation. Rhizobia are poorly motile in soil, while filamentous fungi are known to grow extensively across soil pores. Since root exudates-driven bacterial chemotaxis cannot explain rhizobial long-distance dispersal, mycelia could constitute ideal dispersal networks to help rhizobial enrichment in the legume rhizosphere from bulk soil. Thus, we hypothesized that mycelia networks act as vectors that enable contact between rhizobia and legume and influence subsequent nodulation. By developing a soil microcosm system, we found that a facultatively biotrophic fungus, Phomopsis liquidambaris, helps rhizobial migration from bulk soil to the peanut (Arachis hypogaea) rhizosphere and, hence, triggers peanut-rhizobium nodulation but not seen in the absence of mycelia. Assays of dispersal modes suggested that cell proliferation and motility mediated rhizobial dispersal along mycelia, and fungal exudates might contribute to this process. Furthermore, transcriptomic analysis indicated that genes associated with the cell division, chemosensory system, flagellum biosynthesis, and motility were regulated by Ph. liquidambaris, thus accounting for the detected rhizobial dispersal along hyphae. Our results indicate that rhizobia use mycelia as dispersal networks that migrate to legume rhizosphere and trigger nodulation. This work highlights the importance of mycelial network-based bacterial dispersal in legume-rhizobium symbiosis.
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del Barrio-Duque A, Ley J, Samad A, Antonielli L, Sessitsch A, Compant S. Beneficial Endophytic Bacteria- Serendipita indica Interaction for Crop Enhancement and Resistance to Phytopathogens. Front Microbiol 2019; 10:2888. [PMID: 31921065 PMCID: PMC6930893 DOI: 10.3389/fmicb.2019.02888] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/02/2019] [Indexed: 12/30/2022] Open
Abstract
Serendipita (=Piriformospora) indica is a fungal endophytic symbiont with the capabilities to enhance plant growth and confer resistance to different stresses. However, the application of this fungus in the field has led to inconsistent results, perhaps due to antagonism with other microbes. Here, we studied the impact of individual bacterial isolates from the endophytic bacterial community on the in vitro growth of S. indica. We further analyzed how combinations of bacteria and S. indica influence plant growth and protection against the phytopathogens Fusarium oxysporum and Rhizoctonia solani. Bacterial strains of the genera Bacillus, Enterobacter and Burkholderia negatively affected S. indica growth on plates, whereas Mycolicibacterium, Rhizobium, Paenibacillus strains and several other bacteria from different taxa stimulated fungal growth. To further explore the potential of bacteria positively interacting with S. indica, four of the most promising strains belonging to the genus Mycolicibacterium were selected for further experiments. Some dual inoculations of S. indica and Mycolicibacterium strains boosted the beneficial effects triggered by S. indica, further enhancing the growth of tomato plants, and alleviating the symptoms caused by the phytopathogens F. oxysporum and R. solani. However, some combinations of S. indica and bacteria were less effective than individual inoculations. By analyzing the genomes of the Mycolicibacterium strains, we revealed that these bacteria encode several genes predicted to be involved in the stimulation of S. indica growth, plant development and tolerance to abiotic and biotic stresses. Particularly, a high number of genes related to vitamin and nitrogen metabolism were detected. Taking into consideration multiple interactions on and inside plants, we showed in this study that some bacterial strains may induce beneficial effects on S. indica and could have an outstanding influence on the plant-fungus symbiosis.
