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Yue Y, Hao H, Wang Q, Xiao T, Zhang Y, Chen Q, Chen H, Zhang J. Dynamics of the soil microbial community associated with Morchella cultivation: diversity, assembly mechanism and yield prediction. Front Microbiol 2024; 15:1345231. [PMID: 38426066 PMCID: PMC10903539 DOI: 10.3389/fmicb.2024.1345231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction The artificial cultivation of morels has been a global research focus owing to production variability. Understanding the microbial ecology in cultivated soil is essential to increase morel yield and alleviate pathogen harm. Methods A total of nine Morchella cultivation experiments in four soil field types, forest, paddy, greenhouse, and orchard in Shanghai city were performed to determine the potential ecological relationship between Morchella growth and soil microbial ecology. Results Generally, significant variation was observed in the soil microbial diversity and composition between the different experimental field types. The niche width analysis indicated that the bacterial habitat niche breadth was significantly greater than the fungal community width, which was further confirmed by a null model that revealed that homogeneous selection could explain 46.26 and 53.64% of the variance in the bacterial and fungal assemblies, respectively. Moreover, the neutral community model revealed that stochastic processes dominate the bacterial community in forests and paddies and both the bacterial and fungal communities in orchard crops, whereas deterministic processes mostly govern the fungal community in forests and paddies and both the bacterial and the fungal communities in greenhouses. Furthermore, co-occurrence patterns were constructed, and the results demonstrated that the dynamics of the soil microbial community are related to fluctuations in soil physicochemical characteristics, especially soil potassium. Importantly, structural equation modeling further demonstrated that the experimental soil type significantly affects the potassium content of the soil, which can directly or indirectly promote Morchella yield by inhibiting soil fungal richness. Discussion This was the first study to predict morel yield through soil potassium fertilizer and soil fungal community richness, which provides new insights into deciphering the importance of microbial ecology in morel agroecosystems.
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Affiliation(s)
- Yihong Yue
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Haibo Hao
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qian Wang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Tingting Xiao
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yuchen Zhang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qun Chen
- School of Biology Food and Environment, Hefei University, Hefei, China
| | - Hui Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinjing Zhang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Cailleau G, Hanson BT, Cravero M, Zhioua S, Hilpish P, Ruiz C, Robinson AJ, Kelliher JM, Morales D, Gallegos-Graves LV, Bonito G, Chain PS, Bindschedler S, Junier P. Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1285531. [PMID: 38155707 PMCID: PMC10753826 DOI: 10.3389/ffunb.2023.1285531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/08/2023] [Indexed: 12/30/2023]
Abstract
Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained from Morchella isolates grown in vitro. These investigations included diverse representatives from both Elata and Esculenta Morchella clades. Unique bacterial community compositions were observed across the various structures examined, both within and across individual Morchella isolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genus Pseudomonas and Ralstonia constituted the core bacterial associates of Morchella mycelia and sclerotia, while other genera (e.g., Pedobacter spp., Deviosa spp., and Bradyrhizobium spp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance of Pseudomonas as a key member of the bacteriome was supported by the isolation of several Pseudomonas strains from mycelia during in vitro cultivation. Four of the six mycelial-derived Pseudomonas isolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and various Morchella isolates. Genome sequences obtained from these Pseudomonas isolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence that Pseudomonas spp. are frequently associated with Morchella and these associations may greatly impact fungal physiology.
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Affiliation(s)
- Guillaume Cailleau
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Buck T. Hanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Melissa Cravero
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sami Zhioua
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick Hilpish
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Celia Ruiz
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Aaron J. Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Julia M. Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Demosthenes Morales
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Patrick S.G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
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Buffi M, Cailleau G, Kuhn T, Li Richter XY, Stanley CE, Wick LY, Chain PS, Bindschedler S, Junier P. Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth. MICROLIFE 2023; 4:uqad042. [PMID: 37965130 PMCID: PMC10642649 DOI: 10.1093/femsml/uqad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The 'fungal drops' method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µl drops on a hydrophobic surface at a fixed distance. This system is akin to a two-dimensional (2D) soil-like structure in which aqueous-pockets are intermixed with air-filled pores. The fungus (spores or mycelia) is inoculated into one of the drops, from which hyphal growth and exploration take place. Hyphal structures are assessed at different scales using stereoscopic and microscopic imaging. The former allows to evaluate the local response of regions within the colony (modular behaviour), while the latter can be used for fractal dimension analyses to describe the hyphal network architecture. The method was tested with several species to underpin the transferability to multiple species. In addition, two sets of experiments were carried out to demonstrate its use in fungal biology. First, mycelial reorganization of Fusarium oxysporum was assessed as a response to patches containing different nutrient concentrations. Second, the effect of interactions with the soil bacterium Pseudomonas putida on habitat colonization by the same fungus was assessed. This method appeared as fast and accessible, allowed for a high level of replication, and complements more complex experimental platforms. Coupled with image analysis, the fungal drops method provides new insights into the study of fungal modularity both macroscopically and at a single-hypha level.
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Affiliation(s)
- Matteo Buffi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Thierry Kuhn
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, B304, Bessemer Building, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Patrick S Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, P.O. Box 1663, NM 87545, United States
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Clark KB. Ownership psychology as a "cognitive cell" adaptation: A minimalist model of microbial goods theory. Behav Brain Sci 2023; 46:e330. [PMID: 37813404 DOI: 10.1017/s0140525x23001498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Microbes perfect social interactions with intuitive logics and goal-directed reciprocity. These multilevel, cognition-resembling adaptations in Dictyostelid cellular molds enable individual-to-group viability through public/private bacterial farming and dynamic marketspaces. Like humans and animals, Dictyostelid livestock-ownership depends on environmental sensing, cooperation, and competition. Moreover, social-norm policing of cosmopolitan colonies coordinates farmer decisions, phenotypes, and ownership identities with bacteria herding, privatization, and consumption.
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Affiliation(s)
- Kevin B Clark
- Cures Within Reach, Chicago, IL, USA ; www.linkedin.com/pub/kevin-clark/58/67/19a; https://access-ci.org
- Felidae Conservation Fund, Mill Valley, CA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, USA
- Network for Life Detection (NfoLD), NASA Astrobiology Program, NASA Ames Research Center, Mountain View, CA, USA
- Multi-Omics and Systems Biology & Artificial Intelligence and Machine Learning Analysis Working Groups, NASA GeneLab, NASA Ames Research Center, Mountain View, CA, USA
- Frontier Development Lab, NASA Ames Research Center, Mountain View, CA, USA
- SETI Institute, Mountain View, CA, USA
- Peace Innovation Institute, Netherlands & Stanford University, Palo Alto, CA, USA
- Shared Interest Group for Natural and Artificial Intelligence (sigNAI), Max Planck Alumni Association, Berlin, Germany
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, USA
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Zhang Y, Zhao Q, Uroz S, Gao T, Li J, He F, Rosazlina R, Martin F, Xu L. The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria. Front Microbiol 2023; 14:1257905. [PMID: 37808313 PMCID: PMC10552182 DOI: 10.3389/fmicb.2023.1257905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.
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Affiliation(s)
- Yan Zhang
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
| | - Tianpeng Gao
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
- The Engineering Research Center of Mining Pollution Treatment and Ecological Restoration of Gansu Province, Lanzhou City University, Lanzhou, China
| | - Jing Li
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Fengqin He
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
| | - Rusly Rosazlina
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
| | - Lingling Xu
- Xi'an Key Laboratory of Plant Stress Physiology and Ecological Restoration Technology, Key Laboratory of Natural Product Development and Anticancer Innovative Drug Research in Qinling, School of Biological and Environmental Engineering, Xi'an University, Xi'an, Shaanxi, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, France
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Chen B, Shao G, Zhou T, Fan Q, Yang N, Cui M, Zhang J, Wu X, Zhang B, Zhang R. Dazomet changes microbial communities and improves morel mushroom yield under continuous cropping. Front Microbiol 2023; 14:1200226. [PMID: 37614603 PMCID: PMC10442562 DOI: 10.3389/fmicb.2023.1200226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023] Open
Abstract
Morels (Morchella spp.) are highly prized and popular edible mushrooms. The outdoor cultivation of morels in China first developed at the beginning of the 21st century. Several species, such as Morchella sextelata, M. eximia, and M. importuna, have been commercially cultivated in greenhouses. However, the detriments and obstacles associated with continuous cropping have become increasingly serious, reducing yields and even leading to a complete lack of fructification. It has been reported that the obstacles encountered with continuous morel cropping may be related to changes in the soil microbial community. To study the effect of dazomet treatment on the cultivation of morel under continuous cropping, soil was fumigated with dazomet before morel sowing. Alpha diversity and beta diversity analysis results showed that dazomet treatment altered the microbial communities in continuous cropping soil, which decreased the relative abundance of soil-borne fungal pathogens, including Paecilomyces, Trichoderma, Fusarium, Penicillium, and Acremonium, increased the relative abundance of beneficial soil bacteria, including Bacillius and Pseudomonas. In addition, the dazomet treatment significantly increased the relative abundance of morel mycelia in the soil and significantly improved morel yield under continuous cropping. These results verified the relationship between the obstacles associated with continuous cropping in morels and the soil microbial community and elucidated the mechanism by which the obstacle is alleviated when using dazomet treatment.
