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Wang Y, Zhou Y, Tang F, Cao Q, Bai Y. Mixing of pine and arbuscular mycorrhizal tree species changed soil organic carbon storage by affecting soil microbial characteristics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172630. [PMID: 38677428 DOI: 10.1016/j.scitotenv.2024.172630] [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: 11/14/2023] [Revised: 04/01/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
Pure and mixed pine forests are found all over the world. The mycorrhizal type affects soil microbial activity and carbon sequestration capacity in pure forests. However, the effects of mycorrhizal type on microbial characteristics and carbon sequestration capacity in pine mixed forests remain untested. Further, making it difficult to predict carbon storage of the conversion from pure pine forests to mixed forests at larger scales. Herein, a meta-analysis showed that the contents of soil microbial biomass, mineral-associated organic carbon, and soil organic carbon in pine mixed forests with introduced arbuscular mycorrhizal tree species (PMAM) increased by 26.41 %, 58.55 %, and 27.41 %, respectively, compared to pure pine forests, whereas those of pine mixed forests without arbuscular mycorrhizal tree species (PMEcM) remained unchanged. Furthermore, the effect size of microbial biomass, mineral-associated organic carbon and organic carbon contents in subsoil of PMAM are 56.48 %, 78.49 % and 43.05 %, respectively, which are higher than those in topsoil. The improvement of carbon sinks throughout the PMAM soil profile is positively correlated with increases in microbial biomass and mineral-associated organic carbon in subsoil, according to regression analysis and structural equation modelling. In summary, these results highlight that the positive effects of introducing arbuscular mycorrhizal tree species rather than ectomycorrhizal tree species into pure pine forests on soil microbial biomass and carbon sequestration. The positive link between microbial biomass, mineral-associated organic carbon, and soil organic carbon suggests an underlying mechanism for how soil microorganisms store carbon in pine mixed forests. Nevertheless, our findings also imply that the soil carbon pool of PMAM may be vulnerable under climate change. Based on the above findings, we propose that incorporating mycorrhizal type of tree species and soil thickness into mixed forests management and biodiversity conservation.
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Affiliation(s)
- Yaoxiong Wang
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Yunchao Zhou
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China.
| | - Fenghua Tang
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Qianbin Cao
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Yunxing Bai
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
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2
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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 DOI: 10.1016/j.mib.2024.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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3
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Wang Y, Zou Q. Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences. MICROBIAL ECOLOGY 2024; 87:74. [PMID: 38771320 PMCID: PMC11108897 DOI: 10.1007/s00248-024-02390-3] [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: 01/29/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.
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Affiliation(s)
- Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
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4
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Zhu L, Wang X, Liu L, Le B, Tan C, Dong C, Yao X, Hu B. Fungi play a crucial role in sustaining microbial networks and accelerating organic matter mineralization and humification during thermophilic phase of composting. ENVIRONMENTAL RESEARCH 2024; 254:119155. [PMID: 38754614 DOI: 10.1016/j.envres.2024.119155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Fungi play an important role in the mineralization and humification of refractory organic matter such as lignocellulose during composting. However, limited research on the ecological role of fungi in composting system hindered the development of efficient microbial agents. In this study, six groups of lab-scale composting experiments were conducted to reveal the role of fungal community in composting ecosystems by comparing them with bacterial community. The findings showed that the thermophilic phase was crucial for organic matter degradation and humic acid formation. The Richness index of the fungal community peaked at 1165 during this phase. PCoA analysis revealed a robust thermal stability in the fungal community. Despite temperature fluctuations, the community structure, predominantly governed by Pichia and Candida, remained largely unaltered. The stability of fungal community and the complexity of ecological networks were 1.26 times and 5.15 times higher than those observed in bacterial community, respectively. Fungi-bacteria interdomain interaction markedly enhanced network complexity, contributing to maintain microbial ecological functions. The core fungal species belonging to the family Saccharomycetaceae drove interdomain interaction during thermophilic phase. This study demonstrated the key role of fungi in the composting system, which would provide theoretical guidance for the development of high efficiency composting agents to strengthen the mineralization and humification of organic matter.
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Affiliation(s)
- Lin Zhu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China; College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohan Wang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Liyuan Liu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Boyi Le
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chunxu Tan
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chifei Dong
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangwu Yao
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China; College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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5
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Zhang P, Huguet-Tapia J, Peng Z, Liu S, Obasa K, Block AK, White FF. Genome analysis and hyphal movement characterization of the hitchhiker endohyphal Enterobacter sp. from Rhizoctonia solani. Appl Environ Microbiol 2024; 90:e0224523. [PMID: 38319098 PMCID: PMC10952491 DOI: 10.1128/aem.02245-23] [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: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Bacterial-fungal interactions are pervasive in the rhizosphere. While an increasing number of endohyphal bacteria have been identified, little is known about their ecology and impact on the associated fungal hosts and the surrounding environment. In this study, we characterized the genome of an Enterobacter sp. Crenshaw (En-Cren), which was isolated from the generalist fungal pathogen Rhizoctonia solani, and examined the genetic potential of the bacterium with regard to the phenotypic traits associated with the fungus. Overall, the En-Cren genome size was typical for members of the genus and was capable of free-living growth. The genome was 4.6 MB in size, and no plasmids were detected. Several prophage regions and genomic islands were identified that harbor unique genes in comparison with phylogenetically closely related Enterobacter spp. Type VI secretion system and cyanate assimilation genes were identified from the bacterium, while some common heavy metal resistance genes were absent. En-Cren contains the key genes for indole-3-acetic acid (IAA) and phenylacetic acid (PAA) biosynthesis, and produces IAA and PAA in vitro, which may impact the ecology or pathogenicity of the fungal pathogen in vivo. En-Cren was observed to move along hyphae of R. solani and on other basidiomycetes and ascomycetes in culture. The bacterial flagellum is essential for hyphal movement, while other pathways and genes may also be involved.IMPORTANCEThe genome characterization and comparative genomics analysis of Enterobacter sp. Crenshaw provided the foundation and resources for a better understanding of the ecology and evolution of this endohyphal bacteria in the rhizosphere. The ability to produce indole-3-acetic acid and phenylacetic acid may provide new angles to study the impact of phytohormones during the plant-pathogen interactions. The hitchhiking behavior of the bacterium on a diverse group of fungi, while inhibiting the growth of some others, revealed new areas of bacterial-fungal signaling and interaction, which have yet to be explored.
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Affiliation(s)
- Peiqi Zhang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Jose Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Ken Obasa
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- High Plains Plant Disease Diagnostic Lab, Texas A&M AgriLife Extension Service, Amarillo, Texas, USA
| | - Anna K. Block
- Chemistry Research Unit, US Department of Agriculture-Agricultural Research Service, Gainesville, Florida, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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Hu G, Zhou Y, Mou D, Qu J, Luo L, Duan L, Xu Z, Zou X. Filtration effect of Cordyceps chanhua mycoderm on bacteria and its transport function on nitrogen. Microbiol Spectr 2024; 12:e0117923. [PMID: 38099615 PMCID: PMC10783027 DOI: 10.1128/spectrum.01179-23] [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: 03/19/2023] [Accepted: 11/04/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE During the natural growth of Cordyceps chanhua, it will form a mycoderm structure specialized from hyphae. We found that the bacterial membrane of C. chanhua not only filters environmental bacteria but also absorbs and transports nitrogen elements inside and outside the body of C. chanhua. These findings are of great significance for understanding the stable mechanism of the internal microbial community maintained by C. chanhua and how C. chanhua maintains its own nutritional balance. In addition, this study also enriched our understanding of the differences in bacterial community composition and related bacterial community functions of C. chanhua at different growth stages, which is of great value for understanding the environmental adaptation mechanism, the element distribution network, and the changing process of symbiotic microbial system after Cordyceps fungi infected the host. At the same time, it can also provide a theoretical basis for some important ecological imitation cultivation technology of Cordyceps fungi.
