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Martos I, Domínguez-Núñez JA. Soil Fungal Pathogens in Pinus pinaster Mature Reforestation: Silvicultural Treatments Effects. Pathogens 2024; 13:637. [PMID: 39204238 PMCID: PMC11356966 DOI: 10.3390/pathogens13080637] [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: 05/17/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
Soil fungal communities play a key role in multiple functions and ecosystem services within forest ecosystems. Today, forest ecosystems are subject to multiple environmental and anthropogenic disturbances (e.g., fire or forest management) that mainly lead to changes in vegetation as well as in plant-soil interactions. Soil pathogens play an important role in controlling plant diversity, ecosystem functions, and human and animal health. In this work we analyzed the response of soil plant pathogenic fungi to forest management in a Pinus pinaster reforestation. We started from an experimental design, in which forest thinning and gap cutting treatments were applied at different intensities and sizes, respectively. The fungal communities of plant pathogens in spring were described, and the effect of the silvicultural treatments was evaluated 5 years after their application, as were the possible relationships between soil plant pathogenic fungal communities and other environmental factors. Only a strong low thinning treatment (35% basal area) was able to generate homogeneous changes in soil pathogenic diversity. In the gaps, only the central position showed significant changes in the soil plant pathogenic fungi community.
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Affiliation(s)
| | - Jose Alfonso Domínguez-Núñez
- Department of Forest and Environmental Engineering and Management, Universidad Politécnica de Madrid, C/Jose Antonio Novais, 10, 28040 Madrid, Spain
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2
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Harder CB, Miyauchi S, Virágh M, Kuo A, Thoen E, Andreopoulos B, Lu D, Skrede I, Drula E, Henrissat B, Morin E, Kohler A, Barry K, LaButti K, Salamov A, Lipzen A, Merényi Z, Hegedüs B, Baldrian P, Stursova M, Weitz H, Taylor A, Koriabine M, Savage E, Grigoriev IV, Nagy LG, Martin F, Kauserud H. Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. CELL GENOMICS 2024; 4:100586. [PMID: 38942024 PMCID: PMC11293592 DOI: 10.1016/j.xgen.2024.100586] [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: 07/07/2023] [Revised: 01/28/2024] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway; Department of Biology, Microbial Ecology Group, Biology Department, Lund University, Lund, Sweden; University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, 2100 Copenhagen Ø, Denmark.
| | - Shingo Miyauchi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ella Thoen
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dabao Lu
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Inger Skrede
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France; INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Martina Stursova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Hedda Weitz
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Andy Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK; The James Hutton Institute, Aberdeen, UK
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France.
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
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3
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Jin XH, Wang YC, Li D, Li Y, He HY, Zhang HB. Diverse Mycena Fungi and Their Potential for Gastrodia elata Germination. J Microbiol Biotechnol 2024; 34:1249-1259. [PMID: 38938004 PMCID: PMC11239410 DOI: 10.4014/jmb.2401.01009] [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: 01/10/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/29/2024]
Abstract
It remains to be determined whether there is a geographical distribution pattern and phylogenetic signals for the Mycena strains with seed germination of the orchid plant Gastrodia elata. This study analyzed the community composition and phylogenetics of 72 Mycena strains associated with G. elata varieties (G. elata. f. glauca and G. elata. f. viridis) using multiple gene fragments (ITS+nLSU+SSU). We found that (1) these diverse Mycena phylogenetically belong to the Basidiospore amyloid group. (2) There is a phylogenetic signal of Mycena for germination of G. elata. Those strains phylogenetically close to M. abramsii, M. polygramma, and an unclassified Mycena had significantly higher germination rates than those to M. citrinomarginata. (3) The Mycena distribution depends on geographic site and G. elata variety. Both unclassified Mycena group 1 and the M. abramsii group were dominant for the two varieties of G. elata; in contrast, the M. citrinomarginata group was dominant in G. elata f. glauca but absent in G. elata f. viridis. Our results indicate that the community composition of numerous Mycena resources in the Zhaotong area varies by geographical location and G. elata variety. Importantly, our results also indicate that Mycena's phylogenetic status is correlated with its germination rate.
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Affiliation(s)
- Xiao-Han Jin
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
- School of Ecology and Environmental Science, Yunnan University, Kunming, P.R. China
| | - Yu-Chuan Wang
- Gastrodia Tuber Research Institute of Zhaotong, P.R. China
| | - Dong Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
- School of Ecology and Environmental Science, Yunnan University, Kunming, P.R. China
| | - Yu Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
| | - Hai-Yan He
- The Agriculture and Life Sciences College, Zhaotong University, Zhaotong, P.R. China
- Yunnan Key Laboratory of Gastrodia elