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Zhou J, Liu J, Wang D, Ruan Y, Gong S, Gou J, Zou X. Fungal communities are more sensitive to mildew than bacterial communities during tobacco storage processes. Appl Microbiol Biotechnol 2024; 108:88. [PMID: 38194134 DOI: 10.1007/s00253-023-12882-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024]
Abstract
Mildew poses a significant threat to tobacco production; however, there is limited information on the structure of the abundant and rare microbial subcommunities in moldy tobacco leaves. In this study, we employed high-throughput sequencing technology to discern the disparities in the composition, diversity, and co-occurrence patterns of abundant and rare fungal and bacterial subcommunities between moldy and normal tobacco leaves collected from Guizhou, Shanghai, and Jilin provinces, China. Furthermore, we explored the correlation between microorganisms and metabolites by integrating the metabolic profiles of moldy and normal tobacco leaves. The results showed that the fungi are more sensitive to mildew than bacteria, and that the fungal abundant taxa exhibit greater resistance and environmental adaptability than the rare taxa. The loss of rare taxa results in irreversible changes in the diversity, richness, and composition of the fungal community. Moreover, rare fungal taxa and abundant bacterial taxa played crucial roles in maintaining the stability and functionality of the tobacco microecosystem. In moldy tobacco, however, the disappearance of rare taxa as key nodes resulted in reduced connectivity and stability within the fungal network. In addition, metabolomic analysis showed that the contents of indoles, pyridines, polyketones, phenols, and peptides were significantly enriched in the moldy tobacco leaves, while the contents of amino acids, carbohydrates, lipids, and other compounds were significantly reduced in these leaves. Most metabolites showed negative correlations with Dothideomycetes, Alphaproteobacteria, and Gammaproteobacteria, but showed positive correlations with Eurotiales and Bacilli. This study has demonstrated that abundant fungal taxa are the predominant biological agents responsible for tobacco mildew, while bacteria may indirectly contribute to this process through the production and degradation of metabolites. KEY POINTS: • Fungi exhibited greater sensitivity to mildew of tobacco leaf compared to bacteria • Rare fungal taxa underwent significant damage during the mildew process • Mildew may damage the defense system of the tobacco leaf microecosystem.
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Affiliation(s)
- Jiaxi Zhou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China
- Postdoctoral Research Workstation of China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jing Liu
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Dongfei Wang
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Yibin Ruan
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Shuang Gong
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jianyu Gou
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Xiao Zou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China.
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Luo L, Dai F, Xu Z, Guan J, Fei G, Qu J, Yao M, Xue Y, Zhou Y, Zou X. Core microbes in Cordyceps militaris sclerotia and their nitrogen metabolism-related ecological functions. Microbiol Spectr 2024; 12:e0105324. [PMID: 39162541 PMCID: PMC11448085 DOI: 10.1128/spectrum.01053-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/01/2024] [Indexed: 08/21/2024] Open
Abstract
Cordyceps militaris infects insects and forms sclerotia within the insect remains, establishing insect-microbe complexes. Here, C. militaris sclerotia samples from a single location in China over a 5-year period were subjected to high-throughput DNA sequencing, and the core microbes (which were stably enriched in the sclerotia over the 5 years) were identified. Next, seven bacterial strains were isolated from the C. militaris sclerotia, their biochemical characteristics were assessed, and they were co-cultured with C. militaris to study their effects on C. militaris metabolite production and biomass. Furthermore, the effects of NH4, NO3, and peptone media on C. militaris were compared. The results showed that Rhodococcus, Phyllobacterium, Pseudomonas, Achromobacter, Ensifer, Stenotrophomonas, Sphingobacterium, Variovorax, and Acinetobacter were the core microbes. Although co-culture of C. militaris with the seven bacterial strains isolated from the sclerotia did not directly increase the cordycepin level, they all had NO3 reduction ability, and four had urea decomposition ability. Meanwhile, C. militaris in NH4 medium had an increased cordycepin level compared to C. militaris in the other two media. From this, we inferred that bacteria in the sclerotia can convert NO3 to NH4, and then cordycepin is produced using NH4, which was confirmed by RNA-seq and real-time fluorescence quantitative PCR. Thus, bacteria in the sclerotia may indirectly affect the C. militaris metabolite production by regulating nitrogen metabolism. In summary, there are stable core microbes in the C. militaris sclerotia, and they may directly and indirectly affect the growth and metabolite production of C. militaris. IMPORTANCE The model Cordyceps species Cordyceps militaris is rich in therapeutic compounds. It has recently been demonstrated that symbiotic microbes in sclerotia affect Cordyceps' growth, development, and secondary metabolite production. In this study, core microbes were identified based on C. militaris sclerotia samples obtained from the same site over 5 years. Additionally, bacterial strains isolated from C. militaris sclerotia were found to affect metabolite production and nitrogen utilization, based on functional tests. Moreover, based on the bacterial nitrogen metabolism capacity in the sclerotia and its influence on C. militaris metabolite production, we deduced that bacteria in the sclerotia can indirectly affect C. militaris metabolite production by regulating nitrogen metabolism. This is the first report on how bacteria in the sclerotia affect C. militaris metabolite production from the perspective of the nitrogen cycle. The results increase our understanding of microbial functions in C. militaris sclerotia.
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Affiliation(s)
- Li Luo
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Fei Dai
- Anshun Branch of Guizhou Tobacco Company, Anshun, Guizhou, China
| | - Zhongshun Xu
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Jingqiang Guan
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Gangxiang Fei
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Jiaojiao Qu
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Min Yao
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Yuan Xue
- Anshun Branch of Guizhou Tobacco Company, Anshun, Guizhou, China
| | - Yeming Zhou
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
| | - Xiao Zou
- Institute of Fungus Resources, College of Life Science, Guizhou University, Guiyang, Guizhou, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Guizhou University, Guiyang, Guizhou, China
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Kelliher JM, Johnson LYD, Robinson AJ, Longley R, Hanson BT, Cailleau G, Bindschedler S, Junier P, Chain PSG. Fabricated devices for performing bacterial-fungal interaction experiments across scales. Front Microbiol 2024; 15:1380199. [PMID: 39171270 PMCID: PMC11335632 DOI: 10.3389/fmicb.2024.1380199] [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: 02/02/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.
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Affiliation(s)
- Julia M. Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Leah Y. D. Johnson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aaron J. Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Reid Longley
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Buck T. Hanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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Ali F, Tang Z, Mo G, Zhang B, Ling X, Qiu Z. Taxonomic and functional changes in wheat rhizosphere microbiome caused by imidazoline-based herbicide and genetic modification. ENVIRONMENTAL RESEARCH 2024; 262:119726. [PMID: 39102937 DOI: 10.1016/j.envres.2024.119726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
Genetically modified (GM) crop cultivation has received a lot of attention in recent years due to the substantial public debate. Consequently, an in-depth investigation of excessively used GM herbicide-tolerant crops is a vital step for the biosafety of genetically modified plants. Several studies have been conducted to study the impact of transgenic GM crops on soil microbial composition; however, research into the effects of non-transgenic GM crops is inadequate. In the current work, high-throughput sequencing was used to evaluate the impact of the acetolactate synthase (ALS)-mutant (WK170B), its control (YN19B), and the imazamox (IM) herbicide on the wheat rhizobiome. Under normal growth conditions, our work revealed a minimal impact of ALS-mutant WK170B on the rhizosphere microbiome compared to the control YN10B, except for some cyanobacterial microorganisms that showed a significant increase in abundance. This suggests that the gene mutation could potentially have a beneficial impact on the bacterial communities present in the rhizosphere. Following IM exposure, taxonomic analysis revealed a significant reduction in the relative abundance of Ralstonia pickettii and an unidentified member of the genus Ancylothrix 8 PC. Analyses of both alpha and beta diversity revealed a statistically significant increase in both microbial richness and species diversity. IM-induced relative abundance modulation was also evident through Linear discriminant analysis Effect Size (LEfSe), MetaStat, and heatmap analyses. The SIMPER analysis revealed that the microbial taxa Massilia, Limnobacter, Hydrogenophaga, Ralstonia, Nitrospira, and Ramlibacter exhibited the highest vulnerability to IM exposure. The functional attributes analysis revealed that the relative abundance of genes associated with the extracellular matrix-receptor interaction, which is responsible for structural support and stress response, increased significantly following IM exposure. Collectively, our study identifies key microbial taxa in the wheat rhizobiome that are sensitive to IM herbicides and provides a foundation for assessing the environmental risks associated with IM herbicide use.
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Affiliation(s)
- Farman Ali
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zhaocheng Tang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Gangao Mo
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Baolong Zhang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xitie Ling
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Zeyu Qiu
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Gupta P, Meher MK, Tripathi S, Poluri KM. Nanoformulations for dismantling fungal biofilms: The latest arsenals of antifungal therapy. Mol Aspects Med 2024; 98:101290. [PMID: 38945048 DOI: 10.1016/j.mam.2024.101290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
Globally, fungal infections have evolved as a strenuous challenge for clinicians, particularly in patients with compromised immunity in intensive care units. Fungal co-infection in Covid-19 patients has made the situation more formidable for healthcare practitioners. Surface adhered fungal population known as biofilm often develop at the diseased site to elicit antifungal tolerance and recalcitrant traits. Thus, an innovative strategy is required to impede/eradicate developed biofilm and avoid the formation of new colonies. The development of nanocomposite-based antibiofilm solutions is the most appropriate way to withstand and dismantle biofilm structures. Nanocomposites can be utilized as a drug delivery medium and for fabrication of anti-biofilm surfaces capable to resist fungal colonization. In this context, the present review comprehensively described different forms of nanocomposites and mode of their action against fungal biofilms. Amongst various nanocomposites, efficacy of metal/organic nanoparticles and nanofibers are particularly emphasized to highlight their role in the pursuit of antibiofilm strategies. Further, the inevitable concern of nanotoxicology has also been introduced and discussed with the exigent need of addressing it while developing nano-based therapies. Further, a list of FDA-approved nano-based antifungal formulations for therapeutic usage available to date has been described. Collectively, the review highlights the potential, scope, and future of nanocomposite-based antibiofilm therapeutics to address the fungal biofilm management issue.
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Affiliation(s)
- Payal Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Department of Biotechnology, Graphic Era (Demmed to be Unievrsity), Dehradun, 248001, Uttarakhand, India
| | - Mukesh Kumar Meher
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Shweta Tripathi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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Gallardo-Navarro O, Aguilar-Salinas B, Rocha J, Olmedo-Álvarez G. Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology. Heliyon 2024; 10:e33896. [PMID: 39130413 PMCID: PMC11315108 DOI: 10.1016/j.heliyon.2024.e33896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 06/28/2024] [Indexed: 08/13/2024] Open
Abstract
Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.
