1
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Hamberg L, Vanhatalo J, Velmala S, Taylor AFS, MacKay J, Caron S, Asiegbu FO, Sievänen R, Raumonen P, Hytönen T, Pennanen T. The community of root fungi is associated with the growth rate of Norway spruce (Picea abies). Environ Microbiol 2024; 26:e16662. [PMID: 38840258 DOI: 10.1111/1462-2920.16662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Our study delved into the relationship between root-associated fungi, gene expression and plant morphology in Norway spruce cuttings derived from both slow-and fast-growing trees. We found no clear link between the gene expression patterns of adventitious roots and the growth phenotype, suggesting no fundamental differences in the receptiveness to fungal symbionts between the phenotypes. Interestingly, saplings from slow-growing parental trees exhibited a higher richness of ectomycorrhizal species and larger roots. Some ectomycorrhizal species, typically found on mature spruces, were more prevalent on saplings from slow-growing spruces. The ericoid mycorrhizal fungus, Hyaloscypha hepaticola, showed a stronger association with saplings from fast-growing spruces. Moreover, saplings from slow-growing spruces had a greater number of Ascomycete taxa and free-living saprotrophic fungi. Aboveground sapling stems displayed some phenotypic variation; saplings from fast-growing phenotypes had longer branches but fewer whorls in their stems compared to those from the slow-growing group. In conclusion, the observed root-associated fungi and phenotypic characteristics in young Norway spruces may play a role in their long-term growth rate. This suggests that the early interactions between spruces and fungi could potentially influence their growth trajectory.
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Affiliation(s)
- Leena Hamberg
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Jarno Vanhatalo
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - John MacKay
- Department of Biology, University of Oxford, Oxford, UK
| | - Sébastien Caron
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, Canada
| | - Fred O Asiegbu
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Risto Sievänen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Pasi Raumonen
- Computing Sciences, Tampere University, Tampere, Finland
| | - Tuija Hytönen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Taina Pennanen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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2
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Thanapaul RJRS, Alamneh YA, Finnegan DK, Antonic V, Abu-Taleb R, Czintos C, Boone D, Su W, Sajja VS, Getnet D, Roberds A, Walsh TJ, Bobrov AG. Development of a Combat-Relevant Murine Model of Wound Mucormycosis: A Platform for the Pre-Clinical Investigation of Novel Therapeutics for Wound-Invasive Fungal Diseases. J Fungi (Basel) 2024; 10:364. [PMID: 38786719 PMCID: PMC11122444 DOI: 10.3390/jof10050364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Wound-invasive fungal diseases (WIFDs), especially mucormycosis, have emerged as life-threatening infections during recent military combat operations. Many combat-relevant fungal pathogens are refractory to current antifungal therapy. Therefore, animal models of WIFDs are urgently needed to investigate new therapeutic solutions. Our study establishes combat-relevant murine models of wound mucormycosis using Rhizopus arrhizus and Lichtheimia corymbifera, two Mucorales species that cause wound mucormycosis worldwide. These models recapitulate the characteristics of combat-related wounds from explosions, including blast overpressure exposure, full-thickness skin injury, fascial damage, and muscle crush. The independent inoculation of both pathogens caused sustained infections and enlarged wounds. Histopathological analysis confirmed the presence of necrosis and fungal hyphae in the wound bed and adjacent muscle tissue. Semi-quantification of fungal burden by colony-forming units corroborated the infection. Treatment with liposomal amphotericin B, 30 mg/kg, effectively controlled R. arrhizus growth and significantly reduced residual fungal burden in infected wounds (p < 0.001). This study establishes the first combat-relevant murine model of wound mucormycosis, paving the way for developing and evaluating novel antifungal therapies against combat-associated WIFDs.
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Affiliation(s)
- Rex J. R. Samdavid Thanapaul
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- NRC Research Associateship Programs, National Academies of Sciences, Engineering, and Medicine, Washington, DC 20001, USA
| | - Yonas A. Alamneh
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Daniel K. Finnegan
- Veterinary Services Program, Pathology Department, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Vlado Antonic
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Rania Abu-Taleb
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Christine Czintos
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Dylan Boone
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Wanwen Su
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Venkatasivasai S. Sajja
- Blast Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Derese Getnet
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Ashleigh Roberds
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Thomas J. Walsh
- Departments of Medicine and Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Center for Innovative Therapeutics and Diagnostics, Richmond, VA 23220, USA
| | - Alexander G. Bobrov
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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3
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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. THE NEW PHYTOLOGIST 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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4
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Hao MS, Mazurkewich S, Li H, Kvammen A, Saha S, Koskela S, Inman AR, Nakajima M, Tanaka N, Nakai H, Brändén G, Bulone V, Larsbrink J, McKee LS. Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans. Nat Commun 2024; 15:3429. [PMID: 38653764 PMCID: PMC11039641 DOI: 10.1038/s41467-024-47584-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic proteins found appended to carbohydrate-active enzymes. Soil and marine bacteria secrete such enzymes to scavenge nutrition, and they often use CBMs to improve reaction rates and retention of released sugars. Here we present a structural and functional analysis of the recently established CBM family 92. All proteins analysed bind preferentially to β-1,6-glucans. This contrasts with the diversity of predicted substrates among the enzymes attached to CBM92 domains. We present crystal structures for two proteins, and confirm by mutagenesis that tryptophan residues permit ligand binding at three distinct functional binding sites on each protein. Multivalent CBM families are uncommon, so the establishment and structural characterisation of CBM92 enriches the classification database and will facilitate functional prediction in future projects. We propose that CBM92 proteins may cross-link polysaccharides in nature, and might have use in novel strategies for enzyme immobilisation.
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Affiliation(s)
- Meng-Shu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Scott Mazurkewich
- Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - He Li
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Alma Kvammen
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Srijani Saha
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Salla Koskela
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Nobukiyo Tanaka
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Bedford Park Campus, Sturt Road, SA, 5042, Australia
| | - Johan Larsbrink
- Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden.
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden.
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5
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Bosch J, Dobbler PT, Větrovský T, Tláskal V, Baldrian P, Brabcová V. Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda. FEMS Microbiol Ecol 2024; 100:fiae044. [PMID: 38640440 PMCID: PMC11030162 DOI: 10.1093/femsec/fiae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.
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Affiliation(s)
- Jason Bosch
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Priscila Thiago Dobbler
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
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6
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Li Z, Wu S, Yi Q, Liu Y, Wang J, Nguyen TAH, Ma Y, You F, Chan TS, Klein A, Levett A, Southam G, Alessi DS, Huang Y, Huang L. Arbuscular Mycorrhizal Fungi Drive Organo-Mineral Association in Iron Ore Tailings: Unravelling Microstructure at the Submicron Scale by Synchrotron-Based FTIR and STXM-NEXAFS. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21779-21790. [PMID: 38091466 DOI: 10.1021/acs.est.3c07614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi play an important role in organic matter (OM) stabilization in Fe ore tailings for eco-engineered soil formation. However, little has been understood about the AM fungi-derived organic signature and organo-mineral interactions in situ at the submicron scale. In this study, a compartmentalized cultivation system was used to investigate the role of AM fungi in OM formation and stabilization in tailings. Particularly, microspectroscopic analyses including synchrotron-based transmission Fourier transform infrared (FTIR) and scanning transmission X-ray microspectroscopy combined with near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS) were employed to characterize the chemical signatures at the AM fungal-mineral and mineral-OM interfaces at the submicron scale. The results indicated that AM fungal mycelia developed well in the tailings and entangled mineral particles for aggregation. AM fungal colonization enhanced N-rich OM stabilization through organo-mineral association. Bulk spectroscopic analysis together with FTIR mapping revealed that fungi-derived lipids, proteins, and carbohydrates were associated with Fe/Si minerals. Furthermore, STXM-NEXAFS analysis revealed that AM fungi-derived aromatic, aliphatic, and carboxylic/amide compounds were heterogeneously distributed and trapped by Fe(II)/Fe(III)-bearing minerals originating from biotite-like minerals weathering. These findings imply that AM fungi can stimulate mineral weathering and provide organic substances to associate with minerals, contributing to OM stabilization and aggregate formation as key processes for eco-engineered soil formation in tailings.
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Affiliation(s)
- Zhen Li
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | - Songlin Wu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Yi
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yunjia Liu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jian Wang
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N2 V3, Canada
| | - Tuan A H Nguyen
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yuanying Ma
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fang You
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 30092, Taiwan
| | - Annaleise Klein
- Australian Synchrotron, ANSTO, Melbourne, Victoria 3168, Australia
| | - Alan Levett
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gordon Southam
- School of the Environment, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | - Yuanfang Huang
- College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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7
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Hartmann M, Herzog C, Brunner I, Stierli B, Meyer F, Buchmann N, Frey B. Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition. Front Microbiol 2023; 14:1267270. [PMID: 37840720 PMCID: PMC10570739 DOI: 10.3389/fmicb.2023.1267270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.