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Affiliation(s)
- Gongping Hu
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yeming Zhou
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Dan Mou
- Department of Humanities, Business College of Guizhou University of Finance and Economics, Qiannan, Guizhou, China
| | - Jiaojiao Qu
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
- Tea College, Guizhou University, Guiyang, Guizhou, China
| | - Li Luo
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Lin Duan
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Zhongshun Xu
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Xiao Zou
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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Filippidou S, Price A, Spencer-Jones C, Scales A, Macey MC, Franchi F, Lebogang L, Cavalazzi B, Schwenzer SP, Olsson-Francis K. Diversity of Microbial Mats in the Makgadikgadi Salt Pans, Botswana. Microorganisms 2024; 12:147. [PMID: 38257974 PMCID: PMC10818877 DOI: 10.3390/microorganisms12010147] [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] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
The Makgadikgadi Salt Pans are the remnants of a mega paleo-lake system in the central Kalahari, Botswana. Today, the Makgadikgadi Basin is an arid to semi-arid area receiving water of meteoric origin during the short, wet season. Large microbial mats, which support primary production, are formed due to desiccation during the dry season. This study aimed to characterise the microbial diversity of the microbial mats and the underlying sediment. The focus was the Ntwetwe Pan, located west of the Makgadikgadi Basin. Metagenomic analyses demonstrated that the mats consisted of a high relative abundance of Cyanobacteriota (synonym Cyanobacteria) (20.50-41.47%), Pseudomonadota (synonym Proteobacteria) (15.71 to 32.18%), and Actinomycetota (synonym Actinobacteria) (8.53-32.56%). In the underlying sediments, Pseudomonadota, Actinomycetota, and Euryarchaeota represented over 70% of the community. Localised fluctuations in water content and pH did not significantly affect the microbial diversity of the sediment or the mats.
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Affiliation(s)
- Sevasti Filippidou
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
- School of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alex Price
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Charlotte Spencer-Jones
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
- Department of Geography, Durham University, Durham DH1 3LE, UK
| | - Anthony Scales
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Michael C. Macey
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Fulvio Franchi
- Earth and Environmental Science Department, Botswana International University of Science and Technology, Palapye 10071, Botswana;
- School of Geosciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Lesedi Lebogang
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye 10071, Botswana;
| | - Barbara Cavalazzi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
- Department of Geology, University of Johannesburg, Johannesburg 2006, South Africa
| | - Susanne P. Schwenzer
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Karen Olsson-Francis
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
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8
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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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9
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Al-Salihi SAA, Alberti F. Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides. J Fungi (Basel) 2023; 9:895. [PMID: 37755004 PMCID: PMC10532697 DOI: 10.3390/jof9090895] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 09/28/2023] Open
Abstract
Fungi represents a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. An enzyme's specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. Trichoderma harzianum M10 v1.0 produces many pharmaceutically important molecules; however, their specific biosynthetic pathways remain uncharacterised. Our genomic-based analysis of this species reveals the biosynthetic diversity of its specialised secondary metabolites, where over 50 BGCs were predicted, most of which were listed as polyketide-like compounds associated clusters. Gene annotation of the biosynthetic candidate genes predicted the production of many medically/industrially important compounds including enterobactin, gramicidin, lovastatin, HC-toxin, tyrocidine, equisetin, erythronolide, strobilurin, asperfuranone, cirtinine, protoilludene, germacrene, and epi-isozizaene. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, and the identification of their role in the interaction between this fungus and its biotic/abiotic conditions as well as its role as bio-fungicide.
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Affiliation(s)
| | - Fabrizio Alberti
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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10
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Dijksterhuis J. Endosymbionts: Bacterial hijacking of fungi? Curr Biol 2023; 33:R765-R767. [PMID: 37490862 DOI: 10.1016/j.cub.2023.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Bacteria inside fungal hyphae allow the fungus Rhizopus microsporus to form spores and operate via effectors in 'stealth' mode. When the functionality of one effector is taken away, bacteria are captured in septated cells and die.
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Affiliation(s)
- Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
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11
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Wang Y, Jiménez DJ, Zhang Z, van Elsas JD. Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: a metatranscriptomic study. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:54. [PMID: 36991472 DOI: 10.1186/s13068-023-02289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/25/2023] [Indexed: 03/30/2023]
Abstract
Abstract
Background
In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).
Results
The results indicated that, at 60 rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible (aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180 rpm, at 60 rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180 rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) β-xylosidase/β-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60 rpm.
Conclusions
We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.
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12
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Marine Fungi Select and Transport Aerobic and Anaerobic Bacterial Populations from Polycyclic Aromatic Hydrocarbon-Contaminated Sediments. mBio 2023; 14:e0276122. [PMID: 36786561 PMCID: PMC10127579 DOI: 10.1128/mbio.02761-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The organization of microbial communities in marine sediment relies on complex biotic and abiotic interactions. Among them, the interaction between fungi and bacteria plays a crucial role building specific microbial assemblages, resulting in metabolic networks adapted to environmental conditions. The fungal-bacterial interaction (FBI) includes bacterial translocation via fungal mycelia, allowing bacterial dispersion, and ecological niche colonization. In order to demonstrate that the translocation of bacteria through fungal mycelia involves bacterial selection, the mycelia of two fungi isolated from marine coastal sediment, Alternaria destruens F10.81 and Fusarium pseudonygamai F5.76, showing different strategies for uptake of polycyclic aromatic hydrocarbon (PAH), homogenous internalization and vacuole forming respectively, were used to translocate bacteria through hydrophobic hydrocarbon contaminated sediments. A. destruens F10.81 selected four specific bacteria, while bacterial selection by F. pseudonygamai F5.76 was not evident. Among the bacteria selected by A. destruens F10.81, Spirochaeta litoralis, known as strictly anaerobic bacterium, was identified, indicating that A. destruens F10.81 selects and transports both aerobic and anaerobic bacteria. Such a result is consistent with the observed formation of anoxic micro-niches in areas surrounding and affected by fungal hyphae. Our findings provide new insights on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. IMPORTANCE The study provides advances for understanding fungal-bacterial relationships, particularly on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. The transportation of bacteria via fungal hyphae (fungal highway) results in bacterial selection; in particular, fungal hyphae offer adequate conditions for the transport of both aerobic and anaerobic bacteria through hydrophobic patches for the colonization of novel niches.
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13
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Kennedy PG, Maillard F. Knowns and unknowns of the soil fungal necrobiome. Trends Microbiol 2023; 31:173-180. [PMID: 36100506 DOI: 10.1016/j.tim.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/27/2023]
Abstract
Dead microbial cells, commonly referred to as necromass, are increasingly recognized as an important source of both persistent carbon as well as nutrient availability in soils. Studies of the microbial communities associated with decomposing fungal necromass have accumulated rapidly in recent years across a range of different terrestrial ecosystems. Here we identify the primary ecological patterns regarding the structure and dynamics of the fungal necrobiome as well as highlight new research frontiers that will likely be key to gaining a full understanding of fungal necrobiome composition and its associated role in soil biogeochemical cycling. Because many members of the fungal necrobiome are culturable, combining laboratory functional assays with field-based surveys and experiments will allow ongoing studies of the fungal necrobiome to move from largely descriptive to increasingly predictive.