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Affiliation(s)
- Oscar Gallardo-Navarro
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Bernardo Aguilar-Salinas
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Jorge Rocha
- Centro de Investigaciones Biológicas del Noroeste, S. C., La Paz, Mexico
| | - Gabriela Olmedo-Álvarez
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
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Wang X, Fang J, Li L, Li X, Liu P, Song B, Adams J, Xiao Y, Fang Z. Gongronella sp. w5 hydrolyzes plant sucrose and releases fructose to recruit phosphate-solubilizing bacteria to provide plants with phosphorus. Appl Environ Microbiol 2024; 90:e0053424. [PMID: 38904410 PMCID: PMC11267922 DOI: 10.1128/aem.00534-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
The mechanisms of how plant-beneficial rhizospheric fungi interact with the soil microbial community to promote plant growth by facilitating their phosphorus acquisition are poorly understood. This work supported that a Mucoromycotina fungus, Gongronella sp. w5 (w5), could promote phosphorus uptake of Medicago truncatula by increasing the available phosphorus (P) in the soil. The abundance of phosphate-solubilizing bacteria (PSB) and the activity of alkaline phosphatase (ALP) in alfalfa rhizosphere soil increased after w5 inoculation. Further analysis showed that w5 donated a portion of ALP activity and also stimulated the PSB to secrete ALP during plant-w5-PSB interaction to help release more available P in the rhizosphere of M. truncatula. Unlike most plant-beneficial rhizospheric fungi that mainly acquire hexoses from plants, w5 gained sucrose directly from the host plant and then recruited PSB to aid P acquisition by hydrolyzing sucrose and releasing mainly fructose to induce PSB to secrete ALP. IMPORTANCE This work supported that after absorbing plant sucrose, Gongronella sp. w5 mainly releases sucrose hydrolysis product fructose into the environment. Fructose was used as a carbon source and signaling molecules to induce PSB to co-produce higher alkaline phosphatase activity, releasing soil-available phosphorus and promoting M. truncatula growth. This is the first report that plant-beneficial fungi could directly metabolize sucrose from plants and then recruit PSB to aid P acquisition by providing fructose. Our findings revealed the diversity in pathways of plant-fungi-PSB interactions on soil P acquisition and deepened our understanding of the cooperation of growth-promoting microorganisms in plant rhizosphere.
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Affiliation(s)
- Xiaojie Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Junnan Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Li Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Xing Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Pu Liu
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, China
| | - Bin Song
- School of Geography and Ocean Sciences, Nanjing University, Nanjing, China
| | - Jonathan Adams
- School of Geography and Ocean Sciences, Nanjing University, Nanjing, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
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He L, Sun X, Li S, Zhou W, Yu J, Zhao G. Biogeographic and co-occurrence network differentiation of fungal communities in warm-temperate montane soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174911. [PMID: 39038676 DOI: 10.1016/j.scitotenv.2024.174911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Studying the biogeographic patterns of fungal communities across altitudinal and soil depth gradients is essential for understanding how environmental variations shape the diversity and functionality of these complex ecological assemblages. Here, we evaluated the response and assembly patterns of fungal communities to altitude and soil depth, and the co-occurrence patterns influencing soil fungal metabolic preferences on Dongling Mountain. We observed significant variations in fungal β-diversity, driven by elevation and soil depth, with climatic parameters (MAT and MAP) and nutrient concentrations (TOC, TP, and TN) serving as prominent influencers. Additionally, we found that the multiple substrate-induced respiration rate of fungi degrading various carbon substrates was diminished in high-altitude and subsurface soils compared to low-altitude and surface soils. Stochastic processes play a more important role in controlling fungal community assembly than deterministic processes, with dispersal limitation emerging as the main driver of community assembly. While greater network complexity was evident in the topsoil compared to the subsoil, both layers harbored altitude-sensitive OTUs (asOTUs) that belonging to distinct modules. Moreover, fungal groups sensitive to the same altitude exhibited similar metabolic preferences. The asOTUs designated for lower altitude areas favored unstable carbon substrates (glucose and sucrose), while those designated as higher altitude areas exhibited a preference for recalcitrant carbon (xylan and lignin). This evidence suggests that soil fungal communities respond to environmental changes by trading off their life strategies and metabolic characteristics.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jiantao Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Guanyu Zhao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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Rezaei Z, Moghimi H. Fungal-bacterial consortia: A promising strategy for the removal of petroleum hydrocarbons. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116543. [PMID: 38833981 DOI: 10.1016/j.ecoenv.2024.116543] [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: 12/11/2023] [Revised: 03/21/2024] [Accepted: 06/01/2024] [Indexed: 06/06/2024]
Abstract
Nowadays, petroleum hydrocarbon pollution is one of the most widespread types of contamination that poses a serious threat to both public health and the environment. Among various physicochemical methods, bioremediation is an eco-friendly and cost-effective way to eliminate petroleum hydrocarbon pollutants. The successful degradation of all hydrocarbon components and the achievement of optimal efficiency are necessary for the success of this process. Using potential microbial consortia with rich metabolic networks is a promising strategy for addressing these challenges. Mixed microbial communities, comprising both fungi and bacteria, exhibit diverse synergistic mechanisms to degrade complex hydrocarbon contaminants, including the dissemination of bacteria by fungal hyphae, enhancement of enzyme and secondary metabolites production, and co-metabolism of pollutants. Compared to pure cultures or consortia of either fungi or bacteria, different studies have shown increased bioremediation of particular contaminants when combined fungal-bacterial treatments are applied. However, antagonistic interactions, like microbial competition, and the production of inhibitors or toxins can observed between members. Furthermore, optimizing environmental factors (pH, temperature, moisture, and initial contaminant concentration) is essential for consortium performance. With the advancements in synthetic biology and gene editing tools, it is now feasible to design stable and robust artificial microbial consortia systems. This review presents an overview of using microbial communities for the removal of petroleum pollutants by focusing on microbial degradation pathways, and their interactions. It also highlights the new strategies for constructing optimal microbial consortia, as well as the challenges currently faced and future perspectives of applying fungal-bacterial communities for bioremediation.
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Affiliation(s)
- Zeinab Rezaei
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hamid Moghimi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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10
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Zohair MM, Dongmei W, Shimizu K. Metabolic picture of microbial interaction: chemical crosstalk during co-cultivation between three dominant genera of bacteria and fungi in medicinal plants rhizosphere. Metabolomics 2024; 20:75. [PMID: 38980562 DOI: 10.1007/s11306-024-02138-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/06/2024] [Indexed: 07/10/2024]
Abstract
INTRODUCTION Microbial communities affect several aspects of the earth's ecosystem through their metabolic interaction. The dynamics of this interaction emerge from complex multilevel networks of crosstalk. Elucidation of this interaction could help us to maintain the balance for a sustainable future. OBJECTIVES To investigate the chemical language among highly abundant microbial genera in the rhizospheres of medicinal plants based on the metabolomic analysis at the interaction level. METHODS Coculturing experiments involving three microbial species: Aspergillus (A), Trichoderma (T), and Bacillus (B), representing fungi (A, T) and bacteria (B), respectively. These experiments encompassed various interaction levels, including dual cultures (AB, AT, TB) and triple cultures (ATB). Metabolic profiling by LC-QTOFMS revealed the effect of interaction level on the productivity and diversity of microbial specialized metabolites. RESULTS The ATB interaction had the richest profile, while the bacterial profile in the monoculture condition had the lowest. Two native compounds of the Aspergillus genus, aspergillic acid and the dipeptide asperopiperazine B, exhibited decreased levels in the presence of the AT interaction and were undetectable in the presence of bacteria during the interaction. Trichodermarin N and Trichodermatide D isolated from Trichoderma species exclusively detected during coexistence with bacteria (TB and ATB). These findings indicate that the presence of Bacillus activates cryptic biosynthetic gene clusters in Trichoderma. The antibacterial activity of mixed culture extracts was stronger than that of the monoculture extracts. The TB extract exhibited strong antifungal activity compared to the monoculture extract and other mixed culture treatments. CONCLUSION The elucidation of medicinal plant microbiome interaction chemistry and its effect on the environment will also be of great interest in the context of medicinal plant health Additionally, it sheds light on the content of bioactive constituents, and facilitating the discovery of novel antimicrobials.
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Affiliation(s)
- Moustafa M Zohair
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Research Institute, National Research Centre, Giza, 12622, Egypt
| | - Wang Dongmei
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kuniyoshi Shimizu
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan.
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Maruška A, Mickienė R, Kaškonienė V, Grigiškis S, Stankevičius M, Drevinskas T, Kornyšova O, Donati E, Tiso N, Mikašauskaitė-Tiso J, Zacchini M, Levišauskas D, Ragažinskienė O, Bimbiraitė-Survilienė K, Kanopka A, Dūda G. Searching for Chemical Agents Suppressing Substrate Microbiota in White-Rot Fungi Large-Scale Cultivation. Microorganisms 2024; 12:1242. [PMID: 38930624 PMCID: PMC11206069 DOI: 10.3390/microorganisms12061242] [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: 04/08/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Edible fungi are a valuable resource in the search for sustainable solutions to environmental pollution. Their ability to degrade organic pollutants, extract heavy metals, and restore ecological balance has a huge potential for bioremediation. They are also sustainable food resources. Edible fungi (basidiomycetes or fungi from other divisions) represent an underutilized resource in the field of bioremediation. By maximizing their unique capabilities, it is possible to develop innovative approaches for addressing environmental contamination. The aim of the present study was to find selective chemical agents suppressing the growth of microfungi and bacteria, but not suppressing white-rot fungi, in order to perform large-scale cultivation of white-rot fungi in natural unsterile substrates and use it for different purposes. One application could be the preparation of a matrix composed of wooden sleeper (contaminated with PAHs) and soil for further hazardous waste bioremediation using white-rot fungi. In vitro microbiological methods were applied, such as, firstly, compatibility tests between bacteria and white-rot fungi or microfungi, allowing us to evaluate the interaction between different organisms, and secondly, the addition of chemicals on the surface of a Petri dish with a test strain of microorganisms of white-rot fungi, allowing us to determine the impact of chemicals on the growth of organisms. This study shows that white-rot fungi are not compatible to grow with several rhizobacteria or bacteria isolated from soil and bioremediated waste. Therefore, the impact of several inorganic materials, such as lime (hydrated form), charcoal, dolomite powder, ash, gypsum, phosphogypsum, hydrogen peroxide, potassium permanganate, and sodium hydroxide, was evaluated on the growth of microfungi (sixteen strains), white-rot fungi (three strains), and bacteria (nine strains) in vitro. Charcoal, dolomite powder, gypsum, and phosphogypsum did not suppress the growth either of microfungi or of bacteria in the tested substrate, and even acted as promoters of their growth. The effects of the other agents tested were strain dependent. Potassium permanganate could be used for bacteria and Candida spp. growth suppression, but not for other microfungi. Lime showed promising results by suppressing the growth of microfungi and bacteria, but it also suppressed the growth of white-rot fungi. Hydrogen peroxide showed strong suppression of microfungi, and even had a bactericidal effect on some bacteria, but did not have an impact on white-rot fungi. The study highlights the practical utility of using hydrogen peroxide up to 3% as an effective biota-suppressing chemical agent prior to inoculating white-rot fungi in the large-scale bioremediation of polluted substrates, or in the large-scale cultivation for mushroom production as a foodstuff.