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Affiliation(s)
- Bo Chen
- Institute of Soil and Fertilizer of Guizhou Province, Guiyang, China
| | - Gaige Shao
- Xi'an Agricultural Technology Extension Center, Xi'an, China
| | - Tao Zhou
- Fruit and Vegetable Workstation of Guizhou Province, Guiyang, China
| | - Qinghao Fan
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nuolin Yang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Man Cui
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinwei Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangli Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bangxi Zhang
- Institute of Soil and Fertilizer of Guizhou Province, Guiyang, China
| | - Ruiying Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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Li X, Fu T, Li H, Zhang B, Li W, Zhang B, Wang X, Wang J, Chen Q, He X, Chen H, Zhang Q, Zhang Y, Yang R, Peng Y. Safe Production Strategies for Soil-Covered Cultivation of Morel in Heavy Metal-Contaminated Soils. J Fungi (Basel) 2023; 9:765. [PMID: 37504753 PMCID: PMC10381497 DOI: 10.3390/jof9070765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Morel is a popular edible mushroom with considerable medicinal and economic value which has garnered global popularity. However, the increasing heavy metal (HM) pollution in the soil presents a significant challenge to morels cultivation. Given the susceptibility of morels to HM accumulation, the quality and output of morels are at risk, posing a serious food safety concern that hinders the development of the morel industry. Nonetheless, research on the mechanism of HM enrichment and mitigation strategies in morel remains scarce. The morel, being cultivated in soil, shows a positive correlation between HM content in its fruiting body and the HM content in the soil. Therefore, soil remediation emerges as the most practical and effective approach to tackle HM pollution. Compared to physical and chemical remediation, bioremediation is a low-cost and eco-friendly approach that poses minimal threats to soil composition and structure. HMs easily enriched during morels cultivation were examined, including Cd, Cu, Hg, and Pb, and we assessed soil passivation technology, microbial remediation, strain screening and cultivation, and agronomic measures as potential approaches for HM pollution prevention. The current review underscores the importance of establishing a comprehensive system for preventing HM pollution in morels.
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Affiliation(s)
- Xue Li
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Tianhong Fu
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Hongzhao Li
- Faculty of Food Science and Engineering, Foshan University, Foshan 258000, China
- Key Laboratory for New Technology Research of Vegetable, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Bangxi Zhang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Wendi Li
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
| | - Baige Zhang
- Key Laboratory for New Technology Research of Vegetable, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaomin Wang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Jie Wang
- Qiandongnan Academy of Agricultural Sciences, Kaili 556000, China
| | - Qing Chen
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xuehan He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Chen
- School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China
| | - Qinyu Zhang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yujin Zhang
- School of Pharmacy, Zunyi Medical University, Zunyi 563006, China
| | - Rende Yang
- Soil and Fertilizer Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yutao Peng
- School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China
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Campbell LCE, Kiers ET, Chomicki G. The evolution of plant cultivation by ants. TRENDS IN PLANT SCIENCE 2023; 28:271-282. [PMID: 36372647 DOI: 10.1016/j.tplants.2022.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/11/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Outside humans, true agriculture was previously thought to be restricted to social insects farming fungus. However, obligate farming of plants by ants was recently discovered in Fiji, prompting a re-examination of plant cultivation by ants. Here, we generate a database of plant cultivation by ants, identify three main types, and show that these interactions evolved primarily for shelter rather than food. We find that plant cultivation evolved at least 65 times independently for crops (~200 plant species), and 15 times in farmer lineages (~37 ant taxa) in the Neotropics and Asia/Australasia. Because of their high evolutionary replication, and variation in partner dependence, these systems are powerful models to unveil the steps in the evolution and ecology of insect agriculture.
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Affiliation(s)
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Guillaume Chomicki
- Ecology and Evolutionary Biology, School of Biosciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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Kuhn T, Mamin M, Bindschedler S, Bshary R, Estoppey A, Gonzalez D, Palmieri F, Junier P, Richter XYL. Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211592. [PMID: 36483758 PMCID: PMC9727664 DOI: 10.1098/rsos.211592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.
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Affiliation(s)
- Thierry Kuhn
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Marine Mamin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Redouan Bshary
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
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10
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Lee KK, Kim H, Lee YH. Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations. Front Microbiol 2022; 13:953300. [PMID: 35958158 PMCID: PMC9358436 DOI: 10.3389/fmicb.2022.953300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022] Open
Abstract
Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network's representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.
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Affiliation(s)
- Kiseok Keith Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
- Center for Plant Microbiome Research, Seoul National University, Seoul, South Korea
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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11
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Yu Y, Liu T, Liu L, Chen Y, Tang J, Peng W, Tan H. Application of the mushroom volatile 1-octen-3-ol to suppress a morel disease caused by Paecilomyces penicillatus. Appl Microbiol Biotechnol 2022; 106:4787-4799. [PMID: 35759038 DOI: 10.1007/s00253-022-12038-2] [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: 02/22/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
Abstract
Morels (Morchella spp.) are of great economic and scientific value. Paecilomyces penicillatus can cause white mold disease (WMD) widely emerging on morel ascocarps and is also a potential factor causing morel fructification failure. 1-octen-3-ol is a mushroom volatile compound with broad-spectrum antimicrobial activities. This study aimed to control the morel disease caused by P. penicillatus through suppressing P. penicillatus in the soil cultivated with Morchella sextelata using 1-octen-3-ol. Safe concentration of 1-octen-3-ol was estimated by comparing its inhibitory effect against P. penicillatus and M. sextelata, respectively, with mycelium-growth experiments on agar plates. The results showed that M. sextelata possesses a higher tolerance to 1-octen-3-ol than P. penicillatus with a 1-octen-3-ol concentration between 0 and 200 µL/L. Based on that, a sandy soil was supplemented with low (50 µL/L) or high concentration (200 µL/L) of 1-octen-3-ol. The effects of 1-octen-3-ol on soil microbial communities, WMD incidence, and morel yield were investigated. Compared to the non-supplemented control group, the incidence of WMD and the proportion of Paecilomyces in the soils of low- and high-concentration treatment groups were significantly decreased, corresponding to a significant increase in morel ascocarp yield. It suggests that 1-octen-3-ol effectively suppressed P. penicillatus in the soil, thereby reducing the severity of WMD and improving the morel yield. The diversity of soil bacterial communities was also altered by 1-octen-3-ol supplement. The proportion of Rhodococcus spp. in the soil was positively correlated with the 1-octen-3-ol concentration and ascocarp yield, suggesting its potential role in improving morel yield. KEY POINTS: • A novel method for morel disease suppression was proposed. • Paecilomyces in soil affects white mold disease and fructification yield of morel. • 1-Octen-3-ol suppresses Paecilomyces and alters bacterial community in soil.
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Affiliation(s)
- Yang Yu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Tianhai Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Lixu Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Ying Chen
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Jie Tang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Weihong Peng
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Hao Tan
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China. .,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China. .,Drylands Salinization Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.
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12
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Large-scale commercial cultivation of morels: current state and perspectives. Appl Microbiol Biotechnol 2022; 106:4401-4412. [PMID: 35731306 DOI: 10.1007/s00253-022-12012-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
Abstract
Since morels were first successfully cultivated commercially in Sichuan in 2012, morel cultivation has expanded to more than 20 provinces in China. The highest yield currently reaches 15,000 kg/ha. Morel cultivation is characterized by its environmental friendliness, short cycle length, and high profit. However, the yield obtained is unstable which makes morel cultivation a high-risk industry. Although 10 production cycles have passed, there is still a gap between morel cultivation practice and our basic knowledge of morel biology. This mini-review concentrates on the development needs of morel cultivation. We illustrate the key techniques used in the large-scale commercial cultivation of morels and their relevant studies, including nutritional requirements, mechanisms of nutrient bag, soil type, vegetative and reproductive growth conditions, and disease control. This review will be a useful practical reference for the commercial artificial cultivation of morels and promoting the vital technologies required. KEY POINTS: •Unstable yield still exists after commercial cultivation of morels realized. •There is a gap between cultivation practice and our knowledge of morel biology. •Key techniques are illustrated for morel cultivation practice.
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13
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Yu FM, Jayawardena RS, Thongklang N, Lv ML, Zhu XT, Zhao Q. Morel Production Associated with Soil Nitrogen-Fixing and Nitrifying Microorganisms. J Fungi (Basel) 2022; 8:jof8030299. [PMID: 35330300 PMCID: PMC8950353 DOI: 10.3390/jof8030299] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 02/02/2023] Open
Abstract
True morels (Morchella, Pezizales) cultivated in soil are subject to complex influences from soil microbial communities. To explore the characteristics of soil microbial communities on morel cultivation, and evaluate whether these microbes are related to morel production, we collected 23 soil samples from four counties in Sichuan and Yunnan Provinces, China. Based on ITS and 16S rDNA amplicon sequencing, the alpha diversity analysis indicated that the biodiversity of morel cultivation soil showed a downward trend compared with the bare soil. The results also showed that there were no significant differences in soil microbial communities between OC (bare soil) and OO (after one-year suspension of sowing). This means that, after about one year of stopping sowing, the component and structure of soil that once cultivated morel would be restored. In co-occurrence networks, some noteworthy bacterial microbes involved in nitrogen fixation and nitrification have been identified in soils with high morel yields, such as Arthrobacter, Bradyhizobium, Devosia, Pseudarthrobacter, Pseudolabrys, and Nitrospira. In contrast, in soils with low or no morel yield, some pathogenic fungi accounted for a high proportion, including Gibberella, Microidium, Penicillium, Sarocladium, Streptomyces, and Trichoderma. This study provided valuable information for the isolation and culturing of some beneficial microbes for morel cultivation in further study and, potentially, to harness the power of the microbiome to improve morel production and health.