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Affiliation(s)
- Peter G Kennedy
- Department of Plant & Microbiology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - François Maillard
- Department of Plant & Microbiology, University of Minnesota, Saint Paul, MN 55108, USA
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14
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Omoni VT, Bankole PO, Nwosu TFX, Tennison-Omovoh CA, Ojo AS, Semple KT. Impact of different nitrogen amendments on the biodegradation of 14C-phenanthrene by endophytic fungal strains in liquid culture. Microbiol Res 2023; 266:127223. [DOI: 10.1016/j.micres.2022.127223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/23/2022] [Accepted: 10/05/2022] [Indexed: 11/27/2022]
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15
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Verma S, Azevedo LCB, Pandey J, Khusharia S, Kumari M, Kumar D, Kaushalendra, Bhardwaj N, Teotia P, Kumar A. Microbial Intervention: An Approach to Combat the Postharvest Pathogens of Fruits. PLANTS (BASEL, SWITZERLAND) 2022; 11:3452. [PMID: 36559563 PMCID: PMC9787458 DOI: 10.3390/plants11243452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 09/29/2023]
Abstract
Plants host diverse microbial communities, which undergo a complex interaction with each other. Plant-associated microbial communities provide various benefits to the host directly or indirectly, viz. nutrient acquisition, protection from pathogen invaders, mitigation from different biotic and abiotic stress. Presently, plant-associated microbial strains are frequently utilized as biofertilizers, biostimulants and biocontrol agents in greenhouse and field conditions and have shown satisfactory results. Nowadays, the plant/fruit microbiome has been employed to control postharvest pathogens and postharvest decay, and to maintain the quality or shelf life of fruits. In this context, the intervention of the natural fruit microbiome or the creation of synthetic microbial communities to modulate the functional attributes of the natural microbiome is an emerging aspect. In this regard, we discuss the community behavior of microbes in natural conditions and how the microbiome intervention plays a crucial role in the postharvest management of fruits.
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Affiliation(s)
- Sargam Verma
- Department of Biotechnology, Noida International University, Noida 203201, India
| | - Lucas Carvalho Basilio Azevedo
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Campus Glória—Bloco CCG, Santa Mônica 38408-100, Brazil
| | - Jyoti Pandey
- Department of Biochemistry, Singhania University, Jhunjhunu 333515, India
| | - Saksham Khusharia
- Kuwar SatyaVira College of Engineering and Management, Bijnor 246701, India
| | | | - Dharmendra Kumar
- Department of Zoology, C.M.B.College, Deorh, Ghoghardiha 847402, India
| | - Kaushalendra
- Department of Zoology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Nikunj Bhardwaj
- Department of Zoology, Maharaj Singh College, Maa Shakumbhari University, Saharanpur 247001, India
| | - Pratibha Teotia
- Department of Biotechnology, Noida International University, Noida 203201, India
| | - Ajay Kumar
- Department of Postharvest Science, Agricultural Research Organization (ARO)—Volcani Center, Rishon Lezion 7505101, Israel
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16
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Álvarez-Barragán J, Cravo-Laureau C, Duran R. Fungal-bacterial network in PAH-contaminated coastal marine sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:72718-72728. [PMID: 35614354 DOI: 10.1007/s11356-022-21012-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Fungal microbiome interacts with the other biotic components in coastal sediment playing a key role in the overall coordination of the whole microbial community. These interactions are affected by human activities, such as the constant affluence of polycyclic aromatic hydrocarbons (PAHs). Although fungi and bacteria interactions have been found to play a key role in PAH bioremediation in soil, the effect of PAHs on fungal diversity and their specific interactions with bacteria in coastal sediments are yet to be investigated. The understanding of fungal bacterial interactions under PAH contamination is critical for further bioremediation regarding the important fungal diversity observed in coastal sediment. Here, we investigated the fungal bacterial co-occurrence in PAH-contaminated sediments. The co-occurrence network, constructed with sequencing data (bacterial 16S and fungal 18S rRNA genes barcoding) from 51 PAH-contaminated samples, revealed modules dominated by either fungi or bacteria, reflecting probably the different types of interaction possible between fungi and bacteria. Then, a network constructed from non-contaminated sample data was compared with a network built from the corresponding PAH-contaminated samples issued from a mesocosm experiment. The comparison revealed the effect of PAHs in fungi and bacteria interactions, characterized by a PAH-contaminated network exhibiting less abundant and diverse fungal and bacterial ASVs than the non-contaminated network. However, the links between the remaining ASVs in the PAH-contaminated network showed stronger correlations. Noteworthy, an ASV affiliated to Chrytridiomycota phylum was identified as a keystone fungal ASV forming a module in association with facultative anaerobic and anaerobic bacteria affiliated to the families Prolixibacteraceae, Fusobacteriaceae, and Desulfobulbaceae. These results suggest that fungi promote bacterial anaerobic metabolisms, which are important to cope with the presence of PAHs in sediments. Our study reveals the importance of fungal bacterial interactions in coastal sediments paving the way for future studies to fully understand fungal role in coastal sediment.
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Affiliation(s)
- Joyce Álvarez-Barragán
- Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
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17
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The Wheat Head Blight Pathogen Fusarium graminearum Can Recruit Collaborating Bacteria from Soil. Cells 2022; 11:cells11193004. [PMID: 36230966 PMCID: PMC9563980 DOI: 10.3390/cells11193004] [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: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
In nature, fungal endophytes often have facultative endohyphal bacteria (FEB). Can a model plant pathogenic fungus have them, and does it affect their phenotype? We constructed a growth system/microcosm to allow an F. graminearum isolate to grow through natural soil and then re-isolated it on a gentamicin-containing medium, allowing endohyphal growth of bacteria while killing other bacteria. F. graminearum PH-1 labelled with a His1mCherry gene staining the fungal nuclei fluorescent red was used to confirm the re-isolation of the fungus. Most new re-isolates contained about 10 16SrRNA genes per fungal mCherry gene determined by qPCR. The F. graminearum + FEB holobiont isolates containing the bacteria were sub-cultured several times, and their bacterial contents were stable. Sequencing the bacterial 16SrRNA gene from several Fg-FEB holobiont isolates revealed endophytic bacteria known to be capable of nitrogen fixation. We tested the pathogenicity of one common Fg-FEB holobiont association, F. graminearum + Stenatrophomonas maltophilia, and found increased pathogenicity. The 16SrRNA gene load per fungal His1mCherry gene inside the wheat stayed the same as previously found in vitro. Finally, strong evidence was found for Fg-S. maltophilia symbiotic nitrogen fixation benefitting the fungus.
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18
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Kuhn T, Buffi M, Bindschedler S, Chain PS, Gonzalez D, Stanley CE, Wick LY, Junier P, Richter XYL. Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces. BMC Biol 2022; 20:203. [PMID: 36104696 PMCID: PMC9476585 DOI: 10.1186/s12915-022-01406-z] [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: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/12/2022] Open
Abstract
Background To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements. Results We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells. Conclusions The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01406-z.
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19
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Xiong BJ, Stanley CE, Dusny C, Schlosser D, Harms H, Wick LY. pH Distribution along Growing Fungal Hyphae at Microscale. J Fungi (Basel) 2022; 8:599. [PMID: 35736082 PMCID: PMC9224906 DOI: 10.3390/jof8060599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/06/2023] Open
Abstract
Creating unique microenvironments, hyphal surfaces and their surroundings allow for spatially distinct microbial interactions and functions at the microscale. Using a microfluidic system and pH-sensitive whole-cell bioreporters (Synechocystis sp. PCC6803) attached to hyphae, we spatially resolved the pH along surfaces of growing hyphae of the basidiomycete Coprinopsis cinerea. Time-lapse microscopy analysis of ratiometric fluorescence signals of >2400 individual bioreporters revealed an overall pH drop from 6.3 ± 0.4 (n = 2441) to 5.0 ± 0.3 (n = 2497) within 7 h after pH bioreporter loading to hyphal surfaces. The pH along hyphal surfaces varied significantly (p < 0.05), with pH at hyphal tips being on average ~0.8 pH units lower than at more mature hyphal parts near the entrance of the microfluidic observation chamber. Our data represent the first dynamic in vitro analysis of surface pH along growing hyphae at the micrometre scale. Such knowledge may improve our understanding of spatial, pH-dependent hyphal processes, such as the degradation of organic matter or mineral weathering.