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Affiliation(s)
- Audrius Maruška
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Rūta Mickienė
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Vilma Kaškonienė
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | | | - Mantas Stankevičius
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Tomas Drevinskas
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Olga Kornyšova
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Enrica Donati
- National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (E.D.); (M.Z.)
| | - Nicola Tiso
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Jurgita Mikašauskaitė-Tiso
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Massimo Zacchini
- National Research Council, Area Della Ricerca di Roma 1, Via Salaria Km 29,300, Monterotondo, 00015 Rome, Italy; (E.D.); (M.Z.)
| | - Donatas Levišauskas
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
- Process Control Department, Kaunas University of Technology, Studentų St. 50, LT-51368 Kaunas, Lithuania
| | - Ona Ragažinskienė
- Botanical Garden of Vytautas Magnus University, Ž. E. Žilibero 6, LT-46324 Kaunas, Lithuania;
| | - Kristina Bimbiraitė-Survilienė
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Arvydas Kanopka
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
| | - Gediminas Dūda
- Instrumental Analysis Open Access Centre, Vytautas Magnus University, Vileikos St. 8, LT-40444 Kaunas, Lithuania; (R.M.); (V.K.); (M.S.); (T.D.); (O.K.); (N.T.); (J.M.-T.); (D.L.); (K.B.-S.); (A.K.); (G.D.)
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12
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Wu WF, Li XY, Chen SC, Jin BJ, Wu CY, Li G, Sun CL, Zhu YG, Lin XY. Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172622. [PMID: 38642761 DOI: 10.1016/j.scitotenv.2024.172622] [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: 01/25/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.
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Affiliation(s)
- Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Bing-Jie Jin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Cheng-Liang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
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Xu Z, Li Y, Xu A, Xue L, Soteyome T, Yuan L, Ma Q, Seneviratne G, Hong W, Mao Y, Kjellerup BV, Liu J. Differential alteration in Lactiplantibacillus plantarum subsp. plantarum quorum-sensing systems and reduced Candida albicans yeast survival and virulence gene expression in dual-species interaction. Microbiol Spectr 2024; 12:e0035324. [PMID: 38717160 PMCID: PMC11237386 DOI: 10.1128/spectrum.00353-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 06/06/2024] Open
Abstract
Candida albicans (C. albicans) and Lactiplantibacillus plantarum subsp. plantarum (L. plantarum) are frequently identified in various niches, but their dual-species interaction, especially with C. albicans in yeast form, remains unclear. This study aimed to investigate the dual-species interaction of L. plantarum and C. albicans, including proliferation, morphology, and transcriptomes examined by selective agar plate counting, microscopy, and polymicrobial RNA-seq, respectively. Maintaining a stable and unchanged growth rate, L. plantarum inhibited C. albicans yeast cell proliferation but not hyphal growth. Combining optical microscopy and atomic force microscopy, cell-to-cell direct contact and co-aggregation with L. plantarum cells surrounding C. albicans yeast cells were observed during dual-species interaction. Reduced C. albicans yeast cell proliferation in mixed culture was partially due to L. plantarum cell-free culture supernatant but not the acidic environment. Upon polymicrobial transcriptomics analysis, interesting changes were identified in both L. plantarum and C. albicans gene expression. First, two L. plantarum quorum-sensing systems showed contrary changes, with the activation of lamBDCA and repression of luxS. Second, the upregulation of stress response-related genes and downregulation of cell cycle, cell survival, and cell integrity-related pathways were identified in C. albicans, possibly connected to the stress posed by L. plantarum and the reduced yeast cell proliferation. Third, a large scale of pathogenesis and virulence factors were downregulated in C. albicans, indicating the potential interruption of pathogenic activities by L. plantarum. Fourth, partial metabolism and transport pathways were changed in L. plantarum and C. albicans. The information in this study might aid in understanding the behavior of L. plantarum and C. albicans in dual-species interaction.IMPORTANCEThe anti-Candida albicans activity of Lactiplantibacillus plantarum has been explored in the past decades. However, the importance of C. albicans yeast form and the effect of C. albicans on L. plantarum had also been omitted. In this study, the dual-species interaction of L. plantarum and C. albicans was investigated with a focus on the transcriptomes. Cell-to-cell direct contact and co-aggregation with L. plantarum cells surrounding C. albicans yeast cells were observed. Upon polymicrobial transcriptomics analysis, interesting changes were identified, including contrary changes in two L. plantarum quorum-sensing systems and reduced cell survival-related pathways and pathogenesis determinants in C. albicans.
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Affiliation(s)
- Zhenbo Xu
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Department of Laboratory Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yaqin Li
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Aijuan Xu
- Guangzhou Hybribio Medical Laboratory, Guangzhou, China
| | - Liang Xue
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, China, Guangzhou, Guangdong
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Thanapop Soteyome
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | - Lei Yuan
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qin Ma
- Key Laboratory of Functional Foods, Ministry of Agriculture, Guangdong Key Laboratory of Agricultural Products Processing, Sericultural and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Wei Hong
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yuzhu Mao
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
| | - Birthe V. Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
| | - Junyan Liu
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, College of Light Industry and Food Science, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou, China
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14
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Yang L, Yang Q, Wulu J, Wang Y, Jin W, Yan Z, Zhang Z. Quality analysis and function prediction of soil microbial communities of Polygonatum cyrtonema in two indigenous-origins. Front Microbiol 2024; 15:1410501. [PMID: 38881668 PMCID: PMC11176499 DOI: 10.3389/fmicb.2024.1410501] [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: 04/01/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
Polygonatum cyrtonema Hua (PCH), as an important economic crop, is used as raw industrial materials and traditional Chinese medicine. There are significant variations in the quality of PCH from different geographical origins. It can be due to the change of the endophytic fungi and soil microbial communities of PCH. Therefore, the aim of this study is to investigate the composition and functional prediction of the main microbial communities in the rhizomes and soil of PCH and explore their impact on medicinal quality. High-throughput sequencing techniques targeting ITS and 16S rDNA were employed to compare the structure and biodiversity differences of endophytic fungi in the rhizomes and soil microbial communities of PCH from 12 different locations in Sichuan and Guangxi province. Heatmap analysis was used for comprehensive statistics and visualization of the richness of rhizome and soil microbial communities from all locations. Venn analysis was conducted to determine the total number of shared fungi between rhizomes and soil, and GraphPad Prism analysis was employed to predict and compare the microbial communities related to phenotypes at the genus level in Sichuan and Guangxi. Tax4Fun and Fungild were used for metabolic function prediction of microbial communities in the rhizomes and soil of PCH. The results revealed the identification of 19,387 bacterial amplicon sequence variants (ASVs) in the rhizomes and 37,990 bacterial ASVs in the soil, with 6,889 shared bacterial ASVs. In addition, 2,948 fungal ASVs were identified in the rhizomes and 8,868 in the soil, with 1,893 shared fungal ASVs. Microbial sequencing results indicated that the fungal communities between soil and rhizomes were mainly composed of Ascomycota and Basidiomycota, while bacterial communities included Proteobacteria, Acidobacteria, Bacteroidota, Gammatimonadota, and Firmicutes. Dominant bacterial groups such as Nitrospira, Acidibacter, and fungal groups including Mortierella, Ceratobasidium, and Fusarium were identified as potential contributors to the observed traits. In the top 15 microbial genera, both Sichuan and Guangxi contain 15 bacterial genera, but there are differences in their abundance. Guangxi has three unique fungal genera, including the genera Scleroderma, Russula, and Gliocladiopsis. On the other hand, Sichuan has the unique fungal genus Chamaeota. The correlation analysis between the microbiota and the chemical content from 12 different collecting spots was performed by GraphPad Prism. Burkholderia-Caballeronia-Paraburkholderia, Acidibacter, and Amycolatopsis show an inverse proportionality to total polysaccharides and saponins, while Enterobacter shows a direct proportionality to total polysaccharides and inverse proportionality to saponins. The metabolism pathways show a significant positive correlation with PCH polysaccharides and saponins. This study provide new insights into the mechanisms underlying the quality differences between the two major indigenous areas.
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Affiliation(s)
- Li Yang
- School of Pharmacy, Southwest Minzu University, Chengdu, China
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
| | - Qing Yang
- School of Pharmacy, Southwest Minzu University, Chengdu, China
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
| | - Jiansang Wulu
- School of Pharmacy, Southwest Minzu University, Chengdu, China
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
| | - Yue Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, China
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
| | - Wenfang Jin
- School of Pharmacy, Southwest Minzu University, Chengdu, China
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
| | - Zhigang Yan
- National Engineering Institute for the Research and Development of Endangered Medicinal Resources in Southwest China, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhifeng Zhang
- School of Pharmacy, Southwest Minzu University, Chengdu, China
- Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Southwest Minzu University, Chengdu, China
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15
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Richter A, Blei F, Hu G, Schwitalla JW, Lozano-Andrade CN, Xie J, Jarmusch SA, Wibowo M, Kjeldgaard B, Surabhi S, Xu X, Jautzus T, Phippen CBW, Tyc O, Arentshorst M, Wang Y, Garbeva P, Larsen TO, Ram AFJ, van den Hondel CAM, Maróti G, Kovács ÁT. Enhanced surface colonisation and competition during bacterial adaptation to a fungus. Nat Commun 2024; 15:4486. [PMID: 38802389 PMCID: PMC11130161 DOI: 10.1038/s41467-024-48812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Bacterial-fungal interactions influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Here, we use a co-culture experimental evolution approach to investigate bacterial adaptation to the presence of a fungus, using a simple model of bacterial-fungal interactions encompassing the bacterium Bacillus subtilis and the fungus Aspergillus niger. We find in one evolving population that B. subtilis was selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles possibly provoking an RlmA-dependent cell wall stress. Thus, our results indicate that the presence of the fungus selects for increased surfactin production, which inhibits fungal growth and facilitates the competitive success of the bacterium.