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Affiliation(s)
- Feng-Ming Yu
- Key Laboratory for Plant Diversity and Biotechnology of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (R.S.J.); (N.T.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Ruvishika Shehali Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (R.S.J.); (N.T.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Naritsada Thongklang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (R.S.J.); (N.T.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Meng-Lan Lv
- School of Chemical Engineering, Guizhou Institute of Technology, Guiyang 550003, China;
| | - Xue-Tai Zhu
- College of Life Science, Northwest Normal University, Lanzhou 730070, China;
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biotechnology of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- School of Chemical Engineering, Guizhou Institute of Technology, Guiyang 550003, China;
- Correspondence:
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14
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Xu F, Liao H, Zhang Y, Yao M, Liu J, Sun L, Zhang X, Yang J, Wang K, Wang X, Ding Y, Liu C, Rensing C, Zhang J, Yeh K, Xu W. Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying. THE ISME JOURNAL 2022; 16:801-811. [PMID: 34621017 PMCID: PMC8857228 DOI: 10.1038/s41396-021-01133-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/10/2022]
Abstract
Moderate soil drying (MSD) is a promising agricultural technique that can reduce water consumption and enhance rhizosheath formation promoting drought resistance in plants. The endophytic fungus Piriformospora indica (P. indica) with high auxin production may be beneficial for rhizosheath formation. However, the integrated role of P. indica with native soil microbiome in rhizosheath formation is unclear. Here, we investigated the roles of P. indica and native bacteria on rice rhizosheath formation under MSD using high-throughput sequencing and rice mutants. Under MSD, rice rhizosheath formation was significantly increased by around 30% with P. indica inoculation. Auxins in rice roots and P. indica were responsible for the rhizosheath formation under MSD. Next, the abundance of the genus Bacillus, known as plant growth-promoting rhizobacteria, was enriched in the rice rhizosheath and root endosphere with P. indica inoculation under MSD. Moreover, the abundance of Bacillus cereus (B. cereus) with high auxin production was further increased by P. indica inoculation. After inoculation with both P. indica and B. cereus, rhizosheath formation in wild-type or auxin efflux carrier OsPIN2 complemented line rice was higher than that of the ospin2 mutant. Together, our results suggest that the interaction of the endophytic fungus P. indica with the native soil bacterium B. cereus favors rice rhizosheath formation by auxins modulation in rice and microbes under MSD. This finding reveals a cooperative contribution of P. indica and native microbiota in rice rhizosheath formation under moderate soil drying, which is important for improving water use in agriculture.
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Affiliation(s)
- Feiyun Xu
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hanpeng Liao
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yingjiao Zhang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Minjie Yao
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianping Liu
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Leyun Sun
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xue Zhang
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jinyong Yang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ke Wang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoyun Wang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yexin Ding
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chen Liu
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Christopher Rensing
- grid.256111.00000 0004 1760 2876Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianhua Zhang
- grid.221309.b0000 0004 1764 5980Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Kaiwun Yeh
- grid.19188.390000 0004 0546 0241Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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15
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Van Wylick A, Monclaro AV, Elsacker E, Vandelook S, Rahier H, De Laet L, Cannella D, Peeters E. A review on the potential of filamentous fungi for microbial self-healing of concrete. Fungal Biol Biotechnol 2021; 8:16. [PMID: 34794517 PMCID: PMC8600713 DOI: 10.1186/s40694-021-00122-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Concrete is the most used construction material worldwide due to its abundant availability and inherent ease of manufacturing and application. However, the material bears several drawbacks such as the high susceptibility for crack formation, leading to reinforcement corrosion and structural degradation. Extensive research has therefore been performed on the use of microorganisms for biologically mediated self-healing of concrete by means of CaCO3 precipitation. Recently, filamentous fungi have been recognized as high-potential microorganisms for this application as their hyphae grow in an interwoven three-dimensional network which serves as nucleation site for CaCO3 precipitation to heal the crack. This potential is corroborated by the current state of the art on fungi-mediated self-healing concrete, which is not yet extensive but valuable to direct further research. In this review, we aim to broaden the perspectives on the use of fungi for concrete self-healing applications by first summarizing the major progress made in the field of microbial self-healing of concrete and then discussing pioneering work that has been done with fungi. Starting from insights and hypotheses on the types and principles of biomineralization that occur during microbial self-healing, novel potentially promising candidate species are proposed based on their abilities to promote CaCO3 formation or to survive in extreme conditions that are relevant for concrete. Additionally, an overview will be provided on the challenges, knowledge gaps and future perspectives in the field of fungi-mediated self-healing concrete.
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Affiliation(s)
- Aurélie Van Wylick
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Antonielle Vieira Monclaro
- PhotoBioCatalysis Unit-BTL-Ecole interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium.,Center for Microbial Ecology and Technology (CMET), Department of Biotechnology Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.,Center for Advanced Process Technology and Urban Resource Efficiency (CAPTURE), Frieda Saeysstraat, B-9052, Ghent, Belgium
| | - Elise Elsacker
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.,Newcastle University, Hub for Biotechnology in the Built Environment, Devonshire Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Simon Vandelook
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Hubert Rahier
- Research Group of Physical Chemistry and Polymer Science, Department of Materials and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Lars De Laet
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - David Cannella
- PhotoBioCatalysis Unit-BTL-Ecole interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
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16
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Pu Y, Naikatini A, Pérez‐Escobar OA, Silber M, Renner SS, Chomicki G. Genome-wide transcriptome signatures of ant-farmed Squamellaria epiphytes reveal key functions in a unique symbiosis. Ecol Evol 2021; 11:15882-15895. [PMID: 34824797 PMCID: PMC8601933 DOI: 10.1002/ece3.8258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Farming of fungi by ants, termites, or beetles has led to ecologically successful societies fueled by industrial-scale food production. Another type of obligate insect agriculture in Fiji involves the symbiosis between the ant Philidris nagasau and epiphytes in the genus Squamellaria (Rubiaceae) that the ants fertilize, defend, harvest, and depend on for nesting. All farmed Squamellaria form tubers (domatia) with preformed entrance holes and complex cavity networks occupied by P. nagasau. The inner surface of the domatia consists of smooth-surfaced walls where the ants nest and rear their brood, and warty-surfaced walls where they fertilize their crop by defecation. Here, we use RNA sequencing to identify gene expression patterns associated with the smooth versus warty wall types. Since wall differentiation occurred in the most recent common ancestor of all farmed species of Squamellaria, our study also identifies genetic pathways co-opted following the emergence of agriculture. Warty-surfaced walls show many upregulated genes linked to auxin transport, root development, and nitrogen transport consistent with their root-like function; their defense-related genes are also upregulated, probably to protect these permeable areas from pathogen entry. In smooth-surfaced walls, genes functioning in suberin and wax biosynthesis are upregulated, contributing to the formation of an impermeable ant-nesting area in the domatium. This study throws light on a number of functional characteristics of plant farming by ants and illustrates the power of genomic studies of symbiosis.
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Affiliation(s)
- Yuanshu Pu
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Alivereti Naikatini
- South Pacific Regional HerbariumInstitute of Applied SciencesThe University of the South PacificSuvaFiji
| | | | - Martina Silber
- Systematic Botany and MycologyDepartment of BiologyUniversity of Munich (LMU)MunichGermany
| | | | - Guillaume Chomicki
- Ecology and Evolutionary BiologySchool of BiosciencesUniversity of SheffieldSheffieldUK
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17
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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18
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Orlofsky E, Zabari L, Bonito G, Masaphy S. Changes in soil bacteria functional ecology associated with Morchella rufobrunnea fruiting in a natural habitat. Environ Microbiol 2021; 23:6651-6662. [PMID: 34327796 DOI: 10.1111/1462-2920.15692] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/04/2023]
Abstract
Morchella rufobrunnea is a saprobic edible mushroom, found in a range of ecological niches, indicating nutritional adjustment to different habitats and possible interaction with soil prokaryotic microbiome (SPM). Using the 16S rRNA gene, we examined the SPM of M. rufobrunnea that appeared in a natural habitat in Northern Israel. Three sample types were included: bare soil without mushroom, soil beneath young mushroom initials and soil beneath the mature fruiting body. Morchella rufobrunnea developmental stage was significantly associated with changes in bacterial populations (PERMANOVA, p < 0.0005). Indicator analysis with point-biserial correlation coefficient found 180 operational taxonomic units (OTU) uniquely associated with distinct stages of development. The Functional Annotation of Prokaryotic Taxonomy (FAPROTAX) database helped to infer ecological roles for indicator OTU. The functional ecological progression begins with establishment of a photoautotrophic N-fixing bacterial mat on bare soil. Pioneer heterotrophs including oligotrophs, acidifying nutrient mobilizers and nitrifiers are congruent with appearance of young M. rufobrunnea initials. Under the mature fruiting body, the population changed to saprobes, organic-N degraders, denitrifiers, insect endosymbionts and fungal antagonists. Based on this work, M. rufobrunnea may be able to influence SPM and change the soil nutritional profile.