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Affiliation(s)
- Bi-Jing Xiong
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Claire E. Stanley
- Department of Bioengineering, Imperial College of London, South Kensington Campus, London SW7 2AZ, UK;
| | - Christian Dusny
- Helmholtz Centre for Environmental Research-UFZ, Department of Solar Materials, Permoserstraβe 15, 04318 Leipzig, Germany;
| | - Dietmar Schlosser
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Hauke Harms
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Lukas Y. Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
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20
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Snelders NC, Rovenich H, Thomma BPHJ. Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev 2022; 46:6590816. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts, but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals, but beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, CologneGermany
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21
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You X, Kallies R, Kühn I, Schmidt M, Harms H, Chatzinotas A, Wick LY. Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system. THE ISME JOURNAL 2022; 16:1275-1283. [PMID: 34903848 PMCID: PMC9039081 DOI: 10.1038/s41396-021-01155-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022]
Abstract
Nonmotile microorganisms often enter new habitats by co-transport with motile microorganisms. Here, we report that also lytic phages can co-transport with hyphal-riding bacteria and facilitate bacterial colonization of a new habitat. This is comparable to the concept of biological invasions in macroecology. In analogy to invasion frameworks in plant and animal ecology, we tailored spatially organized, water-unsaturated model microcosms using hyphae of Pythium ultimum as invasion paths and flagellated soil-bacterium Pseudomonas putida KT2440 as carrier for co-transport of Escherichia virus T4. P. putida KT2440 efficiently dispersed along P. ultimum to new habitats and dispatched T4 phages across air gaps transporting ≈0.6 phages bacteria−1. No T4 displacement along hyphae was observed in the absence of carrier bacteria. If E. coli occupied the new habitat, T4 co-transport fueled the fitness of invading P. putida KT2440, while the absence of phage co-transport led to poor colonization followed by extinction. Our data emphasize the importance of hyphal transport of bacteria and associated phages in regulating fitness and composition of microbial populations in water-unsaturated systems. As such co-transport seems analogous to macroecological invasion processes, hyphosphere systems with motile bacteria and co-transported phages could be useful models for testing hypotheses in invasion ecology.
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Affiliation(s)
- Xin You
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstr. 15, 04318, Leipzig, Germany
| | - René Kallies
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstr. 15, 04318, Leipzig, Germany
| | - Ingolf Kühn
- Helmholtz Centre for Environmental Research - UFZ, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120, Halle, Germany.,Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Matthias Schmidt
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Permoserstr. 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstr. 15, 04318, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Antonis Chatzinotas
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstr. 15, 04318, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.,Institute of Biology, Leipzig University, Talstr. 33, Leipzig, 04103, Germany
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstr. 15, 04318, Leipzig, Germany.
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22
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See CR, Keller AB, Hobbie SE, Kennedy PG, Weber PK, Pett-Ridge J. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. GLOBAL CHANGE BIOLOGY 2022; 28:2527-2540. [PMID: 34989058 DOI: 10.1111/gcb.16073] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.
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Affiliation(s)
- Craig R See
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Adrienne B Keller
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter G Kennedy
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
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23
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Omoni VT, Ibeto CN, Lag-Brotons AJ, Bankole PO, Semple KT. Impact of lignocellulosic waste-immobilised white-rot fungi on enhancing the development of 14C-phenanthrene catabolism in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152243. [PMID: 34921880 DOI: 10.1016/j.scitotenv.2021.152243] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/30/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
In this study, an investigation was carried out to explore the the impact of white-rot fungi (WRF) on enhancing the development of phenanthrene catabolism in soil over time (1, 25, 50, 75 and 100 d). The WRF were immobilised on spent brewery grains (SBG) prior to inoculation to the soil. The results showed that SBG-immobilised WRF-amended soils reduced the lag phases and increased the extents of 14C-phenanthrene mineralisation. Greater reductions in the lag phases and increases in the rates of mineralisation were observed in immobilised Trametes versicolor-amended soil compared to the other WRF-amendments. However, the presence of Pleurotus ostreatus and Phanerochaete chrysosporium influenced biodegradation more strongly than the other fungal species. In addition, fungal enzyme activities increased in the amended soils and positively correlated with the extents of 14C-phenanthrene mineralisation in all soil amendments. Maximum ligninolytic enzyme activities were observed in P. ostreatus-amended soil. Microbial populations increased in all amended soils while PAH-degrading fungal numbers increased with increased soil-PAH contact time and strongly positively correlated with fastest rates of mineralisation. The findings presented in this study demonstrate that inoculating the soil with these immobilised WRFs generally enhanced the mineralisation of the 14C-phenanthrene in soil. This has the potential to be used to stimulate or enhance PAH catabolism in field-contaminated soils.
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Affiliation(s)
- Victor T Omoni
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; Department of Microbiology, Federal University of Agriculture, Makurdi P.M.B 2373, Nigeria
| | - Cynthia N Ibeto
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | | | - Paul O Bankole
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; Department of Pure and Applied Botany, Federal University of Agriculture, Abeokuta, Nigeria
| | - Kirk T Semple
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK.
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Mycelia-Assisted Isolation of Non-Host Bacteria Able to Co-Transport Phages. Viruses 2022; 14:v14020195. [PMID: 35215789 PMCID: PMC8877629 DOI: 10.3390/v14020195] [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: 12/08/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/27/2022] Open
Abstract
Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based on the capability of phage-carrying non-host bacteria to move along mycelia out of soil and form colonies in plaques of their co-transported phages. The approach was tested using two model phages of differing surface hydrophobicity, i.e., hydrophobic Escherichia virus T4 (T4) and hydrophilic Pseudoalteromonas phage HS2 (HS2). The phages were mixed into soil and allowed to be transported by soil bacteria along the mycelia of Pythium ultimum. Five phage-carrying bacterial species were isolated (Viridibacillus sp., Enterobacter sp., Serratia sp., Bacillus sp., Janthinobacterium sp.). These bacteria exhibited phage adsorption efficiencies of ≈90–95% for hydrophobic T4 and 30–95% for hydrophilic HS2. The phage adsorption efficiency of Viridibacillus sp. was ≈95% for both phages and twofold higher than T4-or HS2-adsorption to their respective hosts, qualifying Viridibacillus sp. as a potential super carrier for phages. Our approach offers an effective and target-specific way to identify and isolate phage-carrying bacteria in natural and man-made environments.
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Cai F, Zhao Z, Gao R, Chen P, Ding M, Jiang S, Fu Z, Xu P, Chenthamara K, Shen Q, Bayram Akcapinar G, Druzhinina IS. The pleiotropic functions of intracellular hydrophobins in aerial hyphae and fungal spores. PLoS Genet 2021; 17:e1009924. [PMID: 34788288 PMCID: PMC8635391 DOI: 10.1371/journal.pgen.1009924] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/01/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Higher fungi can rapidly produce large numbers of spores suitable for aerial dispersal. The efficiency of the dispersal and spore resilience to abiotic stresses correlate with their hydrophobicity provided by the unique amphiphilic and superior surface-active proteins-hydrophobins (HFBs)-that self-assemble at hydrophobic/hydrophilic interfaces and thus modulate surface properties. Using the HFB-enriched mold Trichoderma (Hypocreales, Ascomycota) and the HFB-free yeast Pichia pastoris (Saccharomycetales, Ascomycota), we revealed that the rapid release of HFBs by aerial hyphae shortly prior to conidiation is associated with their intracellular accumulation in vacuoles and/or lipid-enriched organelles. The occasional internalization of the latter organelles in vacuoles can provide the hydrophobic/hydrophilic interface for the assembly of HFB layers and thus result in the formation of HFB-enriched vesicles and vacuolar multicisternal structures (VMSs) putatively lined up by HFBs. These HFB-enriched vesicles and VMSs can become fused in large tonoplast-like organelles or move to the periplasm for secretion. The tonoplast-like structures can contribute to the maintenance of turgor pressure in aerial hyphae supporting the erection of sporogenic structures (e.g., conidiophores) and provide intracellular force to squeeze out HFB-enriched vesicles and VMSs from the periplasm through the cell wall. We also show that the secretion of HFBs occurs prior to the conidiation and reveal that the even spore coating of HFBs deposited in the extracellular matrix requires microscopic water droplets that can be either guttated by the hyphae or obtained from the environment. Furthermore, we demonstrate that at least one HFB, HFB4 in T. guizhouense, is produced and secreted by wetted spores. We show that this protein possibly controls spore dormancy and contributes to the water sensing mechanism required for the detection of germination conditions. Thus, intracellular HFBs have a range of pleiotropic functions in aerial hyphae and spores and are essential for fungal development and fitness.