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Affiliation(s)
- Anne Richter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Felix Blei
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Guohai Hu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China
| | - Jan W Schwitalla
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jiyu Xie
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Scott A Jarmusch
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Bodil Kjeldgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Surabhi Surabhi
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Xinming Xu
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Theresa Jautzus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Christopher B W Phippen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Olaf Tyc
- Netherlands Institute of Ecology, Wageningen, The Netherlands
- Department of Internal Medicine I, Goethe University Hospital, Frankfurt, Germany
| | - Mark Arentshorst
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Thomas Ostenfeld Larsen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Arthur F J Ram
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark.
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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16
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Li J, Hong M, Lv J, Tang R, Wang R, Yang Y, Liu N. Enhancement on migration and biodegradation of Diaphorobacter sp. LW2 mediated by Pythium ultimum in soil with different particle sizes. Front Microbiol 2024; 15:1391553. [PMID: 38841075 PMCID: PMC11150788 DOI: 10.3389/fmicb.2024.1391553] [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: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction The composition and structure of natural soil are very complex, leading to the difficult contact between hydrophobic organic compounds and degrading-bacteria in contaminated soil, making pollutants hard to be removed from the soil. Several researches have reported the bacterial migration in unsaturated soil mediated by fungal hyphae, but bacterial movement in soil of different particle sizes or in heterogeneous soil was unclear. The remediation of contaminated soil enhanced by hyphae still needs further research. Methods In this case, the migration and biodegradation of Diaphorobacter sp. LW2 in soil was investigated in presence of Pythium ultimum. Results Hyphae could promote the growth and migration of LW2 in culture medium. It was also confirmed that LW2 was able to migrate in the growth direction and against the growth direction along hyphae. Mediated by hyphae, motile strain LW2 translocated over 3 cm in soil with different particle size (CS1, 1.0-2.0 mm; CS2, 0.5-1.0mm; MS, 0.25-0.5 mm and FS, <0.25 mm), and it need shorter time in bigger particle soils. In inhomogeneous soil, hyphae participated in the distribution of introduced bacteria, and the total number of bacteria increased. Pythium ultimum enhanced the migration and survival of LW2 in soil, improving the bioremediation of polluted soil. Discussion The results of this study indicate that the mobilization of degrading bacteria mediated by Pythium ultimum in soil has great potential for application in bioremediation of contaminated soil.
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Affiliation(s)
- Jialu Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Mei Hong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Jing Lv
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Rui Tang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Ruofan Wang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Yadong Yang
- School of Environmental Science and Engineering, Jiangsu Engineering Research Center of Biomass Waste Pyrolytic Carbonization & Application, Yancheng Institute of Technology, Yancheng, China
| | - Na Liu
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
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Jin Z, Jiang F, Wang L, Declerck S, Feng G, Zhang L. Arbuscular mycorrhizal fungi and Streptomyces: brothers in arms to shape the structure and function of the hyphosphere microbiome in the early stage of interaction. MICROBIOME 2024; 12:83. [PMID: 38725008 PMCID: PMC11080229 DOI: 10.1186/s40168-024-01811-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/07/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Fungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other's metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown. RESULTS Here, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P. CONCLUSIONS This work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi. Video Abstract.
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Affiliation(s)
- Zexing Jin
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Feiyan Jiang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Letian Wang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Stéphane Declerck
- Applied Microbiology, Mycology, Earth and Life Institute, Université Catholique de Louvain, Croix du Sud 2, Bte L7.05.06, Louvain-La-Neuve, B-1348, Belgium
| | - Gu Feng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Lin Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China.
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Gorostidi-Aicua M, Reparaz I, Otaegui-Chivite A, García K, Romarate L, Álvarez de Arcaya A, Mendiburu I, Arruti M, Castillo-Triviño T, Moles L, Otaegui D. Bacteria-Fungi Interactions in Multiple Sclerosis. Microorganisms 2024; 12:872. [PMID: 38792701 PMCID: PMC11124083 DOI: 10.3390/microorganisms12050872] [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: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and mycobiome (fungal microbiota) of people with MS (pwMS), and compared them to healthy controls (HC). Through principal coordinate, diversity, and abundance analyses, as well as clustering and cross-kingdom microbial correlation assessments, we uncovered significant differences in the microbial profiles between pwMS and HC. Elevated levels of the fungus Torulaspora and the bacterial family Enterobacteriaceae were observed in pwMS, whereas beneficial bacterial taxa, such as Prevotelladaceae and Dialister, were reduced. Notably, clustering analysis revealed overlapping patterns in the bacteriome and mycobiome data for 74% of the participants, with weakened cross-kingdom interactions evident in the altered microbiota of pwMS. Our findings highlight the dysbiosis of both bacterial and fungal microbiota in MS, characterized by shifts in biodiversity and composition. Furthermore, the distinct disease-associated pattern of fungi-bacteria interactions suggests that fungi, in addition to bacteria, contribute to the pathogenesis of MS. Overall, our study sheds light on the intricate microbial dynamics underlying MS, paving the way for further investigation into the potential therapeutic targeting of the gut microbiota in MS management.
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Affiliation(s)
- Miriam Gorostidi-Aicua
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Iraia Reparaz
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Ane Otaegui-Chivite
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Koldo García
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Leire Romarate
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Amaya Álvarez de Arcaya
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Araba, 01009 Vitoria-Gasteiz, Spain;
| | - Idoia Mendiburu
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Maialen Arruti
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Tamara Castillo-Triviño
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Laura Moles
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - David Otaegui
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
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19
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Loos D, Filho APDC, Dutilh BE, Barber AE, Panagiotou G. A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists. Cell Rep 2024; 43:114046. [PMID: 38581683 DOI: 10.1016/j.celrep.2024.114046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/22/2023] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.
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Affiliation(s)
- Daniel Loos
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Ailton Pereira da Costa Filho
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Bas E Dutilh
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Institute of Biodiversity, Friedrich Schiller University, Jena, Germany; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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20
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Williams A, Sinanaj B, Hoysted GA. Plant-microbe interactions through a lens: tales from the mycorrhizosphere. ANNALS OF BOTANY 2024; 133:399-412. [PMID: 38085925 PMCID: PMC11006548 DOI: 10.1093/aob/mcad191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 04/12/2024]
Abstract
BACKGROUND The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial-fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant-microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant-microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes. SCOPE Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities - particularly in the mycorrhizosphere - and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function. CONCLUSIONS Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.
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Affiliation(s)
- Alex Williams
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Bioscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Grace A Hoysted
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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21
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Probst M, Telagathoti A, Mandolini E, Peintner U. Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils. ENVIRONMENTAL MICROBIOME 2024; 19:20. [PMID: 38566162 PMCID: PMC10985912 DOI: 10.1186/s40793-024-00564-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/24/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover. RESULTS The overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover. CONCLUSION This is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.
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Affiliation(s)
- Maraike Probst
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Anusha Telagathoti
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Edoardo Mandolini
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Ursula Peintner
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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22
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Partida-Martínez LP. Fungal holobionts as blueprints for synthetic endosymbiotic systems. PLoS Biol 2024; 22:e3002587. [PMID: 38607980 PMCID: PMC11014430 DOI: 10.1371/journal.pbio.3002587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Rhizopus microsporus is an example of a fungal holobiont. Strains of this species can harbor bacterial and viral endosymbionts inherited by the next generation. These microbial allies increase pathogenicity and defense and control asexual and sexual reproduction.
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23
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Zhou X, Hu Y, Li H, Sheng J, Cheng J, Zhao T, Zhang Y. Phosphorus addition increases stability and complexity of co-occurrence network of soil microbes in an artificial Leymus chinensis grassland. Front Microbiol 2024; 15:1289022. [PMID: 38601937 PMCID: PMC11004269 DOI: 10.3389/fmicb.2024.1289022] [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: 09/05/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction Understanding the response of cross-domain co-occurrence networks of soil microorganisms to phosphorus stability and the resulting impacts is critical in ecosystems, but the underlying mechanism is unclear in artificial grassland ecosystems. Methods In this study, the effects of four phosphorus concentrations, P0 (0 kg P ha-1), P1 (15.3 kg P ha-1), P2 (30.6 kg P ha-1), and P3 (45.9 kg P ha-1), on the cross-domain co-occurrence network of bacteria and fungi were investigated in an artificial Leymus chinensis grassland in an arid region. Results and discussion The results of the present study showed that phosphorus addition significantly altered the stem number, biomass and plant height of the Leymus chinensis but had no significant effect on the soil bacterial or fungal alpha (ACE) diversity or beta diversity. The phosphorus treatments all increased the cross-domain co-occurrence network edge, node, proportion of positively correlated edges, edge density, average degree, proximity to centrality, and robustness and increased the complexity and stability of the bacterial-fungal cross-domain co-occurrence network after 3 years of continuous phosphorus addition. Among them, fungi (Ascomycota, Basidiomycota, Mortierellomycota and Glomeromycota) play important roles as keystone species in the co-occurrence network, and they are significantly associated with soil AN, AK and EC. Finally, the growth of Leymus chinensis was mainly due to the influence of the soil phosphorus content and AN. This study revealed the factors affecting the growth of Leymus chinense in artificial grasslands in arid areas and provided a theoretical basis for the construction of artificial grasslands.
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Affiliation(s)
- Xiaoguo Zhou
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Yutong Hu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Huijun Li
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiandong Sheng
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Junhui Cheng
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Tingting Zhao
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Yuanmei Zhang
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
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Roberts K, Osme A, De Salvo C, Zoli E, Herrada J, McCormick TS, Ghannoum M, Cominelli F, Di Martino L. Candida tropicalis Affects Candida albicans Virulence by Limiting Its Capacity to Adhere to the Host Intestinal Surface, Leading to Decreased Susceptibility to Colitis in Mice. J Fungi (Basel) 2024; 10:245. [PMID: 38667916 PMCID: PMC11051055 DOI: 10.3390/jof10040245] [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: 02/13/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Candida (C.) infections represent a serious health risk for people affected by inflammatory bowel disease. An important fungal virulence factor is the capacity of the fungus to form biofilms on the colonized surface of the host. This research study aimed to determine the effect of a C. tropicalis and C. albicans co-infection on dextran sodium sulfate (DSS)-induced colitis in mice. The colitis severity was evaluated using histology and a colonoscopy. The mice were mono-inoculated with C. albicans or C. tropicalis or co-challenged with both species. The mice were administered 3% DSS to induce acute colitis. The biofilm activity was assessed using (2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl] 2H-tetrazoliumhydroxide (XTT) and dry-weight assays. The abundance of C. albicans in the colon tissues was assessed by immunohistochemistry. The co-challenged mice showed a decreased colitis severity compared to the mono-inoculated mice. The dry-weight assay demonstrated a marked decrease in C. albicans biofilm production in a C. albicans culture incubated with C. tropicalis supernatant. Immunohistochemical staining showed that C. albicans was more abundant in the mucosa of C. albicans mono-inoculated mice compared to the co-inoculated group. These data indicate an antagonistic microbial interaction between the two Candida species, where C. tropicalis may produce molecules capable of limiting the ability of C. albicans to adhere to the host intestinal surface, leading to a reduction in biofilm formation.