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Affiliation(s)
| | | | | | | | | | - Stéphane Compant
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
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Horner A, Browett SS, Antwis RE. Mixed-Cropping Between Field Pea Varieties Alters Root Bacterial and Fungal Communities. Sci Rep 2019; 9:16953. [PMID: 31740751 PMCID: PMC6861290 DOI: 10.1038/s41598-019-53342-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/29/2019] [Indexed: 01/21/2023] Open
Abstract
Modern agricultural practices have vastly increased crop production but negatively affected soil health. As such, there is a call to develop sustainable, ecologically-viable approaches to food production. Mixed-cropping of plant varieties can increase yields, although impacts on plant-associated microbial communities are unclear, despite their critical role in plant health and broader ecosystem function. We investigated how mixed-cropping between two field pea (Pisum sativum L.) varieties (Winfreda and Ambassador) influenced root-associated microbial communities and yield. The two varieties supported significantly different fungal and bacterial communities when grown as mono-crops. Mixed-cropping caused changes in microbial communities but with differences between varieties. Root bacterial communities of Winfreda remained stable in response to mixed-cropping, whereas those of Ambassador became more similar to Winfreda. Conversely, root fungal communities of Ambassador remained stable under mixed-cropping, and those of Winfreda shifted towards the composition of Ambassador. Microbial co-occurrence networks of both varieties were stronger and larger under mixed-cropping, which may improve stability and resilience in agricultural soils. Both varieties produced slightly higher yields under mixed-cropping, although overall Ambassador plants produced higher yields than Winfreda plants. Our results suggest that variety diversification may increase yield and promote microbial interactions.
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Affiliation(s)
- Anthony Horner
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK.
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Endophytic Bacteria Potentially Promote Plant Growth by Synthesizing Different Metabolites and their Phenotypic/Physiological Profiles in the Biolog GEN III MicroPlate TM Test. Int J Mol Sci 2019; 20:ijms20215283. [PMID: 31652989 PMCID: PMC6862297 DOI: 10.3390/ijms20215283] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/16/2022] Open
Abstract
Endophytic bacteria, as the most promising components of effective, biofertilizers biostimulating and biocontrol preparations, should be very intensively obtained from various plants and studied in terms of the conditions determining the potential ability to promote plant growth. For this reason, endophytic bacteria have been isolated from both stems and roots of up to six systematically distant species of vascular plants: one species belonging to the seedless vascular plants (Monilophyta), and five seed plants (Spermatophyta). The 23 isolated strains represented nine genera: Delftia, Stenotrophomonas, Rhizobium, Brevundimonas, Variovorax, Achromobacter, Novosphingobium, Comamonas and Collimonas, notably which were closely related—belonging to the phylum Proteobacteria. Stenotrophomonas sp. strains showed the greatest ability to synthesize indole-3-acetic acid (IAA)-like compounds, while Achromobacter sp. strains produced the highest levels of siderophores. The presence of the nifH gene and nitrogen binding activity was demonstrated for 95% of the strains tested. Stenotrophomonas maltophila (ES2 strain) showed the highest metabolic activity based on Biolog GEN III test. The ability to solubilize phosphate was determined only for three tested strains from genus: Delftia, Rhizobium and Novosphingobium. The presented work demonstrated that the metabolic and phenotypic properties of plant growth-promoting endophytes are correlated with the genus of bacteria and are not correlated with the host plant species or part of plant (stem, root).
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Wemheuer F, Wemheuer B, Daniel R, Vidal S. Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands. Sci Rep 2019; 9:14183. [PMID: 31578453 PMCID: PMC6775154 DOI: 10.1038/s41598-019-50540-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/10/2019] [Indexed: 01/04/2023] Open
Abstract
Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands (control leaves; CL), within green island areas (GLA) and the surrounding yellow leaf areas (YLA) of leaves with green islands of Acer campestre and A. platanoides. GLA samples of A. campestre and A. platanoides were dominated by Sawadaea polyfida and S. bicornis, respectively, suggesting that these fungi might be responsible for the green islands. We detected a higher fungal richness and diversity in CL compared to GLA samples of A. campestre. Leaf status (CL, GLA, YLA) significantly altered the composition of fungal communities of A. campestre. This was related to differences in fungal community composition between YLA and GLA samples. Site was the main driver of bacterial communities, suggesting that bacterial and fungal endophytes are shaped by different factors. Overall, we observed Acer species-specific responses of endophyte communities towards the presence of green islands and/or leaf type, which might be attributed to several fungi and bacteria specifically associated with one Acer species.
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Affiliation(s)
- Franziska Wemheuer
- Department of Crop Sciences, University of Göttingen, Grisebachstr.6, D-37077, Göttingen, Germany
- Applied Marine and Estuarine Ecology, Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Stefan Vidal
- Department of Crop Sciences, University of Göttingen, Grisebachstr.6, D-37077, Göttingen, Germany.