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Affiliation(s)
- Feng Cai
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Zheng Zhao
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Renwei Gao
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Peijie Chen
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Mingyue Ding
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Siqi Jiang
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Zhifei Fu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Pingyong Xu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Komal Chenthamara
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Qirong Shen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- * E-mail: (QS); (ISD)
| | - Günseli Bayram Akcapinar
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irina S. Druzhinina
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- * E-mail: (QS); (ISD)
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Sharma S, Compant S, Franken P, Ruppel S, Ballhausen MB. It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator. Microorganisms 2021; 9:microorganisms9081566. [PMID: 34442645 PMCID: PMC8398733 DOI: 10.3390/microorganisms9081566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 11/23/2022] Open
Abstract
Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.
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Affiliation(s)
- Shubhangi Sharma
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
| | - Stéphane Compant
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria;
| | - Philipp Franken
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 24, 07743 Jena, Germany
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
| | - Max-Bernhard Ballhausen
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
- Correspondence:
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Telagathoti A, Probst M, Peintner U. Habitat, Snow-Cover and Soil pH, Affect the Distribution and Diversity of Mortierellaceae Species and Their Associations to Bacteria. Front Microbiol 2021; 12:669784. [PMID: 34276602 PMCID: PMC8283828 DOI: 10.3389/fmicb.2021.669784] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/10/2021] [Indexed: 12/21/2022] Open
Abstract
Mortierellaceae species are among the most frequent and globally distributed soil fungi. However, the factors shaping their diversity and distribution remain obscure. Several species have been reported to be associated to bacteria, but the kind and frequency of such associations were not addressed up to now. We hypothesized that such associations could be important for Mortierellaceae ecology. Therefore, our aim was to understand the driving factors responsible for the Mortierellaceae diversity, community composition and bacterial associations in alpine and subalpine habitats. For answering our question, we collected both snow-free and snow-covered soil at sampling sites from different habitats: bare alpine soil in a glacier forefield, alpine dwarf-willow habitats, and high-altitude Pinus cembra forests. The isolations were carried out by direct cultivation without any antibiotics to the isolation media. Altogether, we obtained 389 Mortierellaceae isolates representing 29 operational taxonomic units (OTUs). Many OTUs could be placed to the genera Mortierella sensu stricto, Dissophora, Entomortierella, Gamsiella, Linnemannia, and Podila, but others could not unambiguously be assigned to a genus. Our results demonstrate that both, the distribution as well as the diversity of the Mortierellaceae species, were significantly influenced by habitat, soil pH, and snow-cover. We noticed that >30% of our isolates were associated to a non-contaminant bacterium. The bacteria associated to our Mortierellaceae isolates belonged to seven different genera. Pseudomonas was the most frequently detected genus associated to the isolated Mortierellaceae species and it was found to be species-specific. Mortierellaceae-bacteria pairs, including those with Pseudomonas, were influenced by location, habitat, and snow-cover. The majority of the fungus-bacterium associations were potentially epihyphal, but we also detected potential endohyphal bacterial species belonging to Mycoavidus, Burkholderiaceae, and Paraburkholderia. Taken together, the non-random associations we detected suggest that fungus-bacterium associations are ecologically meaningful - an interesting path that needs to be investigated further.
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Affiliation(s)
| | | | - Ursula Peintner
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
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King WL, Bell TH. Can dispersal be leveraged to improve microbial inoculant success? Trends Biotechnol 2021; 40:12-21. [PMID: 33972105 DOI: 10.1016/j.tibtech.2021.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/24/2023]
Abstract
Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA; Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, USA.
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29
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Junier P, Cailleau G, Palmieri I, Vallotton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, House GL, Morales D, Gallegos-Graves LV, Dichosa AEK, Lupini S, Nguyen HN, Young JD, Rodrigues DF, Parra-Vasquez ANG, Bindschedler S, Chain PSG. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiol Ecol 2021; 97:6095729. [PMID: 33440006 PMCID: PMC7878174 DOI: 10.1093/femsec/fiab003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.
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Affiliation(s)
- Pilar Junier
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Ilona Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Celine Vallotton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Olivia C Trautschold
- Materials Science and Technology, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, CH, 1015, Lausanne, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Danae Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aaron Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Julia M Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Karen Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Demosthenes Morales
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | | | - Armand E K Dichosa
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Simone Lupini
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Hang N Nguyen
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Debora F Rodrigues
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | | | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
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30
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Yuan MM, Kakouridis A, Starr E, Nguyen N, Shi S, Pett-Ridge J, Nuccio E, Zhou J, Firestone M. Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches. mBio 2021; 12:e03509-20. [PMID: 33879589 PMCID: PMC8092305 DOI: 10.1128/mbio.03509-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.
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Affiliation(s)
- Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
| | - Anne Kakouridis
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
| | - Evan Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Nhu Nguyen
- Department of Tropical Plants and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Shengjing Shi
- AgResearch Ltd., Lincoln Science Centre, Christchurch, New Zealand
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Erin Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mary Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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31
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Jiang F, Zhang L, Zhou J, George TS, Feng G. Arbuscular mycorrhizal fungi enhance mineralisation of organic phosphorus by carrying bacteria along their extraradical hyphae. THE NEW PHYTOLOGIST 2021; 230:304-315. [PMID: 33205416 DOI: 10.1111/nph.17081] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 10/26/2020] [Indexed: 05/26/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi gain access to nutrient patches outside the rhizosphere by producing an extensive network of fine hyphae. Here, we focused on establishing the mechanism by which AM fungal hyphae reach discrete organic patches with a cohort of functional bacteria transported in a biofilm on their surface. We investigated the mechanisms and impact of the translocation of phosphate solubilising bacteria (PSB) along AM fungal hyphae in bespoke microcosms. An in vitro culture experiment was also conducted to determine the direct impact of hyphal exudates of AM fungi upon the growth of PSB. The extraradical hyphae of AM fungi can transport PSB to organic phosphorus (P) patches and enhance organic P mineralisation both under in vitro culture and soil conditions. Bacteria move in a thick water film formed around fungal hyphae. However, the bacteria cannot be transferred to the organic P patch without an energy source in the form of hyphal exudates. Our results could be harnessed to better manage plant-microbe interactions and improve the ability of biological inocula involving AM fungi and bacteria to enhance the sustainability of agricultural crops in P limited conditions.
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Affiliation(s)
- Feiyan Jiang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Lin Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Jiachao Zhou
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | | | - Gu Feng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
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Pozo MJ, Zabalgogeazcoa I, Vazquez de Aldana BR, Martinez-Medina A. Untapping the potential of plant mycobiomes for applications in agriculture. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:102034. [PMID: 33827007 DOI: 10.1016/j.pbi.2021.102034] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 05/20/2023]
Abstract
Plant-fungal interactions are widespread in nature, and their multiple benefits for plant growth and health have been amply demonstrated. Endophytic and epiphytic fungi can significantly increase plant resilience, improving plant nutrition, stress tolerance and defence. Although some of these interactions have been known for decades, the relevance of the plant mycobiome within the plant microbiome has been largely underestimated. Our limited knowledge of fungal biology and their interactions with plants in the broader phytobiome context has hampered the development of optimal biotechnological applications in agrosystems and natural ecosystems. Exciting recent technical and knowledge advances in the context of molecular and systems biology open a plethora of opportunities for developing this field of research.