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Affiliation(s)
- Ezra Orlofsky
- Applied Mycology and Microbiology, Migal, Kiryat Shemona, 11016, Israel
| | - Limor Zabari
- Applied Mycology and Microbiology, Migal, Kiryat Shemona, 11016, Israel
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Segula Masaphy
- Applied Mycology and Microbiology, Migal, Kiryat Shemona, 11016, Israel.,Tel Hai Academic College, Kiryat Shemona, 12210, Israel
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19
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Lü BB, Wu GG, Sun Y, Zhang LS, Wu X, Jiang W, Li P, Huang YN, Wang JB, Zhao YC, Liu H, Song LL, Mo Q, Pan AH, Yang Y, Long XQ, Cui WD, Zhang C, Wang X, Tang XM. Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH. Front Microbiol 2021; 12:682356. [PMID: 34354681 PMCID: PMC8329594 DOI: 10.3389/fmicb.2021.682356] [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: 03/18/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
The precious rare edible fungus Morchella conica is popular worldwide for its rich nutrition, savory flavor, and varieties of bioactive components. Due to its high commercial, nutritional, and medicinal value, it has always been a hot spot. However, the molecular mechanism and endophytic bacterial communities in M. conica were poorly understood. In this study, we sequenced, assembled, and analyzed the genome of M. conica SH. Transcriptome analysis reveals significant differences between the mycelia and fruiting body. As shown in this study, 1,329 and 2,796 genes were specifically expressed in the mycelia and fruiting body, respectively. The Gene Ontology (GO) enrichment showed that RNA polymerase II transcription activity-related genes were enriched in the mycelium-specific gene cluster, and nucleotide binding-related genes were enriched in the fruiting body-specific gene cluster. Further analysis of differentially expressed genes in different development stages resulted in finding two groups with distinct expression patterns. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment displays that glycan degradation and ABC transporters were enriched in the group 1 with low expressed level in the mycelia, while taurine and hypotaurine metabolismand tyrosine metabolism-related genes were significantly enriched in the group 2 with high expressed level in mycelia. Moreover, a dynamic shift of bacterial communities in the developing fruiting body was detected by 16S rRNA sequencing, and co-expression analysis suggested that bacterial communities might play an important role in regulating gene expression. Taken together, our study provided a better understanding of the molecular biology of M. conica SH and direction for future research on artificial cultivation.
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Affiliation(s)
- Bei B Lü
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guo G Wu
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yu Sun
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liang S Zhang
- Institute of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiao Wu
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wei Jiang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Peng Li
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan N Huang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jin B Wang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yong C Zhao
- Institute of Edible Fungi, Yunnan Academy of Agricultural Sciences, Yunnan, China
| | - Hua Liu
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li L Song
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qin Mo
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ai H Pan
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xuan Q Long
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Wei D Cui
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Ürümqi, China
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xu Wang
- Department of Pathobiology, Auburn University, Auburn, AL, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Xue M Tang
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
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20
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Shapiro T, Chekanov K, Alexandrova A, Dolnikova G, Ivanova E, Lobakova E. Revealing of Non-Cultivable Bacteria Associated with the Mycelium of Fungi in the Kerosene-Degrading Community Isolated from the Contaminated Jet Fuel. J Fungi (Basel) 2021; 7:jof7010043. [PMID: 33440907 PMCID: PMC7826599 DOI: 10.3390/jof7010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 11/25/2022] Open
Abstract
Fuel (especially kerosene) biodamage is a challenge for global industry. In aviation, where kerosene is a widely used type of fuel, its biodeterioration leads to significant damage. Six isolates of micromycetes from the TS-1 aviation kerosene samples were obtained. Their ability to grow on the fuel was studied, and the difference between biodegradation ability was shown. Micromycetes belonged to the Talaromyces, Penicillium, and Aspergillus genera. It was impossible to obtain bacterial isolates associated with their mycelium. However, 16S rRNA metabarcoding and microscopic observations revealed the presence of bacteria in the micromycete isolates. It seems to be that kerosene-degrading fungi were associated with uncultured bacteria. Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were abundant in the fungal cultures isolated from the TS-1 jet fuel samples. Most genera among these phyla are known as hydrocarbon degraders. Only bacteria-containing micromycete isolates were able to grow on the kerosene. Most likely, kerosene degradation mechanisms are based on synergism of bacteria and fungi.
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Affiliation(s)
- Tatiana Shapiro
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (T.S.); (A.A.); (G.D.); (E.L.)
| | - Konstantin Chekanov
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (T.S.); (A.A.); (G.D.); (E.L.)
- Centre for Humanities Research and Technology, National Research Nuclear University MEPhI, 31 Kashirskoye highway, 115522 Moscow, Russia
- Correspondence:
| | - Alina Alexandrova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (T.S.); (A.A.); (G.D.); (E.L.)
| | - Galina Dolnikova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (T.S.); (A.A.); (G.D.); (E.L.)
| | - Ekaterina Ivanova
- Department of General and Inorganic Chemistry, National University of Oil and Gas “Gubkin University”, 65 Leninsky Prospekt, 119991 Moscow, Russia;
| | - Elena Lobakova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119192 Moscow, Russia; (T.S.); (A.A.); (G.D.); (E.L.)
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21
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Krespach MKC, García-Altares M, Flak M, Hanno Schoeler, Scherlach K, Netzker T, Schmalzl A, Mattern DJ, Schroeckh V, Komor A, Mittag M, Hertweck C, Brakhage AA. Lichen-like association of Chlamydomonas reinhardtii and Aspergillus nidulans protects algal cells from bacteria. THE ISME JOURNAL 2020; 14:2794-2805. [PMID: 32753730 PMCID: PMC7784976 DOI: 10.1038/s41396-020-0731-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 11/09/2022]
Abstract
Organismal interactions within microbial consortia and their responses to harmful intruders remain largely understudied. An important step toward the goal of understanding functional ecological interactions and their evolutionary selection is the study of increasingly complex microbial interaction systems. Here, we discovered a tripartite biosystem consisting of the fungus Aspergillus nidulans, the unicellular green alga Chlamydomonas reinhardtii, and the algicidal bacterium Streptomyces iranensis. Genetic analyses and MALDI-IMS demonstrate that the bacterium secretes the algicidal compound azalomycin F upon contact with C. reinhardtii. In co-culture, A. nidulans attracts the motile alga C. reinhardtii, which becomes embedded and surrounded by fungal mycelium and is shielded from the algicide. The filamentous fungus Sordaria macrospora was susceptible to azalomycin F and failed to protect C. reinhardtii despite chemotactically attracting the alga. Because S. macrospora was susceptible to azalomycin F, this data imply that for protection the fungus needs to be resistant. Formation of the lichen-like association between C. reinhardtii and A. nidulans increased algal growth. The protection depends on the increased amounts of membrane lipids provided by resistant fungi, thereby generating a protective shelter against the bacterial toxin. Our findings reveal a strategy whereby algae survive lethal environmental algicides through cooperation with fungi.
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Affiliation(s)
- Mario K C Krespach
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - María García-Altares
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain
| | - Michal Flak
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hanno Schoeler
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Biologie des Bactéries Intracellulaires, Institut Pasteur, 28 rue du Dr. Roux, 75015, Paris, France
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Anica Schmalzl
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Anna Komor
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Christian Hertweck
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany.
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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22
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Longley R, Benucci GMN, Mills G, Bonito G. Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors. FEMS Microbiol Lett 2020; 366:5585883. [PMID: 31603508 DOI: 10.1093/femsle/fnz215] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Morel mushrooms (Morchella, Pezizales) are highly prized edible fungi. Approaches to cultivate morels indoors in pasteurized composted substrates have been successful for Morchella rufobrunnea. We used DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) ribosomal DNA and 16S rRNA gene to follow bacterial and fungal communities in substrates during indoor morel cultivation. Our goal was to determine changes in microbial communities at key stages of morel cultivation, which included primordia development, fundament initiation, differentiation and maturation. Additionally, we compared microbial communities between trays that successfully fruited to those that produced conidia and primordia but aborted before ascocarp formation (non-fruiting). The prokaryotic community was dominated by Firmicutes belonging to Bacillus and Paenibacillus with a lower abundance of Flavobacteria. At earlier stages, the fungal community was dominated by Pezizomycetes including Morchella and other species, whereas, later in the cropping cycle Sordariomycetes dominated. Additionally, differences were observed between trays with successful fruiting, which were dominated by Gilmaniella; compared to trays that did not fruit, which were dominated by Cephalotrichum. Our findings inform understanding of microbial community dynamics during morel cultivation, and show that fungal genera, such as Gilmaniella, and prokaryotic genera, such as Bacillus, are abundant in substrates that support M. rufobrunnea fruiting.