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Doonan J, Denman S, Pachebat JA, McDonald JE. Genomic analysis of bacteria in the Acute Oak Decline pathobiome. Microb Genom 2019; 5. [PMID: 30625111 PMCID: PMC6412055 DOI: 10.1099/mgen.0.000240] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The UK’s native oak is under serious threat from Acute Oak Decline (AOD). Stem tissue necrosis is a primary symptom of AOD and several bacteria are associated with necrotic lesions. Two members of the lesion pathobiome, Brenneria goodwinii and Gibbsiella quercinecans, have been identified as causative agents of tissue necrosis. However, additional bacteria including Lonsdalea britannica and Rahnella species have been detected in the lesion microbiome, but their role in tissue degradation is unclear. Consequently, information on potential genome-encoded mechanisms for tissue necrosis is critical to understand the role and mechanisms used by bacterial members of the lesion pathobiome in the aetiology of AOD. Here, the whole genomes of bacteria isolated from AOD-affected trees were sequenced, annotated and compared against canonical bacterial phytopathogens and non-pathogenic symbionts. Using orthologous gene inference methods, shared virulence genes that retain the same function were identified. Furthermore, functional annotation of phytopathogenic virulence genes demonstrated that all studied members of the AOD lesion microbiota possessed genes associated with phytopathogens. However, the genome of B. goodwinii was the most characteristic of a necrogenic phytopathogen, corroborating previous pathological and metatranscriptomic studies that implicate it as the key causal agent of AOD lesions. Furthermore, we investigated the genome sequences of other AOD lesion microbiota to understand the potential ability of microbes to cause disease or contribute to pathogenic potential of organisms isolated from this complex pathobiome. The role of these members remains uncertain but some such as G. quercinecans may contribute to tissue necrosis through the release of necrotizing enzymes and may help more dangerous pathogens activate and realize their pathogenic potential or they may contribute as secondary/opportunistic pathogens with the potential to act as accessory species for B. goodwinii. We demonstrate that in combination with ecological data, whole genome sequencing provides key insights into the pathogenic potential of bacterial species whether they be phytopathogens, part-contributors or stimulators of the pathobiome.
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Affiliation(s)
- James Doonan
- 1School of Biological Sciences, Bangor University, Bangor, UK
| | - Sandra Denman
- 2Forest Research, Centre for Forestry and Climate Change, Farnham, UK
| | - Justin A Pachebat
- 3Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Wipf D, Krajinski F, van Tuinen D, Recorbet G, Courty PE. Trading on the arbuscular mycorrhiza market: from arbuscules to common mycorrhizal networks. THE NEW PHYTOLOGIST 2019; 223:1127-1142. [PMID: 30843207 DOI: 10.1111/nph.15775] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/20/2019] [Indexed: 05/08/2023]
Abstract
Arbuscular mycorrhiza (AM) symbiosis occurs between obligate biotrophic fungi of the phylum Glomeromycota and most land plants. The exchange of nutrients between host plants and AM fungi (AMF) is presumed to be the main benefit for the two symbiotic partners. In this review article, we outline the current concepts of nutrient exchanges within this symbiosis (mechanisms and regulation). First, we focus on phosphorus and nitrogen transfer from the fungal partner to the host plant, and on the reciprocal transfer of carbon compounds, with a highlight on a possible interplay between nitrogen and phosphorus nutrition during AM symbiosis. We further discuss potential mechanisms of regulation of these nutrient exchanges linked to membrane dynamics. The review finally addresses the common mycorrhizal networks formed AMF, which interconnect plants from similar and/or different species. Finally the best way to integrate this knowledge and the ensuing potential benefits of AM into sustainable agriculture is discussed.