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Affiliation(s)
- Kyle Roberts
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Abdullah Osme
- Department of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Carlo De Salvo
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (C.D.S.); (F.C.)
| | - Eleonora Zoli
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Janet Herrada
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Thomas S. McCormick
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Mahmoud Ghannoum
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Fabio Cominelli
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (C.D.S.); (F.C.)
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Luca Di Martino
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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25
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Chamard J, Faticov M, Blanchet FG, Chagnon PL, Laforest-Lapointe I. Interplay of biotic and abiotic factors shapes tree seedling growth and root-associated microbial communities. Commun Biol 2024; 7:360. [PMID: 38519711 PMCID: PMC10960049 DOI: 10.1038/s42003-024-06042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Root-associated microbes can alleviate plant abiotic stresses, thus potentially supporting adaptation to a changing climate or to novel environments during range expansion. While climate change is extending plant species fundamental niches northward, the distribution and colonization of mutualists (e.g., arbuscular mycorrhizal fungi) and pathogens may constrain plant growth and regeneration. Yet, the degree to which biotic and abiotic factors impact plant performance and associated microbial communities at the edge of their distribution remains unclear. Here, we use root microscopy, coupled with amplicon sequencing, to study bacterial, fungal, and mycorrhizal root-associated microbial communities from sugar maple seedlings distributed across two temperate-to-boreal elevational gradients in southern Québec, Canada. Our findings demonstrate that soil pH, soil Ca, and distance to sugar maple trees are key drivers of root-associated microbial communities, overshadowing the influence of elevation. Interestingly, changes in root fungal community composition mediate an indirect effect of soil pH on seedling growth, a pattern consistent at both sites. Overall, our findings highlight a complex role of biotic and abiotic factors in shaping tree-microbe interactions, which are in turn correlated with seedling growth. These findings have important ramifications for tree range expansion in response to shifting climatic niches.
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Affiliation(s)
- Joey Chamard
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre Sève, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre d'Étude de la Forêt, Université du Québec à Montréal, Montréal, QC, Canada
| | - Maria Faticov
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada.
- Centre Sève, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada.
- Centre d'Étude de la Forêt, Université du Québec à Montréal, Montréal, QC, Canada.
| | - F Guillaume Blanchet
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
- Département de mathématiques, Université de Sherbrooke, Sherbrooke, QC, Canada
- Département des sciences de la santé communautaire, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre-Luc Chagnon
- Agriculture and Agri-food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Département des Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - Isabelle Laforest-Lapointe
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada.
- Centre Sève, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada.
- Centre d'Étude de la Forêt, Université du Québec à Montréal, Montréal, QC, Canada.
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Vakilchap F, Mohammad Mousavi S. Exploring the untapped practices in bacterial-fungal mixed-based cultures for acidic treatment of metal-enriched printed circuit board waste. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 179:245-261. [PMID: 38493610 DOI: 10.1016/j.wasman.2024.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/17/2023] [Accepted: 02/19/2024] [Indexed: 03/19/2024]
Abstract
This study explores the extraction of metals from spent mobile phone printed circuit boards (SMPhPCBs) to address environmental and resource depletion concerns. The challenges in metal recovery from SMPhPCBs arise due to their complex composition and high metal content. While previous research has primarily focused on using bio-cyanide, bio-sulfate, and bio-ferric compounds from acidophilic bacteria, the potential of bio-oxalic acid for SMPhPCBs treatment and the alteration of their complex structure has not yet been explored. Additionally, this study suggests evaluating the untapped potential of Aspergillus niger in oxalic acid production through mixed cultures with bacteria, marking a pioneering approach. A unique culture of Bacillus megaterium and A. niger was created, inducing bio-stress by bacterial metabolites, including gluconic acid (2683 mg/l) and live/dead bacterial cells in a medium with glucose deficiency. Results demonstrated reducing sugar consumption and oxalic acid over-production in mixed cultures compared to pure cultures, ranging from 1350 to 4951 mg/l at an initial glucose concentration (IGC) of 10 g/l and 4276 to 7460 mg/l at IGC 20 g/l. This over-production is attributed to proposed fungal signaling mechanisms to bacteria. Metal extraction using organic acids and siderophores at 10 g/l pulp density, 24 h, and 60 °C yielded Mn (100 %), Pt (100 %), Pd (70.7 %), Fe (50.8 %), Co (48.3 %), Al (21.8 %), among others. The final valuable residue containing copper, gold, and silver holds potential for future recycling. The study concludes with XRD and FTIR analyses to assess the bioleaching effect on the bio-leached powder.
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Affiliation(s)
- Farzane Vakilchap
- Biotechnology Group, Chemical Engineering Department, Tarbiat Modares University, Tehran, Iran
| | - Seyyed Mohammad Mousavi
- Biotechnology Group, Chemical Engineering Department, Tarbiat Modares University, Tehran, Iran; Modares Environmental Research Institute, Tarbiat Modares University, Tehran, Iran.
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Thomas VE, Antony-Babu S. Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum. ENVIRONMENTAL MICROBIOME 2024; 19:14. [PMID: 38461269 PMCID: PMC10924372 DOI: 10.1186/s40793-024-00558-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2. RESULTS Our results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere. CONCLUSIONS The study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.
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Affiliation(s)
- Vanessa E Thomas
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Sanjay Antony-Babu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
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Hegde S, Khanipov K, Hornett EA, Nilyanimit P, Pimenova M, Saldaña MA, de Bekker C, Golovko G, Hughes GL. Interkingdom interactions shape the fungal microbiome of mosquitoes. Anim Microbiome 2024; 6:11. [PMID: 38454530 PMCID: PMC10921588 DOI: 10.1186/s42523-024-00298-4] [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: 11/21/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The mosquito microbiome is an important modulator of vector competence and vectoral capacity. Unlike the extensively studied bacterial microbiome, fungal communities in the mosquito microbiome (the mycobiome) remain largely unexplored. To work towards getting an improved understanding of the fungi associated with mosquitoes, we sequenced the mycobiome of three field-collected and laboratory-reared mosquito species (Aedes albopictus, Aedes aegypti, and Culex quinquefasciatus). RESULTS Our analysis showed both environment and host species were contributing to the diversity of the fungal microbiome of mosquitoes. When comparing species, Ae. albopictus possessed a higher number of diverse fungal taxa than Cx. quinquefasciatus, while strikingly less than 1% of reads from Ae. aegypti samples were fungal. Fungal reads from Ae. aegypti were < 1% even after inhibiting host amplification using a PNA blocker, indicating that this species lacked a significant fungal microbiome that was amplified using this sequencing approach. Using a mono-association mosquito infection model, we confirmed that mosquito-derived fungal isolates colonize Aedes mosquitoes and support growth and development at comparable rates to their bacterial counterparts. Strikingly, native bacterial taxa isolated from mosquitoes impeded the colonization of symbiotic fungi in Ae. aegypti suggesting interkingdom interactions shape fungal microbiome communities. CONCLUSION Collectively, this study adds to our understanding of the fungal microbiome of different mosquito species, that these fungal microbes support growth and development, and highlights that microbial interactions underpin fungal colonization of these medically relevent species.
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Affiliation(s)
- Shivanand Hegde
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK.
- School of Life Sciences, Keele University, Newcastle, UK.
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Emily A Hornett
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Pornjarim Nilyanimit
- Center of Excellence in Clinical Virology, Faculty of Medicine , Chulalongkorn University, Bangkok, Thailand
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Miguel A Saldaña
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Charissa de Bekker
- Microbiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK.
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Liu Z, Xia Q, Cai J, Wang Z, Yang K, Chen D, Wei J, Chen C, Liu C, Chang W, Li Z, Li X, Yang Y, Yang L, Tan X. Nitrogen Fertilizers Affect Microbial Hitchhiking to the Plant Roots. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4639-4648. [PMID: 38377485 DOI: 10.1021/acs.jafc.3c07623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The phenomenon of microbial hitchhiking, where nonmotile microbes utilize transspecies motility to navigate within their environment, has been observed. However, the underlying factors driving microbial hitchhiking remain unclear. Our study explored how nitrogen fertilizers affect microbial hitchhiking in soil through an in situ planting experiment. We established twelve treatments encompassing the presence and absence of plants, the presence and absence of a filter membrane that is used to prevent hitchhiking, and three nitrogen levels. Results showed that nitrogen influenced bacterial diversity in all soils, an effect thwarted by filter membranes. In the presence of plants, nitrogen significantly affected the bacterial mobility, Bacillus abundance, and plant biomass, but these effects vanished when filters were used. The correlation between motile Bacillus and rhizosphere bacteria was strong without filters at the proper nitrogen levels but weakened with membrane treatments. Thus, plants and nitrogen together, not nitrogen alone, alter the soil microbiome via hitchhiking.
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Affiliation(s)
- Zhibin Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Qini Xia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Cai
- West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ziyuan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kexin Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Dixu Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jiahong Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Cun Chen
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu, Sichuan 611130, China
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Water Resource and Hydropower, Sichuan University, Chengdu, Sichuan 610065, China
| | - Wei Chang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Zhi Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xufeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Liang Yang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Water Resource and Hydropower, Sichuan University, Chengdu, Sichuan 610065, China
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30
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Matteoli FP, Silva AMM, de Araújo VLVP, Feiler HP, Cardoso EJBN. Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks. World J Microbiol Biotechnol 2024; 40:119. [PMID: 38429532 DOI: 10.1007/s11274-024-03926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.