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Affiliation(s)
- Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Claude Herzog
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Folker Meyer
- Data Science, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Argonne National Laboratory, Argonne, IL, United States
- Computation Institute, University of Chicago, Chicago, IL, United States
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Nina Buchmann
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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8
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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9
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Maillard F, Michaud TJ, See CR, DeLancey LC, Blazewicz SJ, Kimbrel JA, Pett-Ridge J, Kennedy PG. Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils. mSystems 2023; 8:e0039023. [PMID: 37338274 PMCID: PMC10469842 DOI: 10.1128/msystems.00390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/21/2023] Open
Abstract
Microbial necromass contributes significantly to both soil carbon (C) persistence and ecosystem nitrogen (N) availability, but quantitative estimates of C and N movement from necromass into soils and decomposer communities are lacking. Additionally, while melanin is known to slow fungal necromass decomposition, how it influences microbial C and N acquisition as well as elemental release into soils remains unclear. Here, we tracked decomposition of isotopically labeled low and high melanin fungal necromass and measured 13C and 15N accumulation in surrounding soils and microbial communities over 77 d in a temperate forest in Minnesota, USA. Mass loss was significantly higher from low melanin necromass, corresponding with greater 13C and 15N soil inputs. A taxonomically and functionally diverse array of bacteria and fungi was enriched in 13C and/or 15N at all sampling points, with enrichment being consistently higher on low melanin necromass and earlier in decomposition. Similar patterns of preferential C and N enrichment of many bacterial and fungal genera early in decomposition suggest that both microbial groups co-contribute to the rapid assimilation of resource-rich soil organic matter inputs. While overall richness of taxa enriched in C was higher than in N for both bacteria and fungi, there was a significant positive relationship between C and N in co-enriched taxa. Collectively, our results demonstrate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate but also necromass C and N release and that both elements are rapidly co-utilized by diverse bacterial and fungal decomposers in natural settings. IMPORTANCE Recent studies indicate that microbial dead cells, particularly those of fungi, play an important role in long-term carbon persistence in soils. Despite this growing recognition, how the resources within dead fungal cells (also known as fungal necromass) move into decomposer communities and soils are poorly quantified, particularly in studies based in natural environments. In this study, we found that the contribution of fungal necromass to soil carbon and nitrogen availability was slowed by the amount of melanin present in fungal cell walls. Further, despite the overall rapid acquisition of carbon and nitrogen from necromass by a diverse range of both bacteria and fungi, melanization also slowed microbial uptake of both elements. Collectively, our results indicate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate, but also necromass carbon and nitrogen release into soil as well as microbial resource acquisition.
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Affiliation(s)
- François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Talia J. Michaud
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Craig R. See
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Lang C. DeLancey
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Peter G. Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
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10
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Lu Z, Kvammen A, Li H, Hao M, Inman AR, Bulone V, McKee LS. A polysaccharide utilization locus from Chitinophaga pinensis simultaneously targets chitin and β-glucans found in fungal cell walls. mSphere 2023; 8:e0024423. [PMID: 37493618 PMCID: PMC10449523 DOI: 10.1128/msphere.00244-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
In nature, complex carbohydrates are rarely found as pure isolated polysaccharides. Instead, bacteria in competitive environments are presented with glycans embedded in heterogeneous matrices such as plant or microbial cell walls. Members of the Bacteroidota phylum thrive in such ecosystems because they are efficient at extracting nutrients from complex substrates, secreting consortia of synergistic enzymes to release metabolizable sugars. Carbohydrate-binding modules (CBMs) are used to target enzymes to substrates, enhancing reaction rate and product release. Additionally, genome organizational tools like polysaccharide utilization loci (PULs) ensure that the appropriate set of enzymes is produced when needed. In this study, we show that the soil bacterium Chitinophaga pinensis uses a PUL and several CBMs to coordinate the activities of enzymes targeting two distinct polysaccharides found in fungal cell walls. We describe the enzymatic activities and carbohydrate-binding behaviors of components of the fungal cell wall utilization locus (FCWUL), which uses multiple chitinases and one β-1,3-glucanase to hydrolyze two different substrates. Unusually, one of the chitinases is appended to a β-glucan-binding CBM, implying targeting to a bulk cell wall substrate rather than to the specific polysaccharide being hydrolyzed. Based on our characterization of the PUL's outer membrane sensor protein, we suggest that the FCWUL is activated by β-1,3-glucans, even though most of its enzymes are chitin-degrading. Our data showcase the complexity of polysaccharide deconstruction in nature and highlight an elegant solution for how multiple different glycans can be accessed using one enzymatic cascade. IMPORTANCE We report that the genome of the soil bacterium Chitinophaga pinensis encodes three multi-modular carbohydrate-active enzymes that work together to hydrolyze the major polysaccharide components found in fungal cell walls (FCWs). The enzymes are all encoded by one polysaccharide utilization locus and are co-expressed, potentially induced in the presence of β-1,3-glucans. We present biochemical characterization of each enzyme, including the appended carbohydrate-binding modules that likely tether the enzymes to a FCW substrate. Finally, we propose a model for how this so-called fungal cell wall utilization locus might enable C. pinensis to metabolize both chitin and β-1,3-glucans found in complex biomass in the soil.
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Affiliation(s)
- Zijia Lu
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alma Kvammen
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - He Li
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mengshu Hao
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annie R. Inman
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincent Bulone
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Lauren S. McKee
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, Stockholm, Sweden
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11
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Cantoran A, Maillard F, Baldrian P, Kennedy PG. Defining a core microbial necrobiome associated with decomposing fungal necromass. FEMS Microbiol Ecol 2023; 99:fiad098. [PMID: 37656873 DOI: 10.1093/femsec/fiad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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Affiliation(s)
- Anahi Cantoran
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Microbial Ecology Group, Department of Biology, Lund University, Naturvetarvägen 22362, Lund, Sweden
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídenská 1083, Prague 142 20, Czech Republic
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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12
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Ouradou A, Veillette M, Bélanger Cayouette A, Corbin S, Boulanger C, Dorner S, Duchaine C, Bédard E. Effect of odor treatment systems on bioaerosol microbial concentration and diversity from wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162419. [PMID: 36858219 DOI: 10.1016/j.scitotenv.2023.162419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/30/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Biofiltration, activated carbon and chemical scrubbing are technologies used for odor control in wastewater treatment plants. These systems may also influence the airborne microbial load in treated air. The study objectives were to 1) evaluate the capacity of three odor control system technologies to reduce the airborne concentration of total bacteria, Legionella, L. pneumophila, non-tuberculous mycobacteria (NTM) and Cladosporium in winter and summer seasons and 2) to describe the microbial ecology of the biofiltration system and evaluate its impact on treated air microbial diversity. A reduction of the total bacterial concentration up to 25 times was observed after odor treatment. Quantification by qPCR revealed the presence of Legionella spp. in all air samples ranging between 26 and 1140 GC/m3, while L. pneumophila was not detected except for three samples below the limit of quantification. A significant increase of up to 25-fold of Legionella spp. was noticed at the outlet of two of the three treatment systems. NTM were ubiquitously detected before air treatment (up to 2500 GC/m3) and were significantly reduced by all 3 systems (up to 13-fold). Cladosporium was measured at low concentrations for each system (< 190 GC/m3), with 68 % of the air samples below the limit of detection. Biodiversity results revealed that biofiltration system is an active process that adapts to air pollutants over time. Legionella spp. were detected in significant abundance in the air once treated in winter (up to 27 %). Nevertheless, the abundance of protozoan hosts is low and does not explain the multiplication of Legionella spp. The season remains the most influential factor shaping biodiversity. In summer only, air biofiltration caused a significant enrichment of the biodiversity. Although odor control technologies are not designed for bacterial mitigation, findings from this study suggest their potential to reduce the abundance of some genera harboring pathogenic species.
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Affiliation(s)
- A Ouradou
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC, Canada.
| | - M Veillette
- Research Center of the University Institute of Cardiology and Pneumology of Quebec-University Laval, Québec, QC, Canada.
| | - A Bélanger Cayouette
- Research Center of the University Institute of Cardiology and Pneumology of Quebec-University Laval, Québec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, University Laval, Québec, QC, Canada.
| | - S Corbin
- City of Repentigny, Repentigny, QC, Canada.
| | | | - S Dorner
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC, Canada.
| | - C Duchaine
- Research Center of the University Institute of Cardiology and Pneumology of Quebec-University Laval, Québec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, University Laval, Québec, QC, Canada; Canada Research Chair on Bioaerosols, University Laval, Québec, QC, Canada.
| | - E Bédard
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC, Canada.
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13
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Kimeklis AK, Gladkov GV, Orlova OV, Afonin AM, Gribchenko ES, Aksenova TS, Kichko AA, Pinaev AG, Andronov EE. The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition. Int J Mol Sci 2023; 24:ijms24076342. [PMID: 37047311 PMCID: PMC10094526 DOI: 10.3390/ijms24076342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.
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Affiliation(s)
- Anastasiia K. Kimeklis
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Department of Applied Ecology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
- Correspondence: (A.K.K.); (E.E.A.)
| | - Grigory V. Gladkov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Olga V. Orlova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Emma S. Gribchenko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Tatiana S. Aksenova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Arina A. Kichko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexander G. Pinaev
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Evgeny E. Andronov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
- Correspondence: (A.K.K.); (E.E.A.)
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14
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Nguyen NH. Fungal Hyphosphere Microbiomes Are Distinct from Surrounding Substrates and Show Consistent Association Patterns. Microbiol Spectr 2023; 11:e0470822. [PMID: 36939352 PMCID: PMC10100729 DOI: 10.1128/spectrum.04708-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
Mat-forming fungi are common in forest and grassland soils across the world, where their activity contributes to important soil ecological processes. These fungi maintain dominance through aggressive and abundant hyphae that modify their internal physical and chemical environments and through these modifications select for what appears to be a suite of mycophilic bacteria. Here, the bacteria associated with the fungal mats of Leucopaxillus gentianeus and Leucopaxillus albissimus from western North America are compared to adjacent nonmat substrates. Within the mats, the bacterial richness and diversity were significantly reduced, and the community composition was significantly different. The bacterial community structure between the two fungal hosts was marginally significant and indicated a shared set of bacterial associates. The genera Burkholderia, Streptomyces, Bacillus, Paenibacillus, and Mycobacterium were significantly abundant within the fungal mats and represent core members of these hypha-rich environments. Comparison with the literature from fungal mat studies worldwide showed that these genera are common and often significantly found within fungal mats, further reinforcing the concept of a mycophilic bacterial guild. These genera are incorporated into a synthesis discussion in the context of our current understanding of the nature of fungal-bacterial interactions and the potential outcomes of these interactions in soil nutrient cycling, plant productivity, and human health. IMPORTANCE Fungi and bacteria are the most abundant and diverse organisms in soils (perhaps more so than any other habitat on earth), and together these microorganisms contribute to broad soil ecosystem processes. There is a suite of bacteria that appears consistently within the physical space called the hyphosphere, the area of influence surrounding fungal hyphae. How these bacteria are selected for, how they are maintained, and what broader ecological functions they perform are subjects of interest in this relatively new field-the cross-kingdom interactions between fungi and bacteria. Understanding their cooccurrence and their interactions can open new realms of understanding in soil ecological processes with global consequences.
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Affiliation(s)
- Nhu H. Nguyen
- University of Hawaiʻi at Mānoa, Honolulu, Hawaiʻi, USA
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15
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Zhang K, Zentella R, Burkey KO, Liao HL, Tisdale RH. Microbial community dynamics responding to nutrient allocation associated with soybean cultivar 'Jake' ozone adaptation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161008. [PMID: 36549524 DOI: 10.1016/j.scitotenv.2022.161008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Tropospheric ozone (O3), a major air pollutant, leads to significant global yield loss in soybean [Glycine max (L.) Merr.]. Soybean cultivar 'Jake' shows O3 resilient traits in above-ground organs, but the root system remains sensitive to elevated O3 (eO3). Changing carbon (C) and nitrogen (N) resource composition during eO3 stress suggests that eO3 presumably alters belowground soil microbial communities and their driven nutrient transformation. Yet, the responses of belowground microbes to eO3 and their feedback on nutrient cycling in 'Jake' are unknown. In this study, we holistically investigated soil microbial communities associated with C and N dynamics and bacterial-fungal inter-kingdom networks in the rhizosphere and bulk soil at different developmental stages of 'Jake' grown under sub-ambient O3 [charcoal-filtered (CF) air, 12 h mean: 20 ppb] or eO3 (12 h mean: 87 ppb). The results demonstrated eO3 significantly decreased fungal diversity and complexity of microbial networks at different 'Jake' developmental stages, whereas bacterial diversity was more tolerant to eO3 in both bulk soil and rhizosphere. In the bulk soil, no O3-responsive microbial biomarkers were found to be associated with C and N content, implying eO3 may stimulate niche-based processes during 'Jake' growth. In contrast, this study identified O3-responsive microbial biomarkers that may contribute to the N acquisition (Chloroflexales) and C dynamics (Caldilineales, Thermomicrobiales, and Hypocreales) in the rhizosphere, which may support the O3 resilience of the 'Jake' cultivar. However, further investigation is required to confirm their specific contributions by determining changes in microbial gene expression. Overall, these findings conduce to an expanding knowledge base that O3 induces temporal and spatial changes in the effects of microbial and nutrient networks in the O3-tolerant agriculture ecosystems.
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Affiliation(s)
- Kaile Zhang
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Rodolfo Zentella
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
| | - Kent O Burkey
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Ripley H Tisdale
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, 27607, NC, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, 27695, NC, USA.
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16
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Kennedy PG, Maillard F. Knowns and unknowns of the soil fungal necrobiome. Trends Microbiol 2023; 31:173-180. [PMID: 36100506 DOI: 10.1016/j.tim.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/27/2023]
Abstract
Dead microbial cells, commonly referred to as necromass, are increasingly recognized as an important source of both persistent carbon as well as nutrient availability in soils. Studies of the microbial communities associated with decomposing fungal necromass have accumulated rapidly in recent years across a range of different terrestrial ecosystems. Here we identify the primary ecological patterns regarding the structure and dynamics of the fungal necrobiome as well as highlight new research frontiers that will likely be key to gaining a full understanding of fungal necrobiome composition and its associated role in soil biogeochemical cycling. Because many members of the fungal necrobiome are culturable, combining laboratory functional assays with field-based surveys and experiments will allow ongoing studies of the fungal necrobiome to move from largely descriptive to increasingly predictive.
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Affiliation(s)
- Peter G Kennedy
- Department of Plant & Microbiology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - François Maillard
- Department of Plant & Microbiology, University of Minnesota, Saint Paul, MN 55108, USA
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17
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Shen Q, Zhang K, Voroney P, Meng L, Xu J, Brookes P. Biodiesel Co-Product enhances microbial stability and beneficial microbial communities along a gradient of soil water content. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159204. [PMID: 36198351 DOI: 10.1016/j.scitotenv.2022.159204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Biodiesel Co-Product (BCP) is a complex carbonaceous liquid formed during the commercial production of biodiesel. Previously, BCP was shown to decrease nitrogen (N) leaching from the soil, but the effects of BCP on the diversity, composition, and structure of soil microbial communities are not well understood. Here, we applied 1.5 mg BCP-C to acidic soil (pH 3.5) at a range of different water contents (from 40 % to 100 % water holding capacity) to investigate the interactions between BCP and increasing water holding capacity on the diversity, composition, and interactions of soil microbial communities. Distance-based multivariate linear model (DistLM) and non-metric multidimensional scaling (NMDS) analyses showed that BCP caused larger changes in fungal than bacterial communities, while soil water content had a greater effect on bacterial communities relative to fungal communities. Co-occurrence network analyses indicated that BCP amendment produced more robust and complex bacterial networks and more stable fungal ones. BCP significantly increased the OTU numbers of beneficial microbes (e.g., Trichoderma spp.) in all water contents, with fewer OTU numbers of putative pathogenetic species (Fusarium spp. and Aspergillus spp.). These findings indicate that BCP addition may be conducive to the health and stability of soil ecosystems.
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Affiliation(s)
- Qunli Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Faculty of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, USA.
| | - Paul Voroney
- Faculty of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Lei Meng
- School of Tropical Crops, Hainan University, Haikou 570228, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Philip Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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18
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Lu Z, Rämgård C, Ergenlioğlu İ, Sandin L, Hammar H, Andersson H, King K, Inman AR, Hao M, Bulone V, McKee LS. Multiple enzymatic approaches to hydrolysis of fungal β-glucans by the soil bacterium Chitinophaga pinensis. FEBS J 2023. [PMID: 36610032 DOI: 10.1111/febs.16720] [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: 08/29/2022] [Revised: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The genome of the soil Bacteroidota Chitinophaga pinensis encodes a large number of glycoside hydrolases (GHs) with noteworthy features and potentially novel functions. Several are predicted to be active on polysaccharide components of fungal and oomycete cell walls, such as chitin, β-1,3-glucan and β-1,6-glucan. While several fungal β-1,6-glucanase enzymes are known, relatively few bacterial examples have been characterised to date. We have previously demonstrated that C. pinensis shows strong growth using β-1,6-glucan as the sole carbon source, with the efficient release of oligosaccharides from the polymer. We here characterise the capacity of the C. pinensis secretome to hydrolyse the β-1,6-glucan pustulan and describe three distinct enzymes encoded by its genome, all of which show different levels of β-1,6-glucanase activity and which are classified into different GH families. Our data show that C. pinensis has multiple tools to deconstruct pustulan, allowing the species' broad utility of this substrate, with potential implications for bacterial biocontrol of pathogens via cell wall disruption. Oligosaccharides derived from fungal β-1,6-glucans are valuable in biomedical research and drug synthesis, and these enzymes could be useful tools for releasing such molecules from microbial biomass, an underexploited source of complex carbohydrates.
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Affiliation(s)
- Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Carl Rämgård
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - İrem Ergenlioğlu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lova Sandin
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Hugo Hammar
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Helena Andersson
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Katharine King
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Mengshu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Centre, Stockholm, Sweden
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19
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Navarrete AA, Aburto F, González-Rocha G, Guzmán CM, Schmidt R, Scow K. Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158508. [PMID: 36063938 DOI: 10.1016/j.scitotenv.2022.158508] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.
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Affiliation(s)
- Alejandro Atenas Navarrete
- Postgrado Facultad de Ciencias Forestales, Universidad de Concepción, Chile; Laboratorio de Investigación en Suelos, Aguas y Bosques (LISAB), Universidad de Concepción, Chile; Iniciativa Foresta Nativa, Universidad de Concepción, Concepción, Chile
| | - Felipe Aburto
- Soil and Crop Sciences Department, Texas A&M University, 370 Olsen Blvd. Heep Center, TX 77845, USA; Departamento de Planificación Territorial y Sistemas Urbanos, Facultad de Ciencias Ambientales, Universidad de Concepción, Chile.