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Affiliation(s)
- Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain.
| | - Iñigo Zabalgogeazcoa
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Beatriz R Vazquez de Aldana
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Ainhoa Martinez-Medina
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
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33
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Steffan BN, Venkatesh N, Keller NP. Let's Get Physical: Bacterial-Fungal Interactions and Their Consequences in Agriculture and Health. J Fungi (Basel) 2020; 6:E243. [PMID: 33114069 PMCID: PMC7712096 DOI: 10.3390/jof6040243] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/01/2023] Open
Abstract
Fungi serve as a biological scaffold for bacterial attachment. In some specialized interactions, the bacteria will invade the fungal host, which in turn provides protection and nutrients for the bacteria. Mechanisms of the physical interactions between fungi and bacteria have been studied in both clinical and agricultural settings, as discussed in this review. Fungi and bacteria that are a part of these dynamic interactions can have altered growth and development as well as changes in microbial fitness as it pertains to antibiotic resistance, nutrient acquisition, and microbial dispersal. Consequences of these interactions are not just limited to the respective microorganisms, but also have major impacts in the health of humans and plants alike. Examining the mechanisms behind the physical interactions of fungi and bacteria will provide us with an understanding of multi-kingdom community processes and allow for the development of therapeutic approaches for disease in both ecological settings.
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Affiliation(s)
- Breanne N. Steffan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; (B.N.S.); (N.V.)
| | - Nandhitha Venkatesh
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; (B.N.S.); (N.V.)
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; (B.N.S.); (N.V.)
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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de Novais CB, Sbrana C, da Conceição Jesus E, Rouws LFM, Giovannetti M, Avio L, Siqueira JO, Saggin Júnior OJ, da Silva EMR, de Faria SM. Mycorrhizal networks facilitate the colonization of legume roots by a symbiotic nitrogen-fixing bacterium. MYCORRHIZA 2020; 30:389-396. [PMID: 32215759 DOI: 10.1007/s00572-020-00948-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/16/2020] [Indexed: 05/22/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) absorb and translocate nutrients from soil to their host plants by means of a wide network of extraradical mycelium (ERM). Here, we assessed whether nitrogen-fixing rhizobia can be transferred to the host legume Glycine max by ERM produced by Glomus formosanum isolate CNPAB020 colonizing the grass Urochloa decumbens. An H-bridge experimental system was developed to evaluate the migration of ERM and of the GFP-tagged Bradyrhizobium diazoefficiens USDA 110 strain across an air gap compartment. Mycorrhizal colonization, nodule formation in legumes, and occurrence of the GFP-tagged strain in root nodules were assessed by optical and confocal laser scanning microscopy. In the presence of non-mycorrhizal U. decumbens, legume roots were neither AMF-colonized nor nodulated. In contrast, G. formosanum ERM crossing the discontinuous compartment connected mycorrhizal U. decumbens and G. max roots, which showed 30-42% mycorrhizal colonization and 7-11 nodules per plant. Fluorescent B. diazoefficiens cells were detected in 94% of G. max root nodules. Our findings reveal that, besides its main activity in nutrient transfer, ERM produced by AMF may facilitate bacterial translocation and the simultaneous associations of plants with beneficial fungi and bacteria, representing an important structure, functional to the establishment of symbiotic relationships.
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Affiliation(s)
- Candido Barreto de Novais
- Instituto de Floresta, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil
| | - Cristiana Sbrana
- CNR-Institute of Agricultural Biology and Biotechnology UOS Pisa, Pisa, Italy.
| | | | | | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Luciano Avio
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - José Oswaldo Siqueira
- DCS-Laboratório de Microbiologia do Solo, Universidade Federal de Lavras, Caixa Postal 3037, Lavras, MG, 37200-000, Brazil
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Suarez C, Ratering S, Weigel V, Sacharow J, Bienhaus J, Ebert J, Hirz A, Rühl M, Schnell S. Isolation of bacteria at different points of Pleurotus ostreatus cultivation and their influence in mycelial growth. Microbiol Res 2019; 234:126393. [PMID: 32036274 DOI: 10.1016/j.micres.2019.126393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/01/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022]
Abstract
Pleurotus ostreatus is one of the most cultivated edible mushrooms worldwide and few approaches have been done to analyze bacterial influence during its cultivation. Therefore, bacteria from commercial spawn, mycelial-colonized straw and fruiting bodies from healthy productive samples were counted, isolated and tested for their mycelial growth promoting ability. Bacterial cell numbers at different steps of the process showed low bacterial cell numbers in spawn and in fruiting bodies inner tissue compared to the high concentration in mycelial-colonized straw. The majority of the 38 isolates belonged to phyla Firmicutes and Actinobacteria were identified as Bacillus, Paenibacillus and Micromonospora species. Similarly, 16S rRNA gene bacterial clones obtained from mycelial biomass DNA samples showed bacterial presence of various genera including Bacillus and Paenibacillus. In the mycelial growth promoting ability tests, 30 isolates negatively affected mycelial growth, two isolates showed no effect on mycelial growth, and six isolates promoted mycelial growth. Moreover, mycelial thickness was influenced in different ways by the bacterial growth. In general, nearly all isolates growth-preventing were isolated from healthy spawn and mycelial-colonized straw, whereas fruiting bodies were the best source for isolation of mycelial growth-promoting bacteria. Characterization of bacterial isolates revealed that growth-preventing isolates exhibited various enzymatic activities in comparison with positive influencing bacteria that exhibited none or weak enzymatic activities. In addition, the influence of volatile compounds being present in the headspace of bi-plate co-cultures on P. ostreatus mycelial growth was demonstrated. The effect of isolates, that promoted mycelial growth in co-cultivation, to reduce P. ostreatus spawn running time, was evaluated on sterilized rye seeds. Results showed that not all mycelial promoted isolates were able to significantly promote P. ostreatus colonization. However, isolate M46F identified as Micromonospora lupini significantly reduce spawn running time. This is one of few studies to estimate cultivable bacteria from healthy samples of P. ostreatus cultivation, to evaluate a bacterial effect on mycelial growth, to show that fruiting bodies are a good source for mycelia growth-promoting isolates, and the first to report a shorter P. ostreatus spawn running time due to bacterial inoculation.
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Victoria Weigel
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Julia Sacharow
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Jackeline Bienhaus
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Janine Ebert
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Anika Hirz
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392, Giessen, Germany
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Bielčik M, Aguilar-Trigueros CA, Lakovic M, Jeltsch F, Rillig MC. The role of active movement in fungal ecology and community assembly. MOVEMENT ECOLOGY 2019; 7:36. [PMID: 31832199 PMCID: PMC6864958 DOI: 10.1186/s40462-019-0180-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/15/2019] [Indexed: 05/16/2023]
Abstract
Movement ecology aims to provide common terminology and an integrative framework of movement research across all groups of organisms. Yet such work has focused on unitary organisms so far, and thus the important group of filamentous fungi has not been considered in this context. With the exception of spore dispersal, movement in filamentous fungi has not been integrated into the movement ecology field. At the same time, the field of fungal ecology has been advancing research on topics like informed growth, mycelial translocations, or fungal highways using its own terminology and frameworks, overlooking the theoretical developments within movement ecology. We provide a conceptual and terminological framework for interdisciplinary collaboration between these two disciplines, and show how both can benefit from closer links: We show how placing the knowledge from fungal biology and ecology into the framework of movement ecology can inspire both theoretical and empirical developments, eventually leading towards a better understanding of fungal ecology and community assembly. Conversely, by a greater focus on movement specificities of filamentous fungi, movement ecology stands to benefit from the challenge to evolve its concepts and terminology towards even greater universality. We show how our concept can be applied for other modular organisms (such as clonal plants and slime molds), and how this can lead towards comparative studies with the relationship between organismal movement and ecosystems in the focus.