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Affiliation(s)
- Filipe Pereira Matteoli
- Laboratory of Microbial Bioinformatics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru, Brazil.
| | - Antonio M M Silva
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Victor L V P de Araújo
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Henrique P Feiler
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Elke J B N Cardoso
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
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31
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Musa OI, Akande SA, Ijah UJJ, Abioye OP, Maude AM, Samuel JO, Mustapha A, Abdulrahim AM, Gusdanis ACG. Biofilms communities in the soil: characteristic and interactions using mathematical model. Res Microbiol 2024; 175:104149. [PMID: 37923049 DOI: 10.1016/j.resmic.2023.104149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
There are many different kinds of microorganisms in the soil, and many of them are biofilms because they can make supracellular compounds. Surface-associated microorganisms in a biofilm are encased in a hydrated extracellular polymeric substance that aids in adherence and survival. Numerous different kinds of microorganisms call the soil home. Strong interactions with and among species are made possible by biofilms; this, in turn, might increase the effectiveness with which organic compounds and poisons in soil are degraded. This encouraged us to take a close look at soil biofilm ecosystems, which we do in this paper. In this research, we will look at how soil biofilms arise and how that affects the composition of microbial communities and their function in the soil. Recent years have seen an uptick in interest in questions about biofilm structure and the social interactions of various bacteria. Many concepts elucidating the underlying mathematics of biofilm growth are also presented. Since biofilms are so widespread, this breakthrough in soil biofilm inquiry might help scientists understand soil microbiomes better. Mathematical models further extrapolate the relationships between microbial communities and gives a more precise information as to what is happening in a biofilm. Biofilms can help plants cope with a variety of environmental challenges. Soil quality, plant nourishment, plant protection, bioremediation, and climate change are all influenced by the interplay of biofilm communities. Thus, biofilms play an important role in the development of environmentally friendly and sustainable agriculture.
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Affiliation(s)
- Ojeba Innocent Musa
- Department of Microbiology, Skyline University Nigeria, Kano State, Nigeria.
| | | | | | - Olabisi Peter Abioye
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Asmau Mohammed Maude
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Job Oloruntoba Samuel
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Adamu Mustapha
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Al-Musbahu Abdulrahim
- Department of Mathematics, Federal University of Technology, Minna Niger State, Nigeria
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32
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Rodriguez KA, Gurung M, Talatala R, Rearick JR, Ruebel ML, Stephens KE, Yeruva L. The Role of Early Life Gut Mycobiome on Child Health. Adv Nutr 2024; 15:100185. [PMID: 38311313 PMCID: PMC10907404 DOI: 10.1016/j.advnut.2024.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
The human gut microbiota is composed of bacteria (microbiota or microbiome), fungi (mycobiome), viruses, and archaea, but most of the research is primarily focused on the bacterial component of this ecosystem. Besides bacteria, fungi have been shown to play a role in host health and physiologic functions. However, studies on mycobiota composition during infancy, the factors that might shape infant gut mycobiota, and implications to child health and development are limited. In this review, we discuss the factors likely shaping gut mycobiota, interkingdom interactions, and associations with child health outcomes and highlight the gaps in our current knowledge of this ecosystem.
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Affiliation(s)
- Kayleigh Amber Rodriguez
- Arkansas Children's Research Institute, Little Rock, AR, United States; University of Arkansas for Medical Sciences, Department of Pediatrics, Division of Infectious Diseases, Little Rock, AR, United States
| | - Manoj Gurung
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Rachelanne Talatala
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States
| | - Jolene R Rearick
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Meghan L Ruebel
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Kimberly E Stephens
- Arkansas Children's Research Institute, Little Rock, AR, United States; University of Arkansas for Medical Sciences, Department of Pediatrics, Division of Infectious Diseases, Little Rock, AR, United States.
| | - Laxmi Yeruva
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States.
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33
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Liu XL, Zhao H, Wang YX, Liu XY, Jiang Y, Tao MF, Liu XY. Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus. Front Microbiol 2024; 15:1346252. [PMID: 38486702 PMCID: PMC10939042 DOI: 10.3389/fmicb.2024.1346252] [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: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
The fungus Rhizopus arrhizus (=R. oryzae) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of R. arrhizus, were identified using live/dead staining, fluorescence in situ hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, Pandoraea sputorum EFB03792 and Mycetohabitans endofungorum EFB03829, were purified from the host fungal strains R. arrhizus XY03792 and XY03829, respectively. Notably, this study marks the first report of Pandoraea as an EFB genus. Compared to its free-living counterparts, P. sputorum EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces R. arrhizus as a new host for EFB M. endofungorum, with EFB contributing to host sporulation. Despite a visibly reduced genome, M. endofungorum EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in R. arrhizus, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within R. arrhizus, laying the groundwork for identifying suitable R. arrhizus strains for fermentation processes.
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Affiliation(s)
- Xiao-Ling Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhao
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Xin Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xin-Ye Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yang Jiang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Meng-Fei Tao
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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34
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Wang M, Ge AH, Ma X, Wang X, Xie Q, Wang L, Song X, Jiang M, Yang W, Murray JD, Wang Y, Liu H, Cao X, Wang E. Dynamic root microbiome sustains soybean productivity under unbalanced fertilization. Nat Commun 2024; 15:1668. [PMID: 38395981 PMCID: PMC10891064 DOI: 10.1038/s41467-024-45925-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.
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Affiliation(s)
- Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An-Hui Ge
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xingzhu Ma
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, China
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiujin Xie
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Like Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengchen Jiang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weibing Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jeremy D Murray
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Maruri-López I, Romero-Contreras YJ, Napsucialy-Mendivil S, González-Pérez E, Aviles-Baltazar NY, Chávez-Martínez AI, Flores-Cuevas EJ, Schwan-Estrada KRF, Dubrovsky JG, Jiménez-Bremont JF, Serrano M. A biostimulant yeast, Hanseniaspora opuntiae, modifies Arabidopsis thaliana root architecture and improves the plant defense response against Botrytis cinerea. PLANTA 2024; 259:53. [PMID: 38294549 PMCID: PMC10830669 DOI: 10.1007/s00425-023-04326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024]
Abstract
MAIN CONCLUSION The biostimulant Hanseniaspora opuntiae regulates Arabidopsis thaliana root development and resistance to Botrytis cinerea. Beneficial microbes can increase plant nutrient accessibility and uptake, promote abiotic stress tolerance, and enhance disease resistance, while pathogenic microorganisms cause plant disease, affecting cellular homeostasis and leading to cell death in the most critical cases. Commonly, plants use specialized pattern recognition receptors to perceive beneficial or pathogen microorganisms. Although bacteria have been the most studied plant-associated beneficial microbes, the analysis of yeasts is receiving less attention. This study assessed the role of Hanseniaspora opuntiae, a fermentative yeast isolated from cacao musts, during Arabidopsis thaliana growth, development, and defense response to fungal pathogens. We evaluated the A. thaliana-H. opuntiae interaction using direct and indirect in vitro systems. Arabidopsis growth was significantly increased seven days post-inoculation with H. opuntiae during indirect interaction. Moreover, we observed that H. opuntiae cells had a strong auxin-like effect in A. thaliana root development during in vitro interaction. We show that 3-methyl-1-butanol and ethanol are the main volatile compounds produced by H. opuntiae. Subsequently, it was determined that A. thaliana plants inoculated with H. opuntiae have a long-lasting and systemic effect against Botrytis cinerea infection, but independently of auxin, ethylene, salicylic acid, or jasmonic acid pathways. Our results demonstrate that H. opuntiae is an important biostimulant that acts by regulating plant development and pathogen resistance through different hormone-related responses.
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Affiliation(s)
- Israel Maruri-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Enrique González-Pérez
- Laboratorio de Biología Molecular de Hongos y Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científca y Tecnológica AC, San Luis Potosí, Mexico
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí (UASLP), Av. Chapultepec 1570, Priv. del Pedregal, 78295, San Luis Potosí, Mexico
| | | | - Ana Isabel Chávez-Martínez
- Laboratorio de Biología Molecular de Hongos y Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científca y Tecnológica AC, San Luis Potosí, Mexico
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | | | - Joseph G Dubrovsky
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Juan Francisco Jiménez-Bremont
- Laboratorio de Biología Molecular de Hongos y Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científca y Tecnológica AC, San Luis Potosí, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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Mészárošová L, Kuťáková E, Kohout P, Münzbergová Z, Baldrian P. Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland. ENVIRONMENTAL MICROBIOME 2024; 19:8. [PMID: 38268048 PMCID: PMC10809484 DOI: 10.1186/s40793-024-00550-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is. RESULTS To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site. CONCLUSIONS Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.
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Affiliation(s)
- Lenka Mészárošová
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic.
- University of Chemistry and Technology, Technická 5, Praha 6, 166 28, Czech Republic.
| | - Eliška Kuťáková
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd 17, Umeå, 901 83, Sweden
| | - Petr Kohout
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
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Staszel-Szlachta K, Lasota J, Szlachta A, Błońska E. The impact of root systems and their exudates in different tree species on soil properties and microorganisms in a temperate forest ecosystem. BMC PLANT BIOLOGY 2024; 24:45. [PMID: 38212695 PMCID: PMC10785385 DOI: 10.1186/s12870-024-04724-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND The species composition of tree stands plays an important role in shaping the properties of forest soils. The aim of our research was to determine the influence on soil properties of the root systems of six species of trees which form forest stands in the temperate climatic zone. The research covered areas including six tree species - Scots pine (Pinus sylvestris L.), European larch (Larix deciduas Mill.), English oak (Quercus robur L.), English ash (Fraxinus excelsior L.), European beech (Fagus sylvatica L.) and European hornbeam (Carpinus betulus L.). In our study, we determined the characteristics of the roots and the amount of carbon excreted alongside their exudates. Enzymatic activity, and the composition and diversity of the fungi and bacteria, were also determined in addition to the basic physicochemical properties of the soil samples. RESULTS A strong relationship between the root characteristics and soil properties, including the pH, basic cation content and phosphorus content, was confirmed. In addition, the enzymatic activity of phosphatase, β-glucosidase, N-acetyl-β-D-glucosaminidase and β-D-cellobiosidase were positively correlated with the root characteristics. The study on soil bacteria across different tree species revealed Proteobacteria and Actinobacteriota to be the most abundant phylum. Fungal analysis showed Basidiomycota and Ascomycota as the dominant phyla. Ascomycota dominated in hornbeam and oak soils. Mortierellomycota was remarkably more present in pine soil. CONCLUSIONS This analysis of root systems and soil properties confirmed the distinctness of ash stands, which were also more abundant in various microorganisms. It was also found that soils affected by different tree species were characterised by varied fungal and bacterial composition. The ash had particularly beneficial impact on soil microbiota.