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Carolina Merino Guzmán
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, BIOREN, Universidad de La Frontera, Chile
| | - Radomir Schmidt
- Working Lands Innovation Center at the Institute of the Environment, University of California, Davis, USA
| | - Kate Scow
- Soil Microbial Ecology Lab, Department of Land, Air and Water Resources, University of California, Davis, USA
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20
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Butterworth NJ, Benbow ME, Barton PS. The ephemeral resource patch concept. Biol Rev Camb Philos Soc 2022; 98:697-726. [PMID: 36517934 DOI: 10.1111/brv.12926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
Ephemeral resource patches (ERPs) - short lived resources including dung, carrion, temporary pools, rotting vegetation, decaying wood, and fungi - are found throughout every ecosystem. Their short-lived dynamics greatly enhance ecosystem heterogeneity and have shaped the evolutionary trajectories of a wide range of organisms - from bacteria to insects and amphibians. Despite this, there has been no attempt to distinguish ERPs clearly from other resource types, to identify their shared spatiotemporal characteristics, or to articulate their broad ecological and evolutionary influences on biotic communities. Here, we define ERPs as any distinct consumable resources which (i) are homogeneous (genetically, chemically, or structurally) relative to the surrounding matrix, (ii) host a discrete multitrophic community consisting of species that cannot replicate solely in any of the surrounding matrix, and (iii) cannot maintain a balance between depletion and renewal, which in turn, prevents multiple generations of consumers/users or reaching a community equilibrium. We outline the wide range of ERPs that fit these criteria, propose 12 spatiotemporal characteristics along which ERPs can vary, and synthesise a large body of literature that relates ERP dynamics to ecological and evolutionary theory. We draw this knowledge together and present a new unifying conceptual framework that incorporates how ERPs have shaped the adaptive trajectories of organisms, the structure of ecosystems, and how they can be integrated into biodiversity management and conservation. Future research should focus on how inter- and intra-resource variation occurs in nature - with a particular focus on resource × environment × genotype interactions. This will likely reveal novel adaptive strategies, aid the development of new eco-evolutionary theory, and greatly improve our understanding of the form and function of organisms and ecosystems.
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Affiliation(s)
- Nathan J. Butterworth
- School of Biological Sciences, Monash University Wellington Road Clayton VIC 3800 Australia
- School of Life Sciences, University of Technology Sydney 15 Broadway Ultimo NSW 2007 Australia
| | - M. Eric Benbow
- Department of Entomology, Department of Osteopathic Medical Specialties, and Ecology, Evolution and Behavior Program Michigan State University 220 Trowbridge Rd East Lansing MI 48824 USA
| | - Philip S. Barton
- Future Regions Research Centre, Federation University University Drive, Mount Helen VIC 3350 Australia
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21
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Martinović T, Kohout P, López-Mondéjar R, Algora Gallardo C, Starke R, Tomšovský M, Baldrian P. Bacterial community in soil and tree roots of Picea abies shows little response to clearcutting. FEMS Microbiol Ecol 2022; 98:6754320. [PMID: 36208910 DOI: 10.1093/femsec/fiac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/15/2022] [Accepted: 10/06/2022] [Indexed: 01/21/2023] Open
Abstract
Clearcutting represents a standard management practice in temperate forests with dramatic consequences for the forest ecosystem. The removal of trees responsible for the bulk of primary production can result in a complex response of the soil microbiome. While studies have shown that tree root-symbiotic ectomycorrhizal fungi disappear from soil and decomposing fine roots of trees become a hotspot for fungal decomposition, the fate of the bacterial component of the soil microbiome following clearcutting is unclear. Here, we investigated the response of bacterial community composition for 2 years following clearcutting of a Picea abies stand in soil, rhizosphere and tree roots, by 16S rRNA amplicon sequencing. While in the first few months after clearcutting there was no significant response of bacterial community composition in the rhizosphere and soil, bacterial communities associated with tree roots underwent more profound changes over time. Acidobacteria were abundant in rhizosphere and soil, while Firmicutes were strongly represented in the roots. In addition, bacterial communities on decomposing roots were significantly different from those on pre-clearcut live roots. Compared with fungi, the response of bacterial communities to clearcutting was much less pronounced, indicating independent development of the two microbial domains.
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Affiliation(s)
- Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Praha 2, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Praha 2, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Camelia Algora Gallardo
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Robert Starke
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
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22
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Liu S, Trevathan-Tackett SM, Jiang Z, Cui L, Wu Y, Zhang X, Li J, Luo H, Huang X. Nutrient loading decreases blue carbon by mediating fungi activities within seagrass meadows. ENVIRONMENTAL RESEARCH 2022; 212:113280. [PMID: 35430277 DOI: 10.1016/j.envres.2022.113280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Coastal pollution, including nutrient loading, can negatively impact seagrass health and cover and may consequently alter soil organic carbon (SOC) accumulation and preservation. Key to understanding how eutrophication impacts SOC cycling in seagrass ecosystems is how nutrient loading changes the sources of carbon being deposited and how these changes in resources, both nutrients and carbon availability, influence soil microbiota community and activity. Currently, the direction and magnitude of nutrient loading impacts on seagrass SOC dynamics are poorly understood at a meadow scale, limiting our ability to reveal the driving mechanisms of SOC remineralisation. The purpose of this study was to assess the response of surface SOC and soil microbiomes to nutrient loading within tropical seagrass meadows. To achieve this, we quantified both total SOC and recalcitrant soil organic carbon (RSOC) concentrations and sources, in addition to the composition of bacterial and fungal communities and soil extracellular enzyme activities. We found that nutrient loading elevated SOC and RSOC content, mainly facilitated by enhanced algal growth. There was no nutrient effect on the soil prokaryotic communities, however, saprotrophic fungi groups (i.e. Trapeliales, Sordaridales, Saccharomycetales and Polyporales) and fungal activities were elevated under high nutrient conditions, including extracellular enzyme activities linked to seagrass-based cellulose and lignin decomposition. This relative increase in RSOC transformation may decrease the relative contribution of seagrass carbon to RSOC pools. Additionally, significantly different fungal communities were observed between adjacent T. hemprichii and E. acoroides areas, which coincided with elevated RSOC-decomposing enzyme activity in T. hemprichii meadows, even though the mixed seagrass meadow received allochthonous SOC and RSOC from the same sources. These results suggest that nutrient loading stimulated fungal activity and community shifts specific to the local seagrass species, thereby causing fine-scale (within-meadow) variability in SOC cycling in response to nutrient loading. This study provides evidence that fungal composition and activity, mediated by human activities (e.g. nutrient loading), can be an important influence on seagrass blue carbon accumulation and remineralisation.
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Affiliation(s)
- Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Stacey M Trevathan-Tackett
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, Victoria, 3125, Australia
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Lijun Cui
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jinlong Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongxue Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
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23
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Zhu X, Zhang Z, Wang Q, Peñuelas J, Sardans J, Lambers H, Li N, Liu Q, Yin H, Liu Z. More soil organic carbon is sequestered through the mycelium pathway than through the root pathway under nitrogen enrichment in an alpine forest. GLOBAL CHANGE BIOLOGY 2022; 28:4947-4961. [PMID: 35582981 DOI: 10.1111/gcb.16263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant roots and associated mycorrhizae exert a large influence on soil carbon (C) cycling. Yet, little was known whether and how roots and ectomycorrhizal (ECM) extraradical mycelia differentially contribute to soil organic C (SOC) accumulation in alpine forests under increasing nitrogen (N) deposition. Using ingrowth cores, the relative contributions of the root pathway (RP; i.e., roots and rhizosphere processes) and mycelium pathway (MP; i.e., extraradical mycelia and hyphosphere processes) to SOC accumulation were distinguished and quantified in an ECM-dominated forest receiving chronic N addition (25 kg N ha-1 year-1 ). Under the non-N addition, the RP facilitated SOC accumulation, although the MP reduced SOC accumulation. Nitrogen addition enhanced the positive effect of RP on SOC accumulation from +18.02 to +20.55 mg C g-1 but counteracted the negative effect of MP on SOC accumulation from -5.62 to -0.57 mg C g-1 , compared with the non-N addition. Compared with the non-N addition, the N-induced SOC accumulation was 1.62-2.21 and 3.23-4.74 mg C g-1 , in the RP and the MP, respectively. The greater contribution of MP to SOC accumulation was mainly attributed to the higher microbial C pump (MCP) efficacy (the proportion of increased microbial residual C to the increased SOC under N addition) in the MP (72.5%) relative to the RP (57%). The higher MCP efficacy in the MP was mainly associated with the higher fungal metabolic activity (i.e., the greater fungal biomass and N-acetyl glucosidase activity) and greater binding efficiency of fungal residual C to mineral surfaces than those of RP. Collectively, our findings highlight the indispensable role of mycelia and hyphosphere processes in the formation and accumulation of stable SOC in the context of increasing N deposition.
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Affiliation(s)
- Xiaomin Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ziliang Zhang
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Qitong Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CEAB-UAB, Cerdanyola del Valles, Catalonia, Spain
- CREAF, Cerdanyola del Valles, Catalonia, Spain
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CEAB-UAB, Cerdanyola del Valles, Catalonia, Spain
- CREAF, Cerdanyola del Valles, Catalonia, Spain
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Na Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Huajun Yin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhanfeng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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24
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High Variability of Fungal Communities Associated with the Functional Tissues and Rhizosphere Soil of Picea abies in the Southern Baltics. FORESTS 2022. [DOI: 10.3390/f13071103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Climate change, which leads to higher temperatures, droughts, and storms, is expected to have a strong effect on both health of forest trees and associated biodiversity. The aim of this study was to investigate the diversity and composition of fungal communities associated with the functional tissues and rhizosphere soil of healthy-looking Picea abies to better understand these fungal communities and their potential effect on tree health in the process of climate change. The study sites included 30 P. abies stands, where needles, shoots, roots, and the rhizosphere soil was sampled. DNA was isolated from individual samples, amplified using ITS2 rRNA as a marker and subjected to high-throughput sequencing. The sequence analysis showed the presence of 232,547 high-quality reads, which following clustering were found to represent 2701 non-singleton fungal OTUs. The highest absolute richness of fungal OTUs was in the soil (1895), then in the needles (1049) and shoots (1002), and the lowest was in the roots (641). The overall fungal community was composed of Ascomycota (58.3%), Basidiomycota (37.2%), Zygomycota (2.5%), Chytridiomycota (1.6%), and Glomeromycota (0.4%). The most common fungi based on sequence read abundance were Aspergillus pseudoglaucus (7.9%), Archaeorhizomyces sp. (3.6%), and Rhinocladiella sp. (2.0%). Pathogens were relatively rare, among which the most common were Phacidium lacerum (1.7%), Cyphellophora sessilis (1.4%), and Rhizosphaera kalkhoffii (1.4%). The results showed that the detected diversity of fungal OTUs was generally high, but their relative abundance varied greatly among different study sites, thereby highlighting the complexity of interactions among the host trees, fungi, and local environmental conditions.