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Affiliation(s)
- Miloš Bielčik
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Carlos A. Aguilar-Trigueros
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Milica Lakovic
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Florian Jeltsch
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
- Department of Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476 Potsdam-Golm, Germany
| | - Matthias C. Rillig
- Institut für Biologie, Plant Ecology, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
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Lohberger A, Spangenberg JE, Ventura Y, Bindschedler S, Verrecchia EP, Bshary R, Junier P. Effect of Organic Carbon and Nitrogen on the Interactions of Morchella spp. and Bacteria Dispersing on Their Mycelium. Front Microbiol 2019; 10:124. [PMID: 30881350 PMCID: PMC6405442 DOI: 10.3389/fmicb.2019.00124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 01/21/2019] [Indexed: 01/14/2023] Open
Abstract
In this study we investigated how the source of organic carbon (Corg) and nitrogen (Norg) affects the interactions between fungi of the genus Morchella and bacteria dispersing along their hyphae (fungal highways; FH). We demonstrated that bacteria using FH increase the hydrolysis of an organic nitrogen source that only the fungus can degrade. Using purified fungal exudates, we found that this increased hydrolysis was due to bacteria enhancing the activity of proteolytic enzymes produced by the fungus. The same effect was shown for various fungal and bacterial strains. The effect of this enhanced proteolytic activity on bacterial and fungal biomass production varied accordingly to the source of Corg and Norg provided. An increase in biomass for both partners 5 days post-inoculation was only attained with a Norg source that the bacterium could not degrade and when additional Corg was present in the medium. In contrast, all other combinations yielded a decrease on biomass production in the co-cultures compared to individual growth. The coupled cycling of Corg and Norg is rarely considered when investigating the role of microbial activity on soil functioning. Our results show that cycling of these two elements can be related through cross-chemical reactions in independent, albeit interacting microbes. In this way, the composition of organic material could greatly alter nutrient turnover due to its effect on the outcome of interactions between fungi and bacteria that disperse on their mycelia.
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Affiliation(s)
- Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Jorge E. Spangenberg
- Stable Isotope and Organic Geochemistry Laboratories, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Yolanda Ventura
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eric P. Verrecchia
- Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Redouan Bshary
- Laboratory of Eco-ethology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Worrich A, Wick LY, Banitz T. Ecology of Contaminant Biotransformation in the Mycosphere: Role of Transport Processes. ADVANCES IN APPLIED MICROBIOLOGY 2018; 104:93-133. [PMID: 30143253 DOI: 10.1016/bs.aambs.2018.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fungi and bacteria often share common microhabitats. Their co-occurrence and coevolution give rise to manifold ecological interactions in the mycosphere, here defined as the microhabitats surrounding and affected by hyphae and mycelia. The extensive structure of mycelia provides ideal "logistic networks" for transport of bacteria and matter in structurally and chemically heterogeneous soil ecosystems. We describe the characteristics of the mycosphere as a unique and highly dynamic bacterial habitat and a hot spot for contaminant biotransformation. In particular, we emphasize the role of the mycosphere for (i) bacterial dispersal and colonization of subsurface interfaces and new habitats, (ii) matter transport processes and contaminant bioaccessibility, and (iii) the functional stability of microbial ecosystems when exposed to environmental fluctuations such as stress or disturbances. Adopting concepts from ecological theory, the chapter disentangles bacterial-fungal impacts on contaminant biotransformation in a systemic approach that interlinks empirical data from microbial ecosystems with simulation data from computational models. This approach provides generic information on key factors, processes, and ecological principles that drive microbial contaminant biotransformation in soil. We highlight that the transport processes create favorable habitat conditions for efficient bacterial contaminant degradation in the mycosphere. In-depth observation, understanding, and prediction of the role of mycosphere transport processes will support the use of bacterial-fungal interactions in nature-based solutions for contaminant biotransformation in natural and man-made ecosystems, respectively.
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Affiliation(s)
- Anja Worrich
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany.
| | - Thomas Banitz
- Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
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39
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Zhang L, Shi N, Fan J, Wang F, George TS, Feng G. Arbuscular mycorrhizal fungi stimulate organic phosphate mobilization associated with changing bacterial community structure under field conditions. Environ Microbiol 2018; 20:2639-2651. [DOI: 10.1111/1462-2920.14289] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/17/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Lin Zhang
- College of Resources and Environmental SciencesChina Agricultural University Beijing 100193 China
| | - Ning Shi
- College of Resources and Environmental SciencesChina Agricultural University Beijing 100193 China
- Institute of Agricultural Resources and EnvironmentShandong Academy of Agricultural Sciences Jinan 250100 China
| | - Jiequn Fan
- Shanghai Academy of Agricultural Sciences Shanghai 201106 People's Republic of China
| | - Fei Wang
- College of Resources and Environmental SciencesChina Agricultural University Beijing 100193 China
| | | | - Gu Feng
- College of Resources and Environmental SciencesChina Agricultural University Beijing 100193 China
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40
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König S, Worrich A, Banitz T, Harms H, Kästner M, Miltner A, Wick LY, Frank K, Thullner M, Centler F. Functional Resistance to Recurrent Spatially Heterogeneous Disturbances Is Facilitated by Increased Activity of Surviving Bacteria in a Virtual Ecosystem. Front Microbiol 2018; 9:734. [PMID: 29696013 PMCID: PMC5904252 DOI: 10.3389/fmicb.2018.00734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial degradation of organic compounds is an important ecosystem function with relevance to, e.g., the cycling of elements or the degradation of organic contaminants. It remains an open question, however, to which extent ecosystems are able to maintain such biodegradation function under recurrent disturbances (functional resistance) and how this is related to the bacterial biomass abundance. In this paper, we use a numerical simulation approach to systematically analyze the dynamic response of a microbial population to recurrent disturbances of different spatial distribution. The spatially explicit model considers microbial degradation, growth, dispersal, and spatial networks that facilitate bacterial dispersal mimicking effects of mycelial networks in nature. We find: (i) There is a certain capacity for high resistance of biodegradation performance to recurrent disturbances. (ii) If this resistance capacity is exceeded, spatial zones of different biodegradation performance develop, ranging from no or reduced to even increased performance. (iii) Bacterial biomass and biodegradation dynamics respond inversely to the spatial fragmentation of disturbances: overall biodegradation performance improves with increasing fragmentation, but bacterial biomass declines. (iv) Bacterial dispersal networks can enhance functional resistance against recurrent disturbances, mainly by reactivating zones in the core of disturbed areas, even though this leads to an overall reduction of bacterial biomass.
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Affiliation(s)
- Sara König
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Environmental Systems Research, University of Osnabrück, Osnabrück, Germany
| | - Anja Worrich
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Thomas Banitz
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Anja Miltner
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Lukas Y. Wick
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Karin Frank
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Environmental Systems Research, University of Osnabrück, Osnabrück, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Martin Thullner
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 505] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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Ghodsalavi B, Svenningsen NB, Hao X, Olsson S, Nicolaisen MH, Al-Soud WA, Sørensen SJ, Nybroe O. A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil. PLoS One 2017; 12:e0187116. [PMID: 29077733 PMCID: PMC5659649 DOI: 10.1371/journal.pone.0187116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/13/2017] [Indexed: 11/18/2022] Open
Abstract
It is important to identify and recover bacteria associating with fungi under natural soil conditions to enable eco-physiological studies, and to facilitate the use of bacterial-fungal consortia in environmental biotechnology. We have developed a novel type of baiting microcosm, where fungal hyphae interact with bacteria under close-to-natural soil conditions; an advantage compared to model systems that determine fungal influences on bacterial communities in laboratory media. In the current approach, the hyphae are placed on a solid support, which enables the recovery of hyphae with associated bacteria in contrast to model systems that compare bulk soil and mycosphere soil. We used the baiting microcosm approach to determine, for the first time, the composition of the bacterial community associating in the soil with hyphae of the phosphate-solubilizer, Penicillium bilaii. By applying a cultivation-independent 16S rRNA gene-targeted amplicon sequencing approach, we found a hypha-associated bacterial community with low diversity compared to the bulk soil community and exhibiting massive dominance of Burkholderia OTUs. Burkholderia is known be abundant in soil environments affected by fungi, but the discovery of this massive dominance among bacteria firmly associating with hyphae in soil is novel and made possible by the current bait approach.