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Affiliation(s)
- Karolina Staszel-Szlachta
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str, 31-425, Krakow, Poland.
| | - Jarosław Lasota
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str, 31-425, Krakow, Poland
| | - Andrzej Szlachta
- Swierklaniec Forest District, Ul. Oswiecimska 19, 42-622, Swierklaniec, Poland
| | - Ewa Błońska
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str, 31-425, Krakow, Poland
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Lewis MT, Miller L, Hu M, Hamby KA. Diffuse Associations Between Drosophila suzukii and Filamentous Fungal Microbes May Alter Caneberry Disease Dynamics. PHYTOPATHOLOGY 2024; 114:137-145. [PMID: 38318843 DOI: 10.1094/phyto-12-22-0470-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Interactions between microorganisms and frugivorous insects can modulate fruit rot disease epidemiology. Insect feeding and/or oviposition wounds may create opportunities for fungal infection. Passive and active dispersal of fungal inoculums by adult insects also increases disease incidence. In fall-bearing raspberries and blackberries, such vectoring interactions could increase crop damage from the invasive pestiferous vinegar fly Drosophila suzukii (spotted-wing drosophila). Periods of peak D. suzukii activity are known to overlap with several species of primary fruit rot pathogen, particularly Botrytis cinerea and Cladosporium cladosporioides, and previous work indicates that larvae co-occur with and feed on various filamentous fungi at low rates. To further our understanding of the epidemiological consequences that may emerge from these associations, we surveyed the filamentous fungal community associated with adult D. suzukii, isolating and molecularly identifying fungi externally and internally (indicating feeding) from field-collected adults over 3 years. We isolated and identified 37 unique genera of fungi in total, including known raspberry pathogens. Most fungi were detected infrequently, and flies acquired and carried fungi externally at higher richness, frequency, and density relative to internally. In a worst-case scenario laboratory vectoring assay, D. suzukii adults were able to transfer B. cinerea and C. cladosporioides to sterile media at 0, 24, 48, and 72 h after exposure to sporulating cultures in Petri dishes. These results collectively suggest an adventitious vectoring association between D. suzukii and fruit rot fungi that has the potential to alter caneberry disease dynamics.
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Affiliation(s)
- Margaret T Lewis
- Department of Entomology, University of Maryland, College Park, MD 20742
| | - Logan Miller
- Department of Entomology, University of Maryland, College Park, MD 20742
| | - Mengjun Hu
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742
| | - Kelly A Hamby
- Department of Entomology, University of Maryland, College Park, MD 20742
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Berrios L, Venturini AM, Ansell TB, Tok E, Johnson W, Willing CE, Peay KG. Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses. ISME COMMUNICATIONS 2024; 4:ycae104. [PMID: 39188310 PMCID: PMC11346365 DOI: 10.1093/ismeco/ycae104] [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: 04/16/2024] [Revised: 07/15/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024]
Abstract
Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
| | - Andressa M Venturini
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
| | - Tillson Bertie Ansell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Esther Tok
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
| | - William Johnson
- Oceans Department, Hopkins Marine Station of Stanford University, 120 Ocean View Blvd., Pacific Grove, CA 93950, United States
| | - Claire E Willing
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, United States
| | - Kabir G Peay
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, United States
- Department of Earth System Science, Stanford University, Stanford, CA 94305, United States
- Woods Institute for the Environment, Stanford University, Stanford, CA 94305, United States
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Dreyling L, Penone C, Schenk NV, Schmitt I, Dal Grande F. Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests. ISME COMMUNICATIONS 2024; 4:ycae012. [PMID: 38500703 PMCID: PMC10945369 DOI: 10.1093/ismeco/ycae012] [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: 12/15/2023] [Revised: 01/18/2024] [Indexed: 03/20/2024]
Abstract
Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.
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Affiliation(s)
- Lukas Dreyling
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Department of Biology, University of Padova, Padua 35122, Italy
- National Biodiversity Future Center (NBFC), Palermo 90133, Italy
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Zhai C, Han L, Xiong C, Ge A, Yue X, Li Y, Zhou Z, Feng J, Ru J, Song J, Jiang L, Yang Y, Zhang L, Wan S. Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167217. [PMID: 37751844 DOI: 10.1016/j.scitotenv.2023.167217] [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: 05/21/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
Soil microbiomes play a critical role in regulating ecosystem multifunctionality. However, whether and how soil protists and microbiome interactions affect ecosystem multifunctionality under climate change is unclear. Here, we transplanted 54 soil monoliths from three typical temperate grasslands (i.e., desert, typical, and meadow steppes) along a precipitation gradient in the Mongolian Plateau and examined their response to nighttime warming, decreased, and increased precipitation. Across the three steppes, nighttime warming only stimulated protistan diversity by 15.61 (absolute change, phylogenetic diversity) but had no effect on ecosystem multifunctionality. Decreased precipitation reduced bacterial (8.78) and fungal (22.28) diversity, but significantly enhanced soil microbiome network complexity by 1.40. Ecosystem multifunctionality was reduced by 0.23 under decreased precipitation, which could be largely attributed to the reduced soil moisture that negatively impacted bacterial and fungal communities. In contrast, increased precipitation had little impact on soil microbial communities. Overall, both bacterial and fungal diversity and network complexity play a fundamental role in maintaining ecosystem multifunctionality in response to drought stress. Protists alter ecosystem multifunctionality by indirectly affecting microbial network complexity. Therefore, not only microbial diversity but also their interactions (regulated by soil protists) should be considered in evaluating the responses of ecosystem multifunctionality, which has important implications for predicting changes in ecosystem functioning under future climate change scenarios.
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Affiliation(s)
- Changchun Zhai
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lili Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Anhui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiaojing Yue
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Ying Li
- School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Zhenxing Zhou
- School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Jiayin Feng
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Jingyi Ru
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Jian Song
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Limei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shiqiang Wan
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China.
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Valadez-Cano C, Olivares-Hernández R, Espino-Vázquez AN, Partida-Martínez LP. Genome-Scale Model of Rhizopus microsporus: Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts. Environ Microbiol 2024; 26:e16551. [PMID: 38072824 DOI: 10.1111/1462-2920.16551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
Rhizopus microsporus often lives in association with bacterial and viral symbionts that alter its biology. This fungal model represents an example of the complex interactions established among diverse organisms in functional holobionts. We constructed a Genome-Scale Model (GSM) of the fungal-bacterial-viral holobiont (iHol). We employed a constraint-based method to calculate the metabolic fluxes to decipher the metabolic interactions of the symbionts with their host. Our computational analyses of iHol simulate the holobiont's growth and the production of the toxin rhizoxin. Analyses of the calculated fluxes between R. microsporus in symbiotic (iHol) versus asymbiotic conditions suggest that changes in the lipid and nucleotide metabolism of the host are necessary for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal-bacterial metabolic interaction, as its production does not compromise fungal growth, and Mycetohabitans bacteria can efficiently consume it. Narnavirus RmNV-20S and RmNV-23S affected the nucleotide metabolism without impacting the fungal-bacterial symbiosis. Our analyses highlighted the metabolic stability of Mycetohabitans throughout its co-evolution with the fungal host. We also predicted changes in reactions of the bacterial metabolism required for the active production of rhizoxin. This iHol is the first GSM of a fungal holobiont.
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Affiliation(s)
- Cecilio Valadez-Cano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Roberto Olivares-Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, Mexico
| | - Astrid N Espino-Vázquez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Laila P Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
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Antón-Herrero R, Chicca I, García-Delgado C, Crognale S, Lelli D, Gargarello RM, Herrero J, Fischer A, Thannberger L, Eymar E, Petruccioli M, D’Annibale A. Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil. J Fungi (Basel) 2023; 9:1205. [PMID: 38132804 PMCID: PMC10745009 DOI: 10.3390/jof9121205] [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: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.
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Affiliation(s)
- Rafael Antón-Herrero
- Department of Agricultural Chemistry and Food Science, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (R.A.-H.); (E.E.)
| | | | - Carlos García-Delgado
- Department of Geology and Geochemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Silvia Crognale
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Davide Lelli
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Romina Mariel Gargarello
- Water, Air and Soil Unit, Eurecat, Centre Tecnològic de Catalunya, 08242 Manresa, Spain; (R.M.G.); (J.H.)
| | - Jofre Herrero
- Water, Air and Soil Unit, Eurecat, Centre Tecnològic de Catalunya, 08242 Manresa, Spain; (R.M.G.); (J.H.)
| | | | | | - Enrique Eymar
- Department of Agricultural Chemistry and Food Science, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (R.A.-H.); (E.E.)
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Alessandro D’Annibale
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
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Chen B, Yu K, Fu L, Wei Y, Liang J, Liao Z, Qin Z, Yu X, Deng C, Han M, Ma H. The diversity, community dynamics, and interactions of the microbiome in the world's deepest blue hole: insights into extreme environmental response patterns and tolerance of marine microorganisms. Microbiol Spectr 2023; 11:e0053123. [PMID: 37861344 PMCID: PMC10883803 DOI: 10.1128/spectrum.00531-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE This study comprehensively examined the community dynamics, functional profiles, and interactions of the microbiome in the world's deepest blue hole. The findings revealed a positive correlation between the α-diversities of Symbiodiniaceae and archaea, indicating the potential reliance of Symbiodiniaceae on archaea in an extreme environment resulting from a partial niche overlap. The negative association between the α-diversity and β-diversity of the bacterial community suggested that the change rule of the bacterial community was consistent with the Anna Karenina effects. The core microbiome comprised nine microbial taxa, highlighting their remarkable tolerance and adaptability to sharp environmental gradient variations. Bacteria and archaea played significant roles in carbon, nitrogen, and sulfur cycles, while fungi contributed to carbon metabolism. This study advanced our understanding of the community dynamics, response patterns, and resilience of microorganisms populating the world's deepest blue hole, thereby facilitating further ecological and evolutional exploration of microbiomes in diverse extreme environments.
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Affiliation(s)
- Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute Co. Ltd. , Qionghai, China
| | - Yuxin Wei
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University , Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Chuanqi Deng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Minwei Han
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Honglin Ma
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University , Nanning, China
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Qiu Y, Zhang K, Zhao Y, Zhao Y, Wang B, Wang Y, He T, Xu X, Bai T, Zhang Y, Hu S. Climate warming suppresses abundant soil fungal taxa and reduces soil carbon efflux in a semi-arid grassland. MLIFE 2023; 2:389-400. [PMID: 38818267 PMCID: PMC10989086 DOI: 10.1002/mlf2.12098] [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: 05/29/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 06/01/2024]
Abstract
Soil microorganisms critically affect the ecosystem carbon (C) balance and C-climate feedback by directly controlling organic C decomposition and indirectly regulating nutrient availability for plant C fixation. However, the effects of climate change drivers such as warming, precipitation change on soil microbial communities, and C dynamics remain poorly understood. Using a long-term field warming and precipitation manipulation in a semi-arid grassland on the Loess Plateau and a complementary incubation experiment, here we show that warming and rainfall reduction differentially affect the abundance and composition of bacteria and fungi, and soil C efflux. Warming significantly reduced the abundance of fungi but not bacteria, increasing the relative dominance of bacteria in the soil microbial community. In particular, warming shifted the community composition of abundant fungi in favor of oligotrophic Capnodiales and Hypocreales over potential saprotroph Archaeorhizomycetales. Also, precipitation reduction increased soil total microbial biomass but did not significantly affect the abundance or diversity of bacteria. Furthermore, the community composition of abundant, but not rare, soil fungi was significantly correlated with soil CO2 efflux. Our findings suggest that alterations in the fungal community composition, in response to changes in soil C and moisture, dominate the microbial responses to climate change and thus control soil C dynamics in semi-arid grasslands.