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25
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Maillard F, Fernandez CW, Mundra S, Heckman KA, Kolka RK, Kauserud H, Kennedy PG. Warming drives a 'hummockification' of microbial communities associated with decomposing mycorrhizal fungal necromass in peatlands. THE NEW PHYTOLOGIST 2022; 234:2032-2043. [PMID: 34559896 DOI: 10.1111/nph.17755] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Dead fungal mycelium (necromass) represents a critical component of soil carbon (C) and nutrient cycles. Assessing how the microbial communities associated with decomposing fungal necromass change as global temperatures rise will help in determining how these belowground organic matter inputs contribute to ecosystem responses. In this study, we characterized the structure of bacterial and fungal communities associated with multiple types of decaying mycorrhizal fungal necromass incubated within mesh bags across a 9°C whole ecosystem temperature enhancement in a boreal peatland. We found major taxonomic and functional shifts in the microbial communities present on decaying mycorrhizal fungal necromass in response to warming. These changes were most pronounced in hollow microsites, which showed convergence towards the necromass-associated microbial communities present in unwarmed hummocks. We also observed a high colonization of ericoid mycorrhizal fungal necromass by fungi from the same genera as the necromass. These results indicate that microbial communities associated with mycorrhizal fungal necromass decomposition are likely to change significantly with future climate warming, which may have strong impacts on soil biogeochemical cycles in peatlands. Additionally, the high enrichment of congeneric fungal decomposers on ericoid mycorrhizal necromass may help to explain the increase in ericoid shrub dominance in warming peatlands.
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Affiliation(s)
- François Maillard
- Department of Plant & Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Christopher W Fernandez
- Department of Plant & Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
- Department of Forestry, Michigan State University, East Lansing, MI, 48824, USA
| | - Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, Oslo, NO-0316, Norway
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | | | - Randall K Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, MN, 55744, USA
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, Oslo, NO-0316, Norway
| | - Peter G Kennedy
- Department of Plant & Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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26
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Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. Best practices in metabarcoding of fungi: From experimental design to results. Mol Ecol 2022; 31:2769-2795. [PMID: 35395127 DOI: 10.1111/mec.16460] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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27
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See CR, Keller AB, Hobbie SE, Kennedy PG, Weber PK, Pett-Ridge J. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. GLOBAL CHANGE BIOLOGY 2022; 28:2527-2540. [PMID: 34989058 DOI: 10.1111/gcb.16073] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.
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Affiliation(s)
- Craig R See
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Adrienne B Keller
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter G Kennedy
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
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D'Alò F, Baldrian P, Odriozola I, Morais D, Větrovský T, Zucconi L, Ripa C, Cannone N, Malfasi F, Onofri S. Composition and functioning of the soil microbiome in the highest altitudes of the Italian Alps and potential effects of climate change. FEMS Microbiol Ecol 2022; 98:6541846. [PMID: 35238906 DOI: 10.1093/femsec/fiac025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/04/2022] [Accepted: 03/01/2022] [Indexed: 11/14/2022] Open
Abstract
As the European Alps are experiencing a strong climate warming; this study analyzed the soil microbiome at different altitudes and among different vegetation types at the Stelvio Pass (Italian Alps), aiming to i) characterize the composition and functional potential of the microbiome of soils and their gene expression during the peak vegetative stage; ii) explore the potential short-term (using open top chambers) and long-term (space-for-time substitutions) effects of increasing temperature on the alpine soil microbiome. We found that the functional potential of the soil microbiome and its expression differed among vegetation types. Microbial α-diversity increased along the altitudinal gradient. At lower altitude, shrubland had the highest proportion of fungi, which was correlated with higher amounts of CAZymes, specific for degrading fungal biomass and recalcitrant plant biopolymers. Subalpine upward vegetation shift could lead a possible loss of species of alpine soils. Shrub encroachment may accelerate higher recalcitrant C decomposition and reduce total ecosystem C storage, increasing the efflux of CO2 to the atmosphere with a positive feedback to warming. Five years of warming had no effect on the composition and functioning of microbial communities, indicating that longer-term warming experiments are needed to investigate the effects of temperature increases on the soil microbiome.
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Affiliation(s)
- Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Caterina Ripa
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Nicoletta Cannone
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Francesco Malfasi
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
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29
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Lebreton A, Zeng Q, Miyauchi S, Kohler A, Dai YC, Martin FM. Evolution of the Mode of Nutrition in Symbiotic and Saprotrophic Fungi in Forest Ecosystems. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012021-114902] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we highlight the main insights that have been gathered from recent developments using large-scale genomics of fungal saprotrophs and symbiotrophs (including ectomycorrhizal and orchid and ericoid mycorrhizal fungi) inhabiting forest ecosystems. After assessing the goals and motivations underlying our approach, we explore our current understanding of the limits and future potential of using genomics to understand the ecological roles of these forest fungi. Comparative genomics unraveled the molecular machineries involved in lignocellulose decomposition in wood decayers, soil and litter saprotrophs, and mycorrhizal symbionts. They also showed that transitions from saprotrophy to mutualism entailed widespread losses of lignocellulose-degrading enzymes; diversification of novel, lineage-specific symbiosis-induced genes; and convergent evolution of genetic innovations that facilitate the accommodationof mutualistic symbionts within their plant hosts. We also identify the major questions that remain unanswered and propose new avenues of genome-based research to understand the role of soil fungi in sustainable forest ecosystems.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Qingchao Zeng
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Köln, Germany, D-50829
| | - Annegret Kohler
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Francis M. Martin
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
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30
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Human ZR, Roets F, Crous CJ, Wingfield MJ, de Beer ZW, Venter SN. Fire impacts bacterial composition in Protea repens (Proteaceae) infructescences. FEMS Microbiol Lett 2021; 368:6385756. [PMID: 34626182 DOI: 10.1093/femsle/fnab132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/07/2021] [Indexed: 01/04/2023] Open
Abstract
The diverse bacterial communities in and around plants provide important benefits, such as protection against pathogens and cycling of essential minerals through decomposition of moribund plant biomass. Biodiverse fynbos landscapes generally have limited deadwood habitats due to the absence of large trees and frequent fire. In this study, we determined the effect of a fire disturbance on the bacterial communities in a fynbos landscape dominated by the shrub Protea repens using 16S ribosomal RNA amplicon sequencing. The bacterial community composition in newly formed fruiting structures (infructescences) and soil at a recently burnt site was different from that in an unburnt site. Bacteria inhabiting P. repens infructescences were similar to well-known taxa from decomposing wood and litter. This suggests a putative role for these aboveground plant structures as reservoirs for postfire decomposer bacteria. The results imply that inordinately frequent fires, which are commonplace in the Anthropocene, are a significant disturbance to bacterial communities and could affect the diversity of potentially important microbes from these landscapes.
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Affiliation(s)
- Zander R Human
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Casparus J Crous
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
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31
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Khokon AM, Schneider D, Daniel R, Polle A. Soil Layers Matter: Vertical Stratification of Root-Associated Fungal Assemblages in Temperate Forests Reveals Differences in Habitat Colonization. Microorganisms 2021; 9:2131. [PMID: 34683452 PMCID: PMC8537680 DOI: 10.3390/microorganisms9102131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Ectomycorrhizal and saprotrophic fungi play pivotal roles in ecosystem functioning. Here, we studied the vertical differentiation of root-associated fungi (RAF) in temperate forests. We analysed RAF assemblages in the organic and mineral soil from 150 experimental forest plots across three biogeographic regions spanning a distance of about 800 km. Saprotrophic RAF showed the highest richness in organic and symbiotrophic RAF in mineral soil. Symbiotrophic RAF exhibited higher relative abundances than saprotrophic fungi in both soil layers. Beta-diversity of RAF was mainly due to turnover between organic and mineral soil and showed regional differences for symbiotrophic and saprotrophic fungi. Regional differences were also found for different phylogenetic levels, i.e., fungal orders and indicator species in the organic and mineral soil, supporting that habitat conditions strongly influence differentiation of RAF assemblages. Important exceptions were fungal orders that occurred irrespective of the habitat conditions in distinct soil layers across the biogeographic gradient: Russulales and Cantharellales (ectomycorrhizal fungi) were enriched in RAF assemblages in mineral soil, whereas saprotrophic Polyporales and Sordariales and ectomycorrhizal Boletales were enriched in RAF assemblages in the organic layer. These results underpin a phylogenetic signature for niche partitioning at the rank of fungal orders and suggest that RAF assembly entails two strategies encompassing flexible and territorial habitat colonization by different fungal taxa.
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Affiliation(s)
- Anis Mahmud Khokon
- Department of Forest Botany and Tree Physiology, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.S.); (R.D.)
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.S.); (R.D.)
| | - Andrea Polle
- Department of Forest Botany and Tree Physiology, University of Göttingen, 37077 Göttingen, Germany;
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McKee LS, La Rosa SL, Westereng B, Eijsink VG, Pope PB, Larsbrink J. Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:559-581. [PMID: 34036727 DOI: 10.1111/1758-2229.12980] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.