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Affiliation(s)
- Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, Univ. Bourgogne, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Franziska Krajinski
- Institute of Biology, Faculty of Life Sciences, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Diederik van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, Univ. Bourgogne, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Ghislaine Recorbet
- Agroécologie, AgroSup Dijon, CNRS, Univ. Bourgogne, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, CNRS, Univ. Bourgogne, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
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Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Miquel Guennoc C, Deveau A, Olsson S, Bonito G, Doktycz MJ, Retterer ST. Increasing access to microfluidics for studying fungi and other branched biological structures. Fungal Biol Biotechnol 2019; 6:1. [PMID: 31198578 PMCID: PMC6556955 DOI: 10.1186/s40694-019-0071-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/15/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve "ready-to-use microfluidics." RESULTS We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we also demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi. CONCLUSIONS This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.
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Affiliation(s)
- Larry J. Millet
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
| | - Jayde Aufrecht
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996 USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27708 USA
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94703 USA
| | - Rytas Vilgalys
- Biology Department, Duke University, Box 90338, Durham, NC 27708 USA
| | - Myka L. Estes
- The Center for Neuroscience, University of California Davis, One Shields Avenue, Davis, CA 95618 USA
| | - Cora Miquel Guennoc
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- Institut national de la recherche agronomique (INRA), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Aurélie Deveau
- Institut national de la recherche agronomique (INRA), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Stefan Olsson
- Fujian Agricultural and Forestry University, Fuzhou City, 350002 Fujian Province China
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
| | - Scott T. Retterer
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
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Eschweiler J, van Holstein-Saj R, Kruidhof HM, Schouten A, Messelink GJ. Tomato Inoculation With a Non-pathogenic Strain of Fusarium oxysporum Enhances Pest Control by Changing the Feeding Preference of an Omnivorous Predator. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Nissinen R, Helander M, Kumar M, Saikkonen K. Heritable Epichloë symbiosis shapes fungal but not bacterial communities of plant leaves. Sci Rep 2019; 9:5253. [PMID: 30918316 PMCID: PMC6437304 DOI: 10.1038/s41598-019-41603-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
Keystone microbial species have driven eco-evolutionary processes since the origin of life. However, due to our inability to detect the majority of microbiota, members of diverse microbial communities of fungi, bacteria and viruses have largely been ignored as keystone species in past literature. Here we tested whether heritable Epichloë species of pooidae grasses modulate microbiota of their shared host plant.
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Affiliation(s)
- Riitta Nissinen
- Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Jyväskylä, Finland.
| | - Marjo Helander
- Department of Biology, 20014 University of Turku, Turku, Finland
| | - Manoj Kumar
- Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Jyväskylä, Finland
| | - Kari Saikkonen
- Biodiversity Unit, 20014 University of Turku, Turku, Finland
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Wemheuer B, Thomas T, Wemheuer F. Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes. Microorganisms 2019; 7:E37. [PMID: 30691243 PMCID: PMC6407066 DOI: 10.3390/microorganisms7020037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/26/2022] Open
Abstract
Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylis glomerata L., Festuca rubra L. and Lolium perenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years.
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Affiliation(s)
- Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Franziska Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
- Division of Agricultural Entomology, Department of Crop Sciences, Georg-August University of Göttingen, D-37077 Göttingen, Germany.
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Zhang S, Merino N, Okamoto A, Gedalanga P. Interkingdom microbial consortia mechanisms to guide biotechnological applications. Microb Biotechnol 2018; 11:833-847. [PMID: 30014573 PMCID: PMC6116752 DOI: 10.1111/1751-7915.13300] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/01/2023] Open
Abstract
Microbial consortia are capable of surviving diverse conditions through the formation of synergistic population-level structures, such as stromatolites, microbial mats and biofilms. Biotechnological applications are poised to capitalize on these unique interactions. However, current artificial co-cultures constructed for societal benefits, including biosynthesis, agriculture and bioremediation, face many challenges to perform as well as natural consortia. Interkingdom microbial consortia tend to be more robust and have higher productivity compared with monocultures and intrakingdom consortia, but the control and design of these diverse artificial consortia have received limited attention. Further, feasible research techniques and instrumentation for comprehensive mechanistic insights have only recently been established for interkingdom microbial communities. Here, we review these recent advances in technology and our current understanding of microbial interaction mechanisms involved in sustaining or developing interkingdom consortia for biotechnological applications. Some of the interactions among members from different kingdoms follow similar mechanisms observed for intrakingdom microbial consortia. However, unique interactions in interkingdom consortia, including endosymbiosis or interkingdom-specific cell-cell interactions, provide improved mitigation to external stresses and inhibitory compounds. Furthermore, antagonistic interactions among interkingdom species can promote fitness, diversification and adaptation, along with the production of beneficial metabolites and enzymes for society. Lastly, we shed light on future research directions to develop study methods at the level of metabolites, genes and meta-omics. These potential research methods could lead to the control and utilization of highly diverse microbial communities.