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Affiliation(s)
- Yunpeng Qiu
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Kangcheng Zhang
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Yunfeng Zhao
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Yexin Zhao
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Bianbian Wang
- Ningxia Yunwu Mountains Grassland Natural Reserve AdministrationGuyuanChina
| | - Yi Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth EnvironmentChinese Academy of SciencesXi'anChina
| | - Tangqing He
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Xinyu Xu
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
- Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Tongshuo Bai
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Yi Zhang
- College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjingChina
| | - Shuijin Hu
- Department of Entomology & Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
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Embacher J, Zeilinger S, Kirchmair M, Neuhauser S. Prokaryote communities associated with different types of tissue formed and substrates inhabited by Serpula lacrymans. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:642-655. [PMID: 37789578 PMCID: PMC10667670 DOI: 10.1111/1758-2229.13191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/07/2023] [Indexed: 10/05/2023]
Abstract
The basidiomycete Serpula lacrymans is responsible for major timber devastation in houses. Basidiomycetes are known to harbour a diverse but poorly understood microbial community of bacteria, archaea, yeasts and filamentous fungi. In this study, we used amplicon-sequencing to analyse the abundance and composition of prokaryotic communities associated with fruiting bodies of S. lacrymans and compared them to communities of surrounding material to access the 'background' community structure. Our findings indicate that bacterial genera cluster depended on sample type and that the main driver for microbial diversity is specimen, followed by sample origin. The most abundant bacterial phylum identified in the fruiting bodies was Pseudomonadota, followed by Actinomycetota and Bacteroidota. The prokaryote community of the mycelium was dominated by Actinomycetota, Halobacterota and Pseudomonadota. Actinomycetota was the most abundant phylum in both environment samples (infested timber and underground scree), followed by Bacillota in wood and Pseudomonadota in underground samples. Nocardioides, Pseudomonas, Pseudonochardia, Streptomyces and Rubrobacter spp. were among others found to comprise the core microbiome of S. lacrymans basidiocarps. This research contributes to the understanding of the holobiont S. lacrymans and gives hints to potential bacterial phyla important for its development and lifestyle.
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Affiliation(s)
- Julia Embacher
- Institute of Microbiology, Universität InnsbruckInnsbruckAustria
| | | | - Martin Kirchmair
- Institute of Microbiology, Universität InnsbruckInnsbruckAustria
| | - Sigrid Neuhauser
- Institute of Microbiology, Universität InnsbruckInnsbruckAustria
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Shi J, Thakur MP. Climate extremes disrupt fungal-bacterial interactions. Nat Microbiol 2023; 8:2226-2229. [PMID: 38030901 DOI: 10.1038/s41564-023-01531-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Affiliation(s)
- Jingjing Shi
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Madhav P Thakur
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
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Elkhairy BM, Salama NM, Desouki AM, Abdelrazek AB, Soliman KA, Ibrahim SA, Khalil HB. Towards unlocking the biocontrol potential of Pichia kudriavzevii for plant fungal diseases: in vitro and in vivo assessments with candidate secreted protein prediction. BMC Microbiol 2023; 23:356. [PMID: 37980509 PMCID: PMC10657120 DOI: 10.1186/s12866-023-03047-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/06/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND Plant fungal pathogens cause substantial economic losses through crop yield reduction and post-harvest storage losses. The utilization of biocontrol agents presents a sustainable strategy to manage plant diseases, reducing the reliance on hazardous chemical. Recently, Pichia kudriavzevii has emerged as a promising biocontrol agent because of its capacity to inhibit fungal growth, offering a potential solution for plant disease management. RESULTS Two novel Pichia kudriavzevii strains, Pk_EgyACGEB_O1 and Pk_EgyACGEB_O2, were isolated from olive brine samples. The microscopic characterization of the strains revealed similar structures. However, there were noticeable differences in their visual morphology. Based on their internal transcribed spacer (ITS) DNA sequences, Pk_EgyACGEB_O1 and Pk_EgyACGEB_O2 strains assigned by GenBank IDs MZ507552.1 and MZ507554.1 shared high sequence similarity (~ 99.8% and 99.5%) with P. kudriavzevii, respectively. Both strains were evaluated in vitro against plant pathogenic fungi. The strains revealed the ability to consistently inhibit fungal growth, with Pk_EgyACGEB_O2 showing higher effectiveness. In addition, both P. kudriavzevii strains effectively controlled grey mold disease caused by B. cinerea in golden delicious apples, suggesting their potential as sustainable and eco-friendly biocontrol agents for post-harvest diseases. Based on a comprehensive bioinformatics pipeline, candidate-secreted proteins responsible for the potent antifungal activity of P. kudriavzevii were identified. A total of 59 proteins were identified as common among the P. kudriavzevii CBS573, SD108, and SD129 strains. Approximately 23% of the secreted proteins in the P. kudriavzevii predicted secretome are hydrolases with various activities, including proteases, lipases, glycosidases, phosphatases, esterases, carboxypeptidases, or peptidases. In addition, a set of cell-wall-related proteins was identified, which might enhance the biocontrol activity of P. kudriavzevii by preserving the structure and integrity of the cell wall. A papain inhibitor was also identified and could potentially offer a supplementary defense against plant pathogens. CONCLUSION Our results revealed the biocontrol capabilities of P. kudriavzevii against plant pathogenic fungi. The research focused on screening novel strains for their ability to inhibit the growth of common pathogens, both in vitro and in vivo. This study shed light on how P. kudriavzevii interacts with fungal pathogens. The findings can help develop effective strategies for managing plant diseases.
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Affiliation(s)
- Bassma Mahmoud Elkhairy
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo, 11241, Egypt
- Biotechnology Labs, NanoFab Technology Company, 6th October, Giza, Egypt
| | - Nabil Mohamed Salama
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo, 11241, Egypt
| | - Abdalrahman Mohammad Desouki
- Department of Plant Pathology, Faculty of Agriculture, Ain Shams University, Postal Code, 68 Hadayek Shoubra, Cairo, 11241, Egypt
| | - Ashraf Bakry Abdelrazek
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo, 11241, Egypt
- Biotechnology Labs, NanoFab Technology Company, 6th October, Giza, Egypt
| | - Khaled Abdelaziz Soliman
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo, 11241, Egypt
| | - Samir Abdelaziz Ibrahim
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo, 11241, Egypt
| | - Hala Badr Khalil
- Department of Genetics, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shoubra, Cairo, 11241, Egypt.
- Biological Sciences Department, College of Science, King Faisal University, Hofuf, Kingdom of Saudi Arabia.
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Khan F, Jeong GJ, Javaid A, Thuy Nguyen Pham D, Tabassum N, Kim YM. Surface adherence and vacuolar internalization of bacterial pathogens to the Candida spp. cells: Mechanism of persistence and propagation. J Adv Res 2023; 53:115-136. [PMID: 36572338 PMCID: PMC10658324 DOI: 10.1016/j.jare.2022.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The co-existence of Candida albicans with the bacteria in the host tissues and organs displays interactions at competitive, antagonistic, and synergistic levels. Several pathogenic bacteria take advantage of such types of interaction for their survival and proliferation. The chemical interaction involves the signaling molecules produced by the bacteria or Candida spp., whereas the physical attachment occurs by involving the surface proteins of the bacteria and Candida. In addition, bacterial pathogens have emerged to internalize inside the C. albicans vacuole, which is one of the inherent properties of the endosymbiotic relationship between the bacteria and the eukaryotic host. AIM OF REVIEW The interaction occurring by the involvement of surface protein from diverse bacterial species with Candida species has been discussed in detail in this paper. An in silico molecular docking study was performed between the surface proteins of different bacterial species and Als3P of C. albicans to explain the molecular mechanism involved in the Als3P-dependent interaction. Furthermore, in order to understand the specificity of C. albicans interaction with Als3P, the evolutionary relatedness of several bacterial surface proteins has been investigated. Furthermore, the environmental factors that influence bacterial pathogen internalization into the Candida vacuole have been addressed. Moreover, the review presented future perspectives for disrupting the cross-kingdom interaction and eradicating the endosymbiotic bacterial pathogens. KEY SCIENTIFIC CONCEPTS OF REVIEW With the involvement of cross-kingdom interactions and endosymbiotic relationships, the bacterial pathogens escape from the environmental stresses and the antimicrobial activity of the host immune system. Thus, the study of interactions between Candida and bacterial pathogens is of high clinical significance.
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Affiliation(s)
- Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
| | - Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Aqib Javaid
- Department of Biotechnology and Bioinformatics, University of Hyderabad, India
| | - Dung Thuy Nguyen Pham
- Institute of Applied Technology and Sustainable Development, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea.
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Nguyen TP, Meng DR, Chang CH, Su PY, Ou CA, Hou PF, Sung HM, Chou CH, Ohme-Takagi M, Huang HJ. Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae. mSphere 2023; 8:e0032423. [PMID: 37750721 PMCID: PMC10597458 DOI: 10.1128/msphere.00324-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species. Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1,030 differentially expressed genes (DEGs) in yeast. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism, and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall, antioxidant, and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of the fungal model. IMPORTANCE Since the use of bacteria-emitted volatile compounds in phytopathogen control is of considerable interest, it is important to understand the molecular mechanisms by which fungi may adapt to microbial volatile compounds (mVCs). Paenarthrobacter ureafaciens is an isolated bacterium from disease-suppressive soil that belongs to the Actinomycetota phylum. P. ureafaciens mVCs showed a potent antifungal effect on phytopathogens, which may contribute to disease suppression in soil. However, our knowledge about the antifungal mechanism of mVCs is limited. This study has proven that mVCs are toxic to fungi due to oxidative stress and mitochondrial dysfunction. To deal with mVC toxicity, antioxidants and physical defenses are required. Furthermore, iron uptake and CAP proteins are required for antimicrobial defense, which is necessary for fungi to deal with the thread from mVCs. This study provides essential foundational knowledge regarding the molecular responses of fungi to inhibitory mVCs.
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Affiliation(s)
- Tri-Phuong Nguyen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - De-Rui Meng
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Han Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
| | - Pei-Yu Su
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chieh-An Ou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Fu Hou
- Kaohsiung District Agricultural Research and Extension Station, Pingtung, Taiwan
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chang-Hung Chou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Masaru Ohme-Takagi
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
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