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Affiliation(s)
- Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
| | | | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
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33
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Ylänne H, Madsen RL, Castaño C, Metcalfe DB, Clemmensen KE. Reindeer control over subarctic treeline alters soil fungal communities with potential consequences for soil carbon storage. GLOBAL CHANGE BIOLOGY 2021; 27:4254-4268. [PMID: 34028938 DOI: 10.1111/gcb.15722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/19/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
The climate-driven encroachment of shrubs into the Arctic is accompanied by shifts in soil fungal communities that could contribute to a net release of carbon from tundra soils. At the same time, arctic grazers are known to prevent the establishment of deciduous shrubs and, under certain conditions, promote the dominance of evergreen shrubs. As these different vegetation types associate with contrasting fungal communities, the belowground consequences of climate change could vary among grazing regimes. Yet, at present, the impact of grazing on soil fungal communities and their links to soil carbon have remained speculative. Here we tested how soil fungal community composition, diversity and function depend on tree vicinity and long-term reindeer grazing regime and assessed how the fungal communities relate to organic soil carbon stocks in an alpine treeline ecotone in Northern Scandinavia. We determined soil carbon stocks and characterized soil fungal communities directly underneath and >3 m away from mountain birches (Betula pubescens ssp. czerepanovii) in two adjacent 55-year-old grazing regimes with or without summer grazing by reindeer (Rangifer tarandus). We show that the area exposed to year-round grazing dominated by evergreen dwarf shrubs had higher soil C:N ratio, higher fungal abundance and lower fungal diversity compared with the area with only winter grazing and higher abundance of mountain birch. Although soil carbon stocks did not differ between the grazing regimes, stocks were positively associated with root-associated ascomycetes, typical to the year-round grazing regime, and negatively associated with free-living saprotrophs, typical to the winter grazing regime. These findings suggest that when grazers promote dominance of evergreen dwarf shrubs, they induce shifts in soil fungal communities that increase soil carbon sequestration in the long term. Thus, to predict climate-driven changes in soil carbon, grazer-induced shifts in vegetation and soil fungal communities need to be accounted for.
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Affiliation(s)
- Henni Ylänne
- Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | | | - Carles Castaño
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Daniel B Metcalfe
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
- Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden
| | - Karina E Clemmensen
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Exploration of social spreading reveals behavior is prevalent among Pedobacter and P. fluorescens isolates, and shows variations in induction of phenotype. Appl Environ Microbiol 2021; 87:e0134421. [PMID: 34288708 DOI: 10.1128/aem.01344-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Within soil, bacteria are found in multi-species communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is critical for investigation of community-level functions. We previously showed that co-cultured Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading (ISS) on a hard agar surface, a behavior which required close contact and depended on the nutritional environment. Here, we investigate whether social spreading is widespread among P. fluorescens and Pedobacter isolates, and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and Pedobacter sp. V48, but is a prevalent behavior found in one clade in the P. fluorescens group and two clades in the Pedobacter genus. We show that the interaction with certain Pedobacter isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As with ISS by Pf0-1+V48, motility of interacting pairs is influenced by the environment, with no spreading behaviors (or induction of motility) observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs the high salt influence was variable. The prevalence of motility phenotypes observed here and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities. Importance Interspecies social spreading (ISS) is an emergent behavior observed when P. fluorescens Pf0-1 and Pedobacter sp. V48 interact, during which both species move together across a surface. Importantly, this environment does not permit movement of either individual species. This group behavior suggests that communities of microbes can function in ways not predictable by knowledge of the individual members. Here we have asked whether ISS is widespread and thus potentially of importance in soil microbial communities. The significance of this research is the demonstration that surface spreading behaviors are not unique to the Pf0-1-V48 interaction, but rather is a more widespread phenomenon observed among members of distinct clades of both P. fluorescens and Pedobacter isolates. Further, we identify differences in mechanism of signaling and nutritional requirements for ISS. Emergent traits resulting from bacterial interactions are widespread and their characterization is necessary for a complete understanding of microbial community function.
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Mayer M, Rewald B, Matthews B, Sanden H, Rosinger C, Katzensteiner K, Gorfer M, Berger H, Tallian C, Berger TW, Godbold DL. Soil fertility relates to fungal-mediated decomposition and organic matter turnover in a temperate mountain forest. THE NEW PHYTOLOGIST 2021; 231:777-790. [PMID: 34013982 PMCID: PMC7611052 DOI: 10.1111/nph.17421] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Fungi are known to exert a significant influence over soil organic matter (SOM) turnover, however understanding of the effects of fungal community structure on SOM dynamics and its consequences for ecosystem fertility is fragmentary. Here we studied soil fungal guilds and SOM decomposition processes along a fertility gradient in a temperate mountain beech forest. High-throughput sequencing was used to investigate fungal communities. Carbon and nitrogen stocks, enzymatic activity and microbial respiration were measured. While ectomycorrhizal fungal abundance was not related to fertility, saprotrophic ascomycetes showed higher relative abundances under more fertile conditions. The activity of oxidising enzymes and respiration rates in mineral soil were related positively to fertility and saprotrophic fungi. In addition, organic layer carbon and nitrogen stocks were lower on the more fertile plots, although tree biomass and litter input were higher. Together, the results indicated a faster SOM turnover at the fertile end of the gradient. We suggest that there is a positive feedback mechanism between SOM turnover and fertility that is mediated by soil fungi to a significant extent. By underlining the importance of fungi for soil fertility and plant growth, these findings furthermore emphasise the dependency of carbon cycling on fungal communities below ground.
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Affiliation(s)
- Mathias Mayer
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, Birmensdorf 8903, Switzerland
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
| | - Boris Rewald
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
| | - Bradley Matthews
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
- Environment Agency Austria, Spittelauer Lände 5, Vienna 1090, Austria
| | - Hans Sanden
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
| | - Christoph Rosinger
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zülpicher Straße 47b, Cologne 50674, Germany
| | - Klaus Katzensteiner
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
| | - Markus Gorfer
- Bioresources Unit, Center for Health & Bioresources, Austrian Institute of Technology GmbH (AIT), Konrad-Lorenz-Straße 24, Tulln 3430, Austria
| | - Harald Berger
- Symbiocyte, Vorgartenstraße 145, Vienna 1020, Austria
| | - Claudia Tallian
- Bioresources Unit, Center for Health & Bioresources, Austrian Institute of Technology GmbH (AIT), Konrad-Lorenz-Straße 24, Tulln 3430, Austria
| | - Torsten W. Berger
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
| | - Douglas L. Godbold
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan Straße 82, Vienna 1190, Austria
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Navarro-Noya YE, Montoya-Ciriaco N, Muñoz-Arenas LC, Hereira-Pacheco S, Estrada-Torres A, Dendooven L. Conversion of a High-Altitude Temperate Forest for Agriculture Reduced Alpha and Beta Diversity of the Soil Fungal Communities as Revealed by a Metabarcoding Analysis. Front Microbiol 2021; 12:667566. [PMID: 34234759 PMCID: PMC8255801 DOI: 10.3389/fmicb.2021.667566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/03/2021] [Indexed: 11/13/2022] Open
Abstract
Land-use change is one of the most important drivers of change in biodiversity. Deforestation for grazing or agriculture has transformed large areas of temperate forest in the central highlands of Mexico, but its impact on soil fungal communities is still largely unknown. In this study, we determined how deforestation of a high-altitude temperate forest for cultivation of maize (Zea mays L.) or husbandry altered the taxonomic, phylogenetic, functional, and beta diversity of soil fungal communities using a 18S rRNA metabarcoding analysis. The true taxonomic and phylogenetic diversity at order q = 1, i.e., considering frequent operational taxonomic units, decreased significantly in the arable, but not in the pasture soil. The beta diversity decreased in the order forest > pasture > arable soil. The ordination analysis showed a clear effect of intensity of land-use as the forest soil clustered closer to pasture than to the arable soil. The most abundant fungal phyla in the studied soils were Ascomycota, Basidiomycota, and Mucoromycota. Deforestation more than halved the relative abundance of Basidiomycota; mostly Agaricomycetes, such as Lactarius and Inocybe. The relative abundance of Glomeromycota decreased in the order pasture > forest > arable soil. Symbiotrophs, especially ectomycorrhizal fungi, were negatively affected by deforestation while pathotrophs, especially animal pathogens, were enriched in the pasture and arable soil. Ectomycorrhizal fungi were more abundant in the forest soil as they are usually associated with conifers. Arbuscular mycorrhizal fungi were more abundant in the pasture than in the arable soil as the higher plant diversity provided more suitable hosts. Changes in fungal communities resulting from land-use change can provide important information for soil management and the assessment of the environmental impact of deforestation and conversion of vulnerable ecosystems such as high-altitude temperate forests.
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Affiliation(s)
- Yendi E Navarro-Noya
- Laboratory of Biotic Interactions, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Nina Montoya-Ciriaco
- Doctorado en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Ligia C Muñoz-Arenas
- Doctorado en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico.,Facultad de Ingeniería Ambiental, UPAEP, Puebla, Mexico
| | | | - Arturo Estrada-Torres
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, CINVESTAV-IPN, Ciudad de México, Mexico
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Tláskal V, Baldrian P. Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition. Front Microbiol 2021; 12:685303. [PMID: 34220772 PMCID: PMC8247643 DOI: 10.3389/fmicb.2021.685303] [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: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 01/01/2023] Open
Abstract
Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.