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Affiliation(s)
- Reid Longley
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd, East Lansing MI, 48823, USA
| | - Gian Maria Niccoló Benucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St, East Lansing MI, 48824, USA
| | - Gary Mills
- Gourmet Mushrooms Inc., 506 E State St, Scottville MI, 49454, USA
| | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd, East Lansing MI, 48823, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St, East Lansing MI, 48824, USA
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23
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Abstract
Diverse forms of cultivation have evolved across the tree of life. Efficient farming requires that the farmer deciphers and actively promotes conditions that increase crop yield. For plant cultivation, this can include evaluating tradeoffs among light, nutrients, and protection against herbivores. It is not understood if, or how, nonhuman farmers evaluate local conditions to increase payoffs. Here, we address this question using an obligate farming mutualism between the ant Philidris nagasau and epiphytic plants in the genus Squamellaria that are cultivated for their nesting sites and floral rewards. We focused on the ants' active fertilization of their crops and their protection against herbivory. We found that ants benefited from cultivating plants in full sun, receiving 7.5-fold more floral food rewards compared to shade-cultivated plants. The higher reward levels correlated with higher levels of crop protection provided by the ants. However, while high-light planting yielded the greatest immediate food rewards, sun-grown crops contained less nitrogen compared to shade-grown crops. This was due to lower nitrogen input from ants feeding on floral rewards instead of insect protein gained from predation. Despite this tradeoff, farming ants optimize crop yield by selectively planting their crops in full sun. Ancestral state reconstructions across this ant-plant clade show that a full-sun farming strategy has existed for millions of years, suggesting that nonhuman farmers have evolved the means to evaluate and balance conflicting crop needs to their own benefit.
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24
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Benucci GMN, Longley R, Zhang P, Zhao Q, Bonito G, Yu F. Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses. PeerJ 2019; 7:e7744. [PMID: 31579614 PMCID: PMC6766373 DOI: 10.7717/peerj.7744] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/25/2019] [Indexed: 12/28/2022] Open
Abstract
Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.
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Affiliation(s)
| | - Reid Longley
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Peng Zhang
- CAS Key Laboratory for East Asia Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Qi Zhao
- CAS Key Laboratory for East Asia Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Gregory Bonito
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.,Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Fuqiang Yu
- CAS Key Laboratory for East Asia Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
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25
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Carrasco J, Preston GM. Growing edible mushrooms: a conversation between bacteria and fungi. Environ Microbiol 2019; 22:858-872. [DOI: 10.1111/1462-2920.14765] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Jaime Carrasco
- Department of Plant SciencesUniversity of Oxford, S Parks Rd Oxford OX1 3RB UK
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH) Autol Spain
| | - Gail M. Preston
- Department of Plant SciencesUniversity of Oxford, S Parks Rd Oxford OX1 3RB UK
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26
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Tan H, Kohler A, Miao R, Liu T, Zhang Q, Zhang B, Jiang L, Wang Y, Xie L, Tang J, Li X, Liu L, Grigoriev IV, Daum C, LaButti K, Lipzen A, Kuo A, Morin E, Drula E, Henrissat B, Wang B, Huang Z, Gan B, Peng W, Martin FM. Multi-omic analyses of exogenous nutrient bag decomposition by the black morel Morchella importuna reveal sustained carbon acquisition and transferring. Environ Microbiol 2019; 21:3909-3926. [PMID: 31314937 DOI: 10.1111/1462-2920.14741] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 12/24/2022]
Abstract
The black morel (Morchella importuna Kuo, O'Donnell and Volk) was once an uncultivable wild mushroom, until the development of exogenous nutrient bag (ENB), making its agricultural production quite feasible and stable. To date, how the nutritional acquisition of the morel mycelium is fulfilled to trigger its fruiting remains unknown. To investigate the mechanisms involved in ENB decomposition, the genome of a cultivable morel strain (M. importuna SCYDJ1-A1) was sequenced and the genes coding for the decay apparatus were identified. Expression of the encoded carbohydrate-active enzymes (CAZymes) was then analyzed by metatranscriptomics and metaproteomics in combination with biochemical assays. The results show that a diverse set of hydrolytic and redox CAZymes secreted by the morel mycelium is the main force driving the substrate decomposition. Plant polysaccharides such as starch and cellulose present in ENB substrate (wheat grains plus rice husks) were rapidly degraded, whereas triglycerides were accumulated initially and consumed later. ENB decomposition led to a rapid increase in the organic carbon content in the surface soil of the mushroom bed, which was thereafter consumed during morel fruiting. In contrast to the high carbon consumption, no significant acquisition of nitrogen was observed. Our findings contribute to an increasingly detailed portrait of molecular features triggering morel fruiting.
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Affiliation(s)
- Hao Tan
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Annegret Kohler
- Université de Lorraine, Institut National de la Recherche Agronomique, UMR Interactions Arbres/Microorganismes, Centre INRA-GrandEst, Champenoux, 54280, France
| | - Renyun Miao
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Tianhai Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Qiang Zhang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Bo Zhang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Lin Jiang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Yong Wang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Liyuan Xie
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Jie Tang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Xiaolin Li
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Lixu Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Emmanuelle Morin
- Université de Lorraine, Institut National de la Recherche Agronomique, UMR Interactions Arbres/Microorganismes, Centre INRA-GrandEst, Champenoux, 54280, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, F-13288, France.,Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, F-13288, France.,Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Bo Wang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Zhongqian Huang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Bingcheng Gan
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Weihong Peng
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Scientific Observing and Experimental Station of Agro-Microbial Resource and Utilization in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Francis M Martin
- Université de Lorraine, Institut National de la Recherche Agronomique, UMR Interactions Arbres/Microorganismes, Centre INRA-GrandEst, Champenoux, 54280, France
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27
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Zhang F, Long L, Hu Z, Yu X, Liu Q, Bao J, Long Z. Analyses of artificial morel soil bacterial community structure and mineral element contents in ascocarp and the cultivated soil. Can J Microbiol 2019; 65:738-749. [PMID: 31206319 DOI: 10.1139/cjm-2018-0600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study explored the differences among various artificial morel cultivations as well as the factors that influence these differences, including soil bacterial community structure, yield, and mineral element contents of ascocarp and the cultivated soil. High-throughput sequencing results revealed that the dominant bacterial phyla in all the samples, including Proteobacteria, Acidobacteria, Chloroflexi, Bacteroides, and Gemmatimonadetes, were found not only in morel soils (experimental group) but also in wheat soil (control group); the highest richness and diversity in the soil bacteria were observed during the primordial differentiation stage. The M6 group exhibited the highest yield (271.8 g/m2) and had an unexpectedly high proportion of Pseudomonas (25.30%) during the primordial differentiation stage, which was 1.77∼194.62 times more than the proportion of Pseudomonas in other samples. Pseudomonas may influence the growth of morel. The mineral element contents of the different soil groups and the ascocarp were determined by electrothermal digestion and inductively coupled plasma mass spectrometry. The results revealed that morel had high enrichment effects on phosphorus (P, bioconcentration factor = 16.83), potassium (K, 2.18), boron (B, 1.47), zinc (Zn, 1.36), copper (Cu, 1.15), and selenium (Se, 2.27). P levels were the highest followed by Se and K, and the mineral element contents in ascocarp were positively correlated with the soil element contents.
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Affiliation(s)
- Fusheng Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Li Long
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Zongyue Hu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Xiaorui Yu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Qingya Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Jinku Bao
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
| | - Zhangfu Long
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China.,Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P.R. China
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28
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Miquel Guennoc C, Rose C, Labbé J, Deveau A. Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls? FEMS Microbiol Ecol 2019; 94:4998851. [PMID: 29788056 DOI: 10.1093/femsec/fiy093] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/16/2018] [Indexed: 12/22/2022] Open
Abstract
Ectomycorrhizal (ECM) fungi establish symbiosis with roots of most trees of boreal and temperate ecosystems and are major drivers of nutrient fluxes between trees and the soil. ECM fungi constantly interact with bacteria all along their life cycle and the extended networks of hyphae provide a habitat for complex bacterial communities. Despite the important effects these bacteria can have on the growth and activities of ECM fungi, little is known about the mechanisms by which these microorganisms interact. Here we investigated the ability of bacteria to form biofilm on the hyphae of the ECM fungus Laccaria bicolor. We showed that the ability to form biofilms on the hyphae of the ECM fungus is widely shared among soil bacteria. Conversely, some fungi, belonging to the Ascomycete class, did not allow for the formation of bacterial biofilms on their surfaces. The formation of biofilms was also modulated by the presence of tree roots and ectomycorrhizae, suggesting that biofilm formation does not occur randomly in soil but that it is regulated by several biotic factors. In addition, our study demonstrated that the formation of bacterial biofilm on fungal hyphae relies on the production of networks of filaments made of extracellular DNA.