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Affiliation(s)
- Shu Zhang
- Global Research Center for Environment and Energy based on Nanomaterials ScienceNational Institute for Material Science1‐1 NamikiTsukubaIbarakiJapan
- Department of Molecular Microbiology and ImmunologyNorris Comprehensive Cancer CenterUniversity of Southern California1441 Eastlake StreetLos AngelesCA90033USA
- Present address:
Section of Infection and ImmunityHerman Ostrow School of DentistryUniversity of Southern CaliforniaCA90089‐0641USA
| | - Nancy Merino
- Earth‐Life Science InstituteTokyo Institute of Technology, 2‐12‐1‐I7E‐323Ookayama, Meguro‐kuTokyo 152‐8550Japan
- Department of Earth SciencesUniversity of Southern California, 835 Bloom Walk, SHS 562Los AngelesCA 90089‐0740USA
| | - Akihiro Okamoto
- Global Research Center for Environment and Energy based on Nanomaterials ScienceNational Institute for Material Science1‐1 NamikiTsukubaIbarakiJapan
| | - Phillip Gedalanga
- Department of Health ScienceCalifornia State University Fullerton, 800 North State College BoulevardFullertonCA 92831‐3599USA
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Jha P, Panwar J, Jha PN. Mechanistic insights on plant root colonization by bacterial endophytes: a symbiotic relationship for sustainable agriculture. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s42398-018-0011-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Yurgel SN, Douglas GM, Dusault A, Percival D, Langille MGI. Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome. Front Microbiol 2018; 9:1187. [PMID: 29922264 PMCID: PMC5996171 DOI: 10.3389/fmicb.2018.01187] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/16/2018] [Indexed: 11/16/2022] Open
Abstract
A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to host-plant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plant-microbe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.
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Affiliation(s)
- Svetlana N. Yurgel
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Gavin M. Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Ashley Dusault
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - David Percival
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 485] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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Vallet M, Vanbellingen QP, Fu T, Le Caer JP, Della-Negra S, Touboul D, Duncan KR, Nay B, Brunelle A, Prado S. An Integrative Approach to Decipher the Chemical Antagonism between the Competing Endophytes Paraconiothyrium variabile and Bacillus subtilis. JOURNAL OF NATURAL PRODUCTS 2017; 80:2863-2873. [PMID: 29139291 DOI: 10.1021/acs.jnatprod.6b01185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An integrative approach combining traditional natural products chemistry, molecular networking, and mass spectrometry imaging has been undertaken to decipher the molecular dialogue between the fungus Paraconiothyrium variabile and the bacterium Bacillus subtilis, which were isolated as endophytes from the conifer Cephalotaxus harringtonia and are characterized by a strong and mutual antibiosis. From this study, we highlight that bacterial surfactins and a fungal tetronic acid are involved in such competition and that the fungus is able to hydrolyze surfactins to fight against the bacterial partner.
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Affiliation(s)
- Marine Vallet
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Quentin P Vanbellingen
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Tingting Fu
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Pierre Le Caer
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Serge Della-Negra
- Institut de Physique Nucléaire, UMR8608, IN2P3-CNRS, Université Paris-Sud, Université Paris-Saclay , 91406, Orsay, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, HW608, University of Strathclyde , 161 Cathedral Street, Glasgow G4 ORE, U.K
| | - Bastien Nay
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Alain Brunelle
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Soizic Prado
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
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