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Affiliation(s)
- Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
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Similarities and Differences among Soil Fungal Assemblages in Managed Forests and Formerly Managed Forest Reserves. FORESTS 2021. [DOI: 10.3390/f12030353] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Unlike the numerous works concerning the effect of management on the forest mycobiome, only a few studies have addressed how fungi from different trophic groups recover from natural and anthropogenic disturbances and develop structural features typical of unmanaged old-growth forests. Our objective is to compare the soil fungal assemblages represented by different functional/trophic groups in protected and managed stands located in European mixed forests dominated by Scots pine. Fungal communities were analyzed using high-throughput Illumina MiSeq sequencing of fungal internal transcribed spacer 1 (ITS1) amplicons. Formerly managed forest reserves (established around 50 years ago) and forests under standard forest management appeared to be similar in terms of total and mean species richness of all fungal operational taxonomic units (OTUs), as well as OTUs assigned to different functional trophic groups. Among the 599 recorded OTUs, 497 (83%) were shared between both management types, whereas 9.5% of taxa were unique to forest reserves and 7.5% were unique to managed stands. Ascomycota and Basidiomycota were the predominant phyla, comprising 88% of all identified fungi. The main functional components of soil fungal assemblages consisted of saprotrophic (42% fungal OTUs; 27% reads) and ectomycorrhizal fungi (16%; 47%). Two-way analysis of similarities (ANOSIM) revealed that both site and management strategy influenced the species composition of soil fungal communities, with site being a primary effect for saprotrophic and ectomycorrhizal fungi. Volume of coarse and very fine woody debris and soil pH significantly influenced the ectomycorrhizal fungal community, whereas saprotrophic fungi were influenced primarily by volume of coarse woody debris and soil nitrate concentration. Among the identified fungal OTUs, 18 red-listed fungal species were identified from both forest reserves and managed forests, comprising two ECM fungi and four saprotrophs from the category of endangered species. Our results suggest that the transformation of fungal diversity after cessation of forest management is rather slow, and that both forest reserves and managed forests help uphold fungal diversity.
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Description of desferrioxamine-producing bacterium Chitinophaga agrisoli sp. nov., isolated from soil. Antonie Van Leeuwenhoek 2021; 114:741-750. [PMID: 33689054 DOI: 10.1007/s10482-021-01554-2] [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: 01/30/2021] [Accepted: 02/25/2021] [Indexed: 10/21/2022]
Abstract
A Gram-stain-negative, non-motile, yellow-pigmented and non-spore forming rod-shaped bacterium, designated strain BN140078T, was isolated from farmland soil, Chungbuk, Republic of Korea. It was able to grow aerobically at 10-40 °C (optimum 28 °C), pH 5.5-7.5 (optimum pH 7.0) and with 0-2.0% (w/v) NaCl concentration (optimum 1.0%) on Reasoner's 2A (R2A) agar medium. Comparative 16S rRNA gene sequence analysis showed that the strain BN140078T had 96.9%, 96.5% and 96.1% 16S rRNA gene similarities with Chitinophaga ginsengihumi KACC 17604T, Chitinophaga rupis KACC 14521T and Chitinophaga japonensis KACC 12057T, respectively. The predominant respiratory quinone was menaquinone MK-7 and the major fatty acids (≥ 5%) were C16:1 ω5c, iso-C15:0, iso-C17:0 3-OH and Summed Feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids were composed of phosphatidylethanolamine, four unidentified amino lipids and six unidentified lipids. The genomic DNA G+C content was 49.5 mol%. The genome of strain BN140078T comprises a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide products. The polyphasic taxonomic study clearly distinguished this strain from its closest phylogenetic neighbors. Thus, we propose that the BN140078T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga agrisoli sp. nov. was proposed. The type strain is BN140078T (=KCTC 62555T = CCTCC AB 2018162T).
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Maillard F, Kennedy PG, Adamczyk B, Heinonsalo J, Buée M. Root presence modifies the long-term decomposition dynamics of fungal necromass and the associated microbial communities in a boreal forest. Mol Ecol 2021; 30:1921-1935. [PMID: 33544953 DOI: 10.1111/mec.15828] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/01/2023]
Abstract
Recent studies have highlighted that dead fungal mycelium represents an important fraction of soil carbon (C) and nitrogen (N) inputs and stocks. Consequently, identifying the microbial communities and the ecological factors that govern the decomposition of fungal necromass will provide critical insight into how fungal organic matter (OM) affects forest soil C and nutrient cycles. Here, we examined the microbial communities colonising fungal necromass during a multiyear decomposition experiment in a boreal forest, which included incubation bags with different mesh sizes to manipulate both plant root and microbial decomposer group access. Necromass-associated bacterial and fungal communities were taxonomically and functionally rich throughout the 30 months of incubation, with increasing abundances of oligotrophic bacteria and root-associated fungi (i.e., ectomycorrhizal, ericoid mycorrhizal and endophytic fungi) in the late stages of decomposition in the mesh bags to which they had access. Necromass-associated β-glucosidase activity was highest at 6 months, while leucine aminopeptidase peptidase was highest at 18 months. Based on an asymptotic decomposition model, root presence was associated with an initial faster rate of fungal necromass decomposition, but resulted in higher amounts of fungal necromass retained at later sampling times. Collectively, these results indicate that microbial community composition and enzyme activities on decomposing fungal necromass remain dynamic years after initial input, and that roots and their associated fungal symbionts result in the slowing of microbial necromass turnover with time.
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Affiliation(s)
- François Maillard
- INRAE, UMR IAM, Université de Lorraine, Nancy, France.,Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | | | - Jussi Heinonsalo
- Department of Microbiology, University of Helsinki, Helsinki, Finland.,Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, Finland.,Finnish Meteorological Institute, Helsinki, Finland
| | - Marc Buée
- INRAE, UMR IAM, Université de Lorraine, Nancy, France
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Netherway T, Bengtsson J, Krab EJ, Bahram M. Biotic interactions with mycorrhizal systems as extended nutrient acquisition strategies shaping forest soil communities and functions. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood’s properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.
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Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats. PLoS One 2020; 15:e0244682. [PMID: 33378355 PMCID: PMC7773206 DOI: 10.1371/journal.pone.0244682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.
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See CR, Fernandez CW, Conley AM, DeLancey LC, Heckman KA, Kennedy PG, Hobbie SE. Distinct carbon fractions drive a generalisable two‐pool model of fungal necromass decomposition. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Craig R. See
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Chris W. Fernandez
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Anna M. Conley
- Department of Chemistry Carleton College Northfield MN USA
| | - Lang C. DeLancey
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | | | - Peter G. Kennedy
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Sarah E. Hobbie
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
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Castaño C, Camarero JJ, Zas R, Sampedro L, Bonet JA, Alday JG, Oliva J. Insect defoliation is linked to a decrease in soil ectomycorrhizal biomass and shifts in needle endophytic communities. TREE PHYSIOLOGY 2020; 40:1712-1725. [PMID: 32785638 DOI: 10.1093/treephys/tpaa104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Insect outbreaks of increasing frequency and severity in forests are predicted due to climate change. Insect herbivory is known to promote physiological changes in forest trees. However, little is known about whether these plant phenotypic adjustments have cascading effects on tree microbial symbionts such as fungi in roots and foliage. We studied the impact of defoliation by the pine processionary moth in two infested Pinus nigra forests through a multilevel sampling of defoliated and non-defoliated trees. We measured tree growth, nutritional status and carbon allocation to chemical defenses. Simultaneously, we analysed the putative impact of defoliation on the needle endophytes and on the soil fungal communities. Higher concentrations of chemical defenses were found in defoliated trees, likely as a response to defoliation; however, no differences in non-structural carbohydrate reserves were found. In parallel to the reductions in tree growth and changes in chemical defenses, we observed shifts in the composition of needle endophytic and soil fungal communities in defoliated trees. Defoliated trees consistently corresponded with a lower biomass of ectomycorrhizal fungi in both sites, and a higher alpha diversity and greater relative abundance of belowground saprotrophs and pathogens. However, ectomycorrhizal alpha diversity was similar between non-defoliated and defoliated trees. Specific needle endophytes in old needles were strongly associated with non-defoliated trees. The potential role of these endophytic fungi in pine resistance should be further investigated. Our study suggests that lower biomass of ectomycorrhizal fungi in defoliated trees might slow down tree recovery since fungal shifts might affect tree-mycorrhizal feedbacks and can potentially influence carbon and nitrogen cycling in forest soils.
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Affiliation(s)
- Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - J Julio Camarero
- Instituto Pirenaico de Ecología (IPE-CSIC), 50192 Zaragoza, Spain
| | - Rafael Zas
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo 28, 36080 Pontevedra, Spain
| | - Luis Sampedro
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo 28, 36080 Pontevedra, Spain
| | - José Antonio Bonet
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
| | - Josu G Alday
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
| | - Jonàs Oliva
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
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46
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Kim D, Chae N, Kim M, Nam S, Kim E, Lee H. Soil water content as a critical factor for stable bacterial community structure and degradative activity in maritime Antarctic soil. J Microbiol 2020; 58:1010-1017. [PMID: 33263894 DOI: 10.1007/s12275-020-0490-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 12/26/2022]
Abstract
Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature (Ts) and volumetric soil water content (SWC) in maritime tundra. Under an 8°C soil warming scenario, two customized microcosm systems with maritime Antarctic soils were incubated to investigate the differential influence of SWC on the bacterial community and degradation activity of humic substances (HS), the largest constituent of soil organic carbon and a key component of the terrestrial ecosystem. When the microcosm soil (KS1-4Feb) was incubated for 90 days (T = 90) at a constant SWC of ~32%, the initial HS content (167.0 mg/g of dried soil) decreased to 156.0 mg (approximately 6.6% loss, p < 0.05). However, when another microcosm soil (KS1-4Apr) was incubated with SWCs that gradually decreased from 37% to 9% for T = 90, HS degradation was undetected. The low HS degradative activity persisted, even after the SWC was restored to 30% with water supply for an additional T = 30. Overall bacterial community structure remained relatively stable at a constant SWC setting (KS1-4Feb). In contrast, we saw marked shifts in the bacterial community structure with the changing SWC regimen (KS1-4Apr), suggesting that the soil bacterial communities are vulnerable to drying and re-wetting conditions. These microcosm experiments provide new information regarding the effects of constant SWC and higher Ts on bacterial communities for HS degradation in maritime Antarctic tundra soil.