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Affiliation(s)
- Cora Miquel Guennoc
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Christophe Rose
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, 54000 Nancy, France
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Aurélie Deveau
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
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29
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Liu W, Cai Y, He P, Chen L, Bian Y. Comparative transcriptomics reveals potential genes involved in the vegetative growth of Morchella importuna. 3 Biotech 2019; 9:81. [PMID: 30800592 PMCID: PMC6374242 DOI: 10.1007/s13205-019-1614-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/02/2019] [Indexed: 12/16/2022] Open
Abstract
True morels (Morchella spp.) are edible, medicinal mushrooms which have recently been artificially cultivated in China but stable production remains a problem. Here, we describe complete and comprehensive transcriptome of Morchella importuna at the stages of vegetative mycelium (VM), initial sclerotium (IS) and mature sclerotium (MS) by deep transcriptional sequencing and de novo assembly for the first time and which will potentially provide useful information for improving its cultivation. A total of 26,496 genes were identified with a contig N50 length of 1763 bp and an average length of over 1064 bp. Additionally, 11,957 open reading frames (ORFs) were predicted and 9676 of them (80.9%) were annotated. The 2605 differentially expressed genes (DEGs) identified by gene expression clustering were mainly involved with energy metabolism and could be divided into three broad clusters, of which genes in cluster_1 and cluster_2 were involved in the metabolic process of carbohydrate, polysaccharide, hydrolase, caprolactam, beta-galactosidase, and disaccharide, respectively. Genes in cluster_3 were the largest category, mainly identified with the catalytic activity and transporter activity. Overall, the enzymes involved in the carbohydrate metabolism were highly expressed, and the CAZyme (carbohydrate-active enzyme) genes were significantly expressed within cluster_3. For expression verification, 16 CAZYme genes were selected for qRT-PCR, and the results suggested that the catabolism of carbohydrates occurs mainly in the vegetative mycelium stage, and the anabolism of the energy-rich substances is the main event of mycelial growth and sclerotial morphogenesis of M. importuna.
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Affiliation(s)
- Wei Liu
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Wuhan, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, Hubei China
| | - Yingli Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, 430070 Wuhan, China
| | - Peixin He
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, 450001 Zhengzhou, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Wuhan, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, Hubei China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Wuhan, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, Hubei China
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30
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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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31
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Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev 2018; 42:335-352. [PMID: 29471481 DOI: 10.1093/femsre/fuy008] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 02/16/2018] [Indexed: 12/14/2022] Open
Abstract
Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.
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Affiliation(s)
- Aurélie Deveau
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27705, USA.,Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Mathieu Paoletti
- Institut de Biologie et Génétique Cellulaire, UMR 5095 CNRS et Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux cedex, France
| | - Matthias Becker
- IGZ, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland.,Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sophie Mieszkin
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Larry J Millet
- Joint Institute for Biological Science, University of Tennessee, and the Biosciences Division of Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Torino, 10125 Torino, Italy
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry, G. Mahlerlaan 3004, 1081 LA, Amsterdam, The Netherlands
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Jan Dirk van Elsas
- Microbial Ecology group, GELIFES, University of Groningen, 9747 Groningen, The Netherlands
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
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32
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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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33
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Haq IU, Zwahlen RD, Yang P, van Elsas JD. The Response of Paraburkholderia terrae Strains to Two Soil Fungi and the Potential Role of Oxalate. Front Microbiol 2018; 9:989. [PMID: 29896162 PMCID: PMC5986945 DOI: 10.3389/fmicb.2018.00989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/27/2018] [Indexed: 12/18/2022] Open
Abstract
Fungal-associated Paraburkholderia terrae strains in soil have been extensively studied, but their sensing strategies to locate fungi in soil have remained largely elusive. In this study, we investigated the behavior of five mycosphere-isolated P. terrae strains [including the type-3 secretion system negative mutant BS001-ΔsctD and the type strain DSM 17804T] with respect to their fungal-sensing strategies. The putative role of oxalic acid as a signaling molecule in the chemotaxis toward soil fungi, as well as a potential carbon source, was assessed. First, all P. terrae strains, including the type strain, were found to sense, and show a chemotactic response toward, the different levels of oxalic acid (0.1, 0.5, and 0.8%) applied at a distance. The chemotactic responses were faster and stronger at lower concentrations (0.1%) than at higher ones. We then tested the chemotactic responses of all strains toward exudates of the soil fungi Lyophyllum sp. strain Karsten and Trichoderma asperellum 302 used in different dilutions (undiluted, 1:10, 1:100 diluted) versus the control. All P. terrae strains showed significant directed chemotactic behavior toward the exudate source, with full-strength exudates inciting the strongest responses. In a separate experiment, strain BS001 was shown to be able to grow on oxalate-amended (0.1 and 0.5%) mineral medium M9. Chemical analyses of the fungal secretomes using proton nuclear magnetic resonance (1H NMR), next to high-performance liquid chromatography (HPLC), indeed revealed the presence of oxalic acid (next to glycerol, acetic acid, formic acid, and fumaric acid) in the supernatants of both fungi. In addition, citric acid was found in the Lyophyllum sp. strain Karsten exudates. Given the fact that, next to oxalic acid, the other compounds can also serve as C and energy sources for P. terrae, the two fungi clearly offer ecological benefits to this bacterium. The oxalic acid released by the two fungi may have primarily acted as a signaling molecule, and, as a "second option," a carbon source for P. terrae strains like BS001.
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Affiliation(s)
- Irshad Ul Haq
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands.,Department of Microbiology, University of Haripur, Haripur, Pakistan
| | - Reto Daniel Zwahlen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Pu Yang
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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34
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Chomicki G, Janda M, Renner SS. The assembly of ant-farmed gardens: mutualism specialization following host broadening. Proc Biol Sci 2018; 284:rspb.2016.1759. [PMID: 28298344 DOI: 10.1098/rspb.2016.1759] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Ant-gardens (AGs) are ant/plant mutualisms in which ants farm epiphytes in return for nest space and food rewards. They occur in the Neotropics and Australasia, but not in Africa, and their evolutionary assembly remains unclear. We here use phylogenetic frameworks for important AG lineages in Australasia, namely the ant genus Philidris and domatium-bearing ferns (Lecanopteris) and flowering plants in the Apocynaceae (Hoya and Dischidia) and Rubiaceae (Myrmecodia, Hydnophytum, Anthorrhiza, Myrmephytum and Squamellaria). Our analyses revealed that in these clades, diaspore dispersal by ants evolved at least 13 times, five times in the Late Miocene and Pliocene in Australasia and seven times during the Pliocene in Southeast Asia, after Philidris ants had arrived there, with subsequent dispersal between these two areas. A uniquely specialized AG system evolved in Fiji at the onset of the Quaternary. The farming in the same AG of epiphytes that do not offer nest spaces suggests that a broadening of the ants' plant host spectrum drove the evolution of additional domatium-bearing AG-epiphytes by selecting on pre-adapted morphological traits. Consistent with this, we found a statistical correlation between the evolution of diaspore dispersal by ants and domatia in all three lineages. Our study highlights how host broadening by a symbiont has led to new farming mutualisms.
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Affiliation(s)
- Guillaume Chomicki
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
| | - Milan Janda
- Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.,Laboratorio Nacional de Análisis y Síntesis Ecológica, ENES, UNAM, Antigua Carretera a Pátzcuaro 8701, Morelia, Mexico
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
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35
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Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. Nat Commun 2018; 9:336. [PMID: 29362365 PMCID: PMC5780524 DOI: 10.1038/s41467-017-02522-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/07/2017] [Indexed: 11/29/2022] Open
Abstract
Most studies of bacterial motility have examined small-scale (micrometer–centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes. Interactions with other microbes may inhibit or facilitate the dispersal of bacteria. Here, Zhang et al. use cheese rind microbiomes as a model to show that physical networks created by filamentous fungi can affect the dispersal of motile bacteria and thus shape the diversity of microbial communities.
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36
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Aleklett K, Kiers ET, Ohlsson P, Shimizu TS, Caldas VE, Hammer EC. Build your own soil: exploring microfluidics to create microbial habitat structures. ISME JOURNAL 2017; 12:312-319. [PMID: 29135971 PMCID: PMC5776464 DOI: 10.1038/ismej.2017.184] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/25/2017] [Accepted: 09/15/2017] [Indexed: 11/23/2022]
Abstract
Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.