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Affiliation(s)
- Behnoushsadat Ghodsalavi
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Nanna Bygvraa Svenningsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Xiuli Hao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Stefan Olsson
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
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Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
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Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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Bárta J, Tahovská K, Šantrůčková H, Oulehle F. Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching. Sci Rep 2017; 7:9738. [PMID: 28851897 PMCID: PMC5575336 DOI: 10.1038/s41598-017-08554-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/14/2017] [Indexed: 02/06/2023] Open
Abstract
Nitrogen leaching owing to elevated acid deposition remains the main ecosystem threat worldwide. We aimed to contribute to the understanding of the highly variable nitrate losses observed in Europe after acid deposition retreat. Our study proceeded in adjacent beech and spruce forests undergoing acidification recovery and differing in nitrate leaching. We reconstructed soil microbial functional characteristics connected with nitrogen and carbon cycling based on community composition. Our results showed that in the more acidic spruce soil with high carbon content, where Acidobacteria and Actinobacteria were abundant (Proteo:Acido = 1.3), the potential for nitrate reduction and loss via denitrification was high (denitrification: dissimilative nitrogen reduction to ammonium (DNRA) = 3). In the less acidic beech stand with low carbon content, but high nitrogen availability, Proteobacteria were more abundant (Proteo:Acido = 1.6). Proportionally less nitrate could be denitrified there (denitrification:DNRA = 1), possibly increasing its availability. Among 10 potential keystone species, microbes capable of DNRA were identified in the beech soil while instead denitrifiers dominated in the spruce soil. In spite of the former acid deposition impact, distinct microbial functional guilds developed under different vegetational dominance, resulting in different N immobilization potentials, possibly influencing the ecosystem's nitrogen retention ability.
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Affiliation(s)
- Jiří Bárta
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Karolina Tahovská
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Hana Šantrůčková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Filip Oulehle
- Czech Geological Survey, Department of Environmental Geochemistry and Biogeochemistry, Prague, 118 21, Czech Republic
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45
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Yang P, Zhang M, van Elsas JD. Role of flagella and type four pili in the co-migration of Burkholderia terrae BS001 with fungal hyphae through soil. Sci Rep 2017; 7:2997. [PMID: 28592860 PMCID: PMC5462819 DOI: 10.1038/s41598-017-02959-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/21/2017] [Indexed: 12/25/2022] Open
Abstract
Burkholderia terrae BS001 has previously been found to be able to disperse along with growing fungal hyphae in soil, with the type-3 secretion system having a supportive role in this movement. In this study, we focus on the role of two motility- and adherence-associated appendages, i.e. type-4 pili (T4P) and flagella. Electron microcopy and motility testing revealed that strain BS001 produces polar flagella and can swim on semi-solid R2A agar. Flagellum- and T4P-negative mutants were then constructed to examine the ecological roles of the respective systems. Both in liquid media and on swimming agar, the mutant strains showed similar fitness to the wild-type strain in mixed culture. The flagellar mutant had completely lost its flagella, as well as its swimming capacity. It also lost its co-migration ability with two soil-exploring fungi, Lyophyllum sp. strain Karsten and Trichoderma asperellum 302, in soil microcosms. In contrast, the T4P mutant showed reduced surface twitching motility, whereas its co-migration ability in competition with the wild-type strain was slightly reduced. We conclude that the co-migration of strain BS001 with fungal hyphae through soil is dependent on the presence of functional flagella conferring swimming motility, with the T4P system having a minor effect.
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Affiliation(s)
- Pu Yang
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Miaozhi Zhang
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Kooliyottil R, Dandurand LM, Knudsen GR. Prospecting fungal parasites of the potato cyst nematode Globodera pallida using a rapid screening technique. J Basic Microbiol 2017; 57:386-392. [PMID: 28375550 DOI: 10.1002/jobm.201600683] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/12/2017] [Indexed: 11/09/2022]
Abstract
Seven filamentous fungal species were isolated from individual eggs of Globodera pallida cysts collected from infested fields in Shelley Idaho, USA and identified as Chaetomium globosum, Fusarium oxysporum, Fusarium solani, Fusarium tricinctum, Microdochium bolleyi, Purpureocillium lilacinum, and Plectosphaerella cucumerina. Their ability to reduce infection by G. pallida in planta were assessed in simple, reproducible micro-rhizosphere chambers (micro-ROCs). All fungi reduced G. pallida infection in potato, but greatest reduction was observed with C. globosum at an average reduction of 76%. Further non-destructive methods were developed to rapidly assess biological control potential of putative fungal strains by staining the infectious second stage juveniles of G. pallida with the live fluorescent stain PKH26. In comparisons between the standard, invasive acid fuchsin method and use of the live stain PKH26, no significant difference in infection level of G. pallida was observed whether roots were stained with PKH26 or acid fuchsin. For both methods, a similar reduction (77% for acid fuchsin, and 78% for PKH26 stain) in invasion of infectious stage of G. pallida was observed when potato plants were inoculated with C. globosum compared to non-inoculated potato.
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Affiliation(s)
- Rinu Kooliyottil
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho
| | - Louise-Marie Dandurand
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho
| | - Guy R Knudsen
- Soil and Land Resources Division, University of Idaho, Moscow, Idaho
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Oh SY, Fong JJ, Park MS, Lim YW. Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil. PLoS One 2016; 11:e0168573. [PMID: 27977803 PMCID: PMC5158061 DOI: 10.1371/journal.pone.0168573] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/03/2016] [Indexed: 02/01/2023] Open
Abstract
Tricholoma matsutake, the pine mushroom, is a valuable forest product with high economic value in Asia, and plays an important ecological role as an ectomycorrhizal fungus. Around the host tree, T. matsutake hyphae generate a distinctive soil aggregating environment called a fairy ring, where fruiting bodies form. Because T. matsutake hyphae dominate the soil near the fairy ring, this species has the potential to influence the microbial community. To explore the influence of T. matsutake on the microbial communities, we compared the microbial community and predicted bacterial function between two different soil types-T. matsutake dominant and T. matsutake minor. DNA sequence analyses showed that fungal and bacterial diversity were lower in the T. matsutake dominant soil compared to T. matsutake minor soil. Some microbial taxa were significantly more common in the T. matsutake dominant soil across geographic locations, many of which were previously identified as mycophillic or mycorrhiza helper bacteria. Between the two soil types, the predicted bacterial functional profiles (using PICRUSt) had significantly distinct KEGG modules. Modules for amino acid uptake, carbohydrate metabolism, and the type III secretion system were higher in the T. matsutake dominant soil than in the T. matsutake minor soil. Overall, similar microbial diversity, community structure, and bacterial functional profiles of the T. matsutake dominant soil across geographic locations suggest that T. matsutake may generate a dominance effect.
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Affiliation(s)
- Seung-Yoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jonathan J. Fong
- Science Unit, Lingnan University, Tuen Mun, New Territories, Hong Kong
| | - Myung Soo Park
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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Simon A, Hervé V, Al-Dourobi A, Verrecchia E, Junier P. An in situ inventory of fungi and their associated migrating bacteria in forest soils using fungal highway columns. FEMS Microbiol Ecol 2016; 93:fiw217. [PMID: 27797964 DOI: 10.1093/femsec/fiw217] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/04/2016] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
Soils are complex ecosystems in which fungi and bacteria co-exist and interact. Fungal highways are a kind of interaction by which bacteria use fungal hyphae to disperse in soils. Despite the fact that fungal highways have been studied in laboratory models, the diversity of fungi and bacteria interacting in this way in soils is still unknown. Fungal highway columns containing two different culture media were used as a selective method to study the identity of fungi and bacteria able to migrate along the hyphae in three forest soils. Regardless of the soil type, fungi of the genus Mortierella (phylum Zygomycota) were selected inside the columns. In contrast, a diverse community of bacteria dominated by Firmicutes and Proteobacteria was observed. The results confirm the importance of bacteria affiliated to Burkholderia as potentially associated migrating bacteria in soils and indicate that other groups such as Bacillus and Clostridium are also highly enriched in the co-colonization of a new habitat (columns) associated to Mortierella. The diversity of potentially associated migrating bacteria brings a novel perspective on the indirect metabolic capabilities that could be favored by r-strategist fungi and supports the fact that these fungi should be considered as crucial actors in soil functioning.
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Affiliation(s)
- Anaele Simon
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,Biogeosciences laboratory, Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Andrej Al-Dourobi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eric Verrecchia
- Biogeosciences laboratory, Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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