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Affiliation(s)
- Dockyu Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| | - Namyi Chae
- Institutes of Life Sciences and Natural Resources, Korea University, Seoul, 02841, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sungjin Nam
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eungbin Kim
- Department of Systems Biology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyoungseok Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
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Collins CG, Spasojevic MJ, Alados CL, Aronson EL, Benavides JC, Cannone N, Caviezel C, Grau O, Guo H, Kudo G, Kuhn NJ, Müllerová J, Phillips ML, Pombubpa N, Reverchon F, Shulman HB, Stajich JE, Stokes A, Weber SE, Diez JM. Belowground impacts of alpine woody encroachment are determined by plant traits, local climate, and soil conditions. GLOBAL CHANGE BIOLOGY 2020; 26:7112-7127. [PMID: 32902066 DOI: 10.1111/gcb.15340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 08/26/2020] [Indexed: 05/17/2023]
Abstract
Global climate and land use change are causing woody plant encroachment in arctic, alpine, and arid/semi-arid ecosystems around the world, yet our understanding of the belowground impacts of this phenomenon is limited. We conducted a globally distributed field study of 13 alpine sites across four continents undergoing woody plant encroachment and sampled soils from both woody encroached and nearby herbaceous plant community types. We found that woody plant encroachment influenced soil microbial richness and community composition across sites based on multiple factors including woody plant traits, site level climate, and abiotic soil conditions. In particular, root symbiont type was a key determinant of belowground effects, as Nitrogen-fixing woody plants had higher soil fungal richness, while Ecto/Ericoid mycorrhizal species had higher soil bacterial richness and symbiont types had distinct soil microbial community composition. Woody plant leaf traits indirectly influenced soil microbes through their impact on soil abiotic conditions, primarily soil pH and C:N ratios. Finally, site-level climate affected the overall magnitude and direction of woody plant influence, as soil fungal and bacterial richness were either higher or lower in woody encroached versus herbaceous soils depending on mean annual temperature and precipitation. All together, these results document global impacts of woody plant encroachment on soil microbial communities, but highlight that multiple biotic and abiotic pathways must be considered to scale up globally from site- and species-level patterns. Considering both the aboveground and belowground effects of woody encroachment will be critical to predict future changes in alpine ecosystem structure and function and subsequent feedbacks to the global climate system.
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Affiliation(s)
- Courtney G Collins
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Marko J Spasojevic
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Emma L Aronson
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | | | | | - Chatrina Caviezel
- Department of Environmental Sciences, Physical Geography and Environmental Change, University of Basel, Basel, Switzerland
| | - Oriol Grau
- Global Ecology Unit, Campus de Bellaterra (UAB), CREAF, Barcelona, Spain
- Cirad, UMR EcoFoG (AgroParisTech, CNRS, Inra, Univ Antilles, Univ Guyane), Kourou, French Guiana
| | - Hui Guo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Gaku Kudo
- Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Nikolas J Kuhn
- Department of Environmental Sciences, Physical Geography and Environmental Change, University of Basel, Basel, Switzerland
| | - Jana Müllerová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Michala L Phillips
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- US Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología (INECOL), Pátzcuaro, Mexico
| | - Hannah B Shulman
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Alexia Stokes
- University Montpellier, AMAP, INRAE, CIRAD, IRD, CNRS, Montpellier, France
| | - Sören E Weber
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
- Institut für Evolutionsbiologie und Umweltwissenschaften, Universität Zürich, Zürich, Switzerland
| | - Jeffrey M Diez
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
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Albright MBN, Johansen R, Thompson J, Lopez D, Gallegos-Graves LV, Kroeger ME, Runde A, Mueller RC, Washburne A, Munsky B, Yoshida T, Dunbar J. Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition. Front Microbiol 2020; 11:542220. [PMID: 33240225 PMCID: PMC7677502 DOI: 10.3389/fmicb.2020.542220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
Discovering widespread microbial processes that drive unexpected variation in carbon cycling may improve modeling and management of soil carbon (Prescott, 2010; Wieder et al., 2015a, 2018). A first step is to identify community features linked to carbon cycle variation. We addressed this challenge using an epidemiological approach with 206 soil communities decomposing Ponderosa pine litter in 618 microcosms. Carbon flow from litter decomposition was measured over a 6-week incubation. Cumulative CO2 from microbial respiration varied two-fold among microcosms and dissolved organic carbon (DOC) from litter decomposition varied five-fold, demonstrating large functional variation despite constant environmental conditions where strong selection is expected. To investigate microbial features driving DOC concentration, two microbial community cohorts were delineated as "high" and "low" DOC. For each cohort, communities from the original soils and from the final microcosm communities after the 6-week incubation with litter were taxonomically profiled. A logistic model including total biomass, fungal richness, and bacterial richness measured in the original soils or in the final microcosm communities predicted the DOC cohort with 72 (P < 0.05) and 80 (P < 0.001) percent accuracy, respectively. The strongest predictors of the DOC cohort were biomass and either fungal richness (in the original soils) or bacterial richness (in the final microcosm communities). Successful forecasting of functional patterns after lengthy community succession in a new environment reveals strong historical contingencies. Forecasting future community function is a key advance beyond correlation of functional variance with end-state community features. The importance of taxon richness-the same feature linked to carbon fate in gut microbiome studies-underscores the need for increased understanding of biotic mechanisms that can shape richness in microbial communities independent of physicochemical conditions.
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Affiliation(s)
| | - Renee Johansen
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Deanna Lopez
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Marie E. Kroeger
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andreas Runde
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Rebecca C. Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Alex Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Thomas Yoshida
- Chemical Diagnostics and Engineering, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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Park KH, Oh SY, Yoo S, Fong JJ, Kim CS, Jo JW, Lim YW. Influence of Season and Soil Properties on Fungal Communities of Neighboring Climax Forests ( Carpinus cordata and Fraxinus rhynchophylla). Front Microbiol 2020; 11:572706. [PMID: 33193174 PMCID: PMC7655983 DOI: 10.3389/fmicb.2020.572706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 11/13/2022] Open
Abstract
Trees in forest ecosystems constantly interact with the soil fungal community, and this interaction plays a key role in nutrient cycling. The diversity of soil fungal communities is affected by both environmental factors and host tree species. We investigated the influence of both of these factors by examining the total fungal communities in the rhizospheric soil of climax tree species that have similar ecological roles (Carpinus cordata, an ectomycorrhizal [ECM] tree, and Fraxinus rhynchophylla, an arbuscular mycorrhizal [AM] tree) in temperate forests with continental climates of Mt. Jeombong, South Korea. Fungal communities were assessed by Illumina-MiSeq sequencing the internal transcribed spacer (ITS) region of environmental DNA, and comparing their environmental factors (season and soil properties). We found that soil fungi of the two forest types differed in terms of community structure and ecological guild composition. The total fungal community composition changed significantly with seasons and soil properties in the F. rhynchophylla forest, but not in the C. cordata forest. However, potassium and carbon were significantly correlated with fungal diversity in both forests, and a positive correlation was found only between symbiotrophs of C. cordata and the carbon to nitrogen (C/N) ratio. Thus, the effects of environmental factors on soil fungal communities depended on the host trees, but some factors were common in both forests. Our results indicate that individual tree species should be considered when anticipating how the fungal communities will respond to environmental change.
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Affiliation(s)
- Ki Hyeong Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, South Korea
| | - Shinnam Yoo
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | | | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Jong Won Jo
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
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Štursová M, Kohout P, Human ZR, Baldrian P. Production of Fungal Mycelia in a Temperate Coniferous Forest Shows Distinct Seasonal Patterns. J Fungi (Basel) 2020; 6:E190. [PMID: 32993121 PMCID: PMC7712845 DOI: 10.3390/jof6040190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
In temperate forests, climate seasonality restricts the photosynthetic activity of primary producers to the warm season from spring to autumn, while the cold season with temperatures below the freezing point represents a period of strongly reduced plant activity. Although soil microorganisms are active all-year-round, their expressions show seasonal patterns. This is especially visible on the ectomycorrhizal fungi, the most abundant guild of fungi in coniferous forests. We quantified the production of fungal mycelia using ingrowth sandbags in the organic layer of soil in temperate coniferous forest and analysed the composition of fungal communities in four consecutive seasons. We show that fungal biomass production is as low as 0.029 µg g-1 of sand in December-March, while it reaches 0.122 µg g-1 in June-September. The majority of fungi show distinct patterns of seasonal mycelial production, with most ectomycorrhizal fungi colonising ingrowth bags in the spring or summer, while the autumn and winter colonisation was mostly due to moulds. Our results indicate that fungal taxa differ in their seasonal patterns of mycelial production. Although fungal biomass turnover appears all-year-round, its rates are much faster in the period of plant activity than in the cold season.
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Affiliation(s)
- Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (P.K.); (Z.R.H.)
| | | | | | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (P.K.); (Z.R.H.)
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