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Affiliation(s)
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | | | - Victor Ea Caldas
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,AMOLF Institute, Amsterdam, The Netherlands
| | - Edith C Hammer
- Department of Microbial Ecology, Lund University, Lund, Sweden
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37
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Worrich A, Stryhanyuk H, Musat N, König S, Banitz T, Centler F, Frank K, Thullner M, Harms H, Richnow HH, Miltner A, Kästner M, Wick LY. Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments. Nat Commun 2017; 8:15472. [PMID: 28589950 PMCID: PMC5467244 DOI: 10.1038/ncomms15472] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/29/2017] [Indexed: 12/22/2022] Open
Abstract
Fungal–bacterial interactions are highly diverse and contribute to many ecosystem processes. Their emergence under common environmental stress scenarios however, remains elusive. Here we use a synthetic microbial ecosystem based on the germination of Bacillus subtilis spores to examine whether fungal and fungal-like (oomycete) mycelia reduce bacterial water and nutrient stress in an otherwise dry and nutrient-poor microhabitat. We find that the presence of mycelia enables the germination and subsequent growth of bacterial spores near the hyphae. Using a combination of time of flight- and nanoscale secondary ion mass spectrometry (ToF- and nanoSIMS) coupled with stable isotope labelling, we link spore germination to hyphal transfer of water, carbon and nitrogen. Our study provides direct experimental evidence for the stimulation of bacterial activity by mycelial supply of scarce resources in dry and nutrient-free environments. We propose that mycelia may stimulate bacterial activity and thus contribute to sustaining ecosystem functioning in stressed habitats. The maintenance of bacterial and fungal activity is essential for ecosystem functioning, particularly in dry soils where the two phyla co-exist. Here, Worrich and colleagues show experimentally that mycelia traffic water and nutrients and thereby stimulate bacterial activity in stressful conditions.
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Affiliation(s)
- Anja Worrich
- Department of Environmental Biotechnology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sara König
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Thomas Banitz
- Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Karin Frank
- Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany.,University of Osnabrück, Institute for Environmental Systems Research, Barbarastaße 12, 49076 Osnabrück, Germany
| | - Martin Thullner
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Anja Miltner
- Department of Environmental Biotechnology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
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Abstract
Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.
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Affiliation(s)
- Kabir G Peay
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Peter G Kennedy
- Department of Plant Biology, University of Minnesota.,Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Jennifer M Talbot
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
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Liu Q, Liu H, Chen C, Wang J, Han Y, Long Z. Effects of element complexes containing Fe, Zn and Mn on artificial morel's biological characteristics and soil bacterial community structures. PLoS One 2017; 12:e0174618. [PMID: 28350840 PMCID: PMC5370159 DOI: 10.1371/journal.pone.0174618] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 03/12/2017] [Indexed: 12/29/2022] Open
Abstract
This study described the effects of elements (including Fe, Zn, Mn and their complexes) on the following factors in artificial morel cultivation: the characteristics of mycelia and sclerotia, soil bacterial community structures, yields and contents of microelements. The results indicated that the groups containing Mn significantly promoted mycelia growth rates, and all the experimental groups resulted in higher yields than the control (P<0.01), although their mycelia and sclerotia did not show obvious differences. It was also found that Proteobacteria, Chloroflexi, Bacteroides, Firmicutes, Actinobacteria, Acidobacteria and Nitrospirae were the dominated bacterial phyla. The Zn·Fe group had an unexpectedly high proportion (75.49%) of Proteobacteria during the primordial differentiation stage, while Pseudomonas also occupied a high proportion (5.52%) in this group. These results suggested that different trace elements clearly affected morel yields and soil bacterial community structures, particularly due to the high proportions of Pseudomonas during the primordial differentiation stage.
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Affiliation(s)
- Qingya Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Huimei Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Ciqiong Chen
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Jinmei Wang
- Sichuan Tongfeng Science & Technology Co. Ltd, Chengdu, P.R. China
| | - Yu Han
- Sichuan Tongfeng Science & Technology Co. Ltd, Chengdu, P.R. China
| | - Zhangfu Long
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
- * E-mail:
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40
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Nazir R, Mazurier S, Yang P, Lemanceau P, van Elsas JD. The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent. Front Microbiol 2017; 8:38. [PMID: 28197129 PMCID: PMC5282467 DOI: 10.3389/fmicb.2017.00038] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/06/2017] [Indexed: 12/14/2022] Open
Abstract
Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve efficient association strategies. The purpose of this review is to examine the mechanisms that underpin the bacterial interactions with fungi in soil and other systems, with special focus on the type III secretion system (T3SS). Starting with a brief description of the versatility of the T3SS as an interaction system with diverse eukaryotic hosts, we subsequently examine the recent advances made in our understanding of its contribution to interactions with soil fungi. The analysis used data sets ranging from circumstantial evidence to gene-knockout-based experimental data. The initial finding that the abundance of T3SSs in microbiomes is often enhanced in fungal-affected habitats like the mycosphere and the mycorrhizosphere is now substantiated with in-depth knowledge of the specific systems involved. Different fungal–interactive bacteria, in positive or negative associations with partner fungi, harbor and express T3SSs, with different ecological outcomes. In some particular cases, bacterial T3SSs have been shown to modulate the physiology of its fungal partner, affecting its ecological characteristics and consequently shaping its own habitat. Overall, the analyses of the collective data set revealed that diverse T3SSs have assumed diverse roles in the interactions of bacteria with host fungi, as driven by ecological and evolutionary niche requirements.
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Affiliation(s)
- Rashid Nazir
- Department of Environmental Sciences, COMSATS Institute of Information TechnologyAbbottabad, Pakistan; Department of Soil Environmental Science, Research Centre for Eco-environmental Sciences - Chinese Academy of SciencesBeijing, China
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Pu Yang
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
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41
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Haq IU, Dini-Andreote F, van Elsas JD. Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions. MICROBIAL ECOLOGY 2017; 73:236-252. [PMID: 27844108 PMCID: PMC5209427 DOI: 10.1007/s00248-016-0885-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/24/2016] [Indexed: 05/05/2023]
Abstract
In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1-day 3; T2-day 5), contact between both partner organisms was absent, whereas in the final stage (T3-day 8), the two populations made intimate physical contact. Overall, a strong modulation of the strain BS001 gene expression patterns was found. First, the stationary-phase sigma factor RpoS, and numerous genes under its control, were strongly expressed as a response to the soil extract agar, and this extended over the whole temporal regime. In the system, B. terrae BS001 apparently perceived the presence of the fungal hyphae already at the early experimental stages (T1, T2), by strongly upregulating a suite of chemotaxis and flagellar motility genes. With respect to specific metabolism and energy generation, a picture of differential involvement in different metabolic routes was obtained. Initial (T1, T2) up- or downregulation of ethanolamine and mandelate uptake and utilization pathways was substituted by a strong investment, in the presence of the fungus, in the expression of putative metabolic gene clusters (T3). Specifically at T3, five clustered genes that are potentially involved in energy generation coupled to an oxidative stress response, and two genes encoding short-chain dehydrogenases/oxidoreductases (SDR), were highly upregulated. In contrast, the dnaE2 gene (related to general stress response; encoding error-prone DNA polymerase) was transcriptionally downregulated at this stage. This study revealed that B. terrae BS001, from a stress-induced state, resulting from the soil extract agar milieu, responds positively to fungal hyphae that encroach upon it, in a temporally dynamic manner. The response is characterized by phases in which the modulation of (1) chemotaxis, (2) metabolic activity, and (3) oxidative stress responses are key mechanisms.
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Affiliation(s)
- Irshad Ul Haq
- Microbial Ecology Group, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Francisco Dini-Andreote
- Microbial Ecology Group, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Group, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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42
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Catch me if you can: dispersal and foraging of Bdellovibrio bacteriovorus 109J along mycelia. ISME JOURNAL 2016; 11:386-393. [PMID: 27824344 DOI: 10.1038/ismej.2016.135] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/17/2016] [Accepted: 08/29/2016] [Indexed: 11/08/2022]
Abstract
To cope with heterogeneous environments and resource distributions, filamentous fungi have evolved a spatially extensive growth enabling their hyphae to penetrate air-water interfaces and pass through air-filled pores. Such mycelia are also known to act as dispersal networks for the mobilisation of bacteria ('fungal highways') and connection of microbial microhabitats. Hitherto, however, nothing is known about the effect of mycelia-based dispersal on interactions between bacterial predators and their prey and concomitant effects on biomass formation. We here hypothesise that mycelia enable the contact between predators and their prey and shape a prey's population. We investigated the impact of predation by Bdellovibrio bacteriovorus 109J on the growth of its potential prey Pseudomonas fluorescens LP6a in the presence of mycelia. Our data give evidence that hyphae increase the accessibility of the prey to B. bacteriovorus 109J and, hence, allow for efficient foraging and shaping of prey populations not seen in the absence of mycelia. To test our hypothesis tailored microbial landscapes were used for better reduction of emerging properties in complex systems. Our data suggest that mycelia have substantial influence on prey-predator relationship and hereby may promote the structure of prey and predator populations and, hence, may be a determinant for biomass formation in heterogeneous environments.
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43
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Johnston SR, Boddy L, Weightman AJ. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol 2016; 92:fiw179. [PMID: 27559028 DOI: 10.1093/femsec/fiw179] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 01/02/2023] Open
Abstract
The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research.
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Affiliation(s)
- Sarah R Johnston
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
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44
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Worrich A, König S, Banitz T, Centler F, Frank K, Thullner M, Harms H, Miltner A, Wick LY, Kästner M. Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress. Front Microbiol 2016; 7:1214. [PMID: 27536297 PMCID: PMC4971104 DOI: 10.3389/fmicb.2016.01214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/21/2016] [Indexed: 11/13/2022] Open
Abstract
Contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. Over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. Here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of osmotic potentials (ΔΨo) using model ecosystems exhibiting a heterogeneous distribution of the soil-borne bacterium Pseudomonas putida KT2440. Three systematically manipulated scenarios allowed us to cover the effects of (i) substrate diffusion, (ii) substrate diffusion and autonomous bacterial dispersal, and (iii) substrate diffusion and autonomous as well as mediated bacterial dispersal along glass fiber networks mimicking fungal hyphae. To quantify the relative importance of the different spatial processes, we compared these heterogeneous scenarios to a reference value obtained for each ΔΨo by means of a quasi-optimal scenario in which degraders were ab initio homogeneously distributed. Substrate diffusion as the sole spatial process was insufficient to counteract the disadvantage due to spatial degrader heterogeneity at ΔΨo ranging from 0 to -1 MPa. In this scenario, only 13.8-21.3% of the quasi-optimal biodegradation performance could be achieved. In the same range of ΔΨo values, substrate diffusion in combination with bacterial dispersal allowed between 68.6 and 36.2% of the performance showing a clear downwards trend with decreasing ΔΨo. At -1.5 MPa, however, this scenario performed worse than the diffusion scenario, possibly as a result of energetic disadvantages associated with flagellum synthesis and emerging requirements to exceed a critical population density to resist osmotic stress. Network-mediated bacterial dispersal kept biodegradation almost consistently high with an average of 70.7 ± 7.8%, regardless of the strength of the osmotic stress. We propose that especially fungal network-mediated bacterial dispersal is a key process to achieve high functionality of heterogeneous microbial ecosystems also at reduced osmotic potentials. Thus, mechanical stress by, for example, soil homogenization should be kept low in order to preserve fungal network integrity.
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Affiliation(s)
- Anja Worrich
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; UFZ - Helmholtz Centre for Environmental Research, Department of Environmental BiotechnologyLeipzig, Germany
| | - Sara König
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; UFZ - Helmholtz Centre for Environmental Research, Department of Ecological ModellingLeipzig, Germany
| | - Thomas Banitz
- UFZ - Helmholtz Centre for Environmental Research, Department of Ecological Modelling Leipzig, Germany
| | - Florian Centler
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Karin Frank
- UFZ - Helmholtz Centre for Environmental Research, Department of Ecological ModellingLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany; Institute for Environmental Systems Research, University of OsnabrückOsnabrück, Germany
| | - Martin Thullner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Hauke Harms
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Anja Miltner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology Leipzig, Germany
| | - Lukas Y Wick
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Matthias Kästner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology Leipzig, Germany
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45
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Otto S, Banitz T, Thullner M, Harms H, Wick LY. Effects of Facilitated Bacterial Dispersal on the Degradation and Emission of a Desorbing Contaminant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6320-6326. [PMID: 27195517 DOI: 10.1021/acs.est.6b00567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The quantitative relationship between a compound's availability for biological removal and ecotoxicity is a key issue for retrospective risk assessment and remediation approaches. Here, we investigated the impact of facilitated bacterial dispersal at a model soil-atmosphere interface on the release, degradation, and outgassing of a semivolatile contaminant. We designed a laboratory microcosm with passive dosing of phenanthrene (PHE) to a model soil-atmosphere interface (agar surface) in the presence and absence of glass fibers known to facilitate the dispersal of PHE-degrading Pseudomonas fluorescens LP6a. We observed that glass fibers (used as a model to mimic a fungal hyphal network) resulted in (i) increased bacterial surface coverage, (ii) effective degradation of matrix-bound PHE, and (iii) substantially reduced PHE emission to locations beyond the contamination zone even at low bacterial surface coverage. Our data suggest that bacterial dispersal networks such as mycelia promote the optimized spatial arrangement of microbial populations to allow for effective contaminant degradation and reduction of potential hazard to organisms beyond a contaminated zone.
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Affiliation(s)
| | | | | | - Hauke Harms
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e, 04103 Leipzig, Germany
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46
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Mycelium-Like Networks Increase Bacterial Dispersal, Growth, and Biodegradation in a Model Ecosystem at Various Water Potentials. Appl Environ Microbiol 2016; 82:2902-2908. [PMID: 26944849 DOI: 10.1128/aem.03901-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/02/2016] [Indexed: 11/20/2022] Open
Abstract
Fungal mycelia serve as effective dispersal networks for bacteria in water-unsaturated environments, thereby allowing bacteria to maintain important functions, such as biodegradation. However, poor knowledge exists on the effects of dispersal networks at various osmotic (Ψo) and matric (Ψm) potentials, which contribute to the water potential mainly in terrestrial soil environments. Here we studied the effects of artificial mycelium-like dispersal networks on bacterial dispersal dynamics and subsequent effects on growth and benzoate biodegradation at ΔΨo and ΔΨm values between 0 and -1.5 MPa. In a multiple-microcosm approach, we used a green fluorescent protein (GFP)-tagged derivative of the soil bacterium Pseudomonas putida KT2440 as a model organism and sodium benzoate as a representative of polar aromatic contaminants. We found that decreasing ΔΨo and ΔΨm values slowed bacterial dispersal in the system, leading to decelerated growth and benzoate degradation. In contrast, dispersal networks facilitated bacterial movement at ΔΨo and ΔΨm values between 0 and -0.5 MPa and thus improved the absolute biodegradation performance by up to 52 and 119% for ΔΨo and ΔΨm, respectively. This strong functional interrelationship was further emphasized by a high positive correlation between population dispersal, population growth, and degradation. We propose that dispersal networks may sustain the functionality of microbial ecosystems at low osmotic and matric potentials.
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47
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Oldfield CA, Evans JP. Twelve years of repeated wild hog activity promotes population maintenance of an invasive clonal plant in a coastal dune ecosystem. Ecol Evol 2016; 6:2569-78. [PMID: 27110354 PMCID: PMC4834338 DOI: 10.1002/ece3.2045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 02/01/2016] [Accepted: 02/08/2016] [Indexed: 11/15/2022] Open
Abstract
Invasive animals can facilitate the success of invasive plant populations through disturbance. We examined the relationship between the repeated foraging disturbance of an invasive animal and the population maintenance of an invasive plant in a coastal dune ecosystem. We hypothesized that feral wild hog (Sus scrofa) populations repeatedly utilized tubers of the clonal perennial, yellow nutsedge (Cyperus esculentus) as a food source and evaluated whether hog activity promoted the long‐term maintenance of yellow nutsedge populations on St. Catherine's Island, Georgia, United States. Using generalized linear mixed models, we tested the effect of wild hog disturbance on permanent sites for yellow nutsedge culm density, tuber density, and percent cover of native plant species over a 12‐year period. We found that disturbance plots had a higher number of culms and tubers and a lower percentage of native live plant cover than undisturbed control plots. Wild hogs redisturbed the disturbed plots approximately every 5 years. Our research provides demographic evidence that repeated foraging disturbances by an invasive animal promote the long‐term population maintenance of an invasive clonal plant. Opportunistic facultative interactions such as we demonstrate in this study are likely to become more commonplace as greater numbers of introduced species are integrated into ecological communities around the world.
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Affiliation(s)
- Callie A Oldfield
- Department of Biology The University of the South Sewanee Tennessee 37383
| | - Jonathan P Evans
- Department of Biology The University of the South Sewanee Tennessee 37383
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48
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Johns NI, Blazejewski T, Gomes AL, Wang HH. Principles for designing synthetic microbial communities. Curr Opin Microbiol 2016; 31:146-153. [PMID: 27084981 DOI: 10.1016/j.mib.2016.03.010] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 01/21/2023]
Abstract
Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of synthetic microbial communities. Here, we review recent experimental, analytical and computational advances to study and build multi-species microbial communities with defined functions and behavior for various applications. We also highlight outstanding challenges and future directions to advance this field.
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Affiliation(s)
- Nathan I Johns
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, USA
| | - Tomasz Blazejewski
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, USA
| | - Antonio Lc Gomes
- Department of Systems Biology, Columbia University Medical Center, New York, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA.
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49
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Ben-Jacob E, Finkelshtein A, Ariel G, Ingham C. Multispecies Swarms of Social Microorganisms as Moving Ecosystems. Trends Microbiol 2016; 24:257-269. [DOI: 10.1016/j.tim.2015.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
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50
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Hervé V, Ketter E, Pierrat JC, Gelhaye E, Frey-Klett P. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood. PLoS One 2016; 11:e0147100. [PMID: 26824755 PMCID: PMC4732817 DOI: 10.1371/journal.pone.0147100] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 12/29/2015] [Indexed: 11/18/2022] Open
Abstract
Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.
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Affiliation(s)
- Vincent Hervé
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
- * E-mail:
| | - Elodie Ketter
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
| | - Jean-Claude Pierrat
- INRA, UMR 1092 LERFOB, F-54280 Champenoux, France
- AgroParisTech, UMR 1092 LERFOB, F-54000 Nancy, France
| | - Eric Gelhaye
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
| | - Pascale Frey-Klett
- INRA, Interactions Arbres–Microorganismes, UMR1136, F-54280 Champenoux, France
- Université de Lorraine, Interactions Arbres–Microorganismes, UMR1136, F-54500 Vandoeuvre-lès-Nancy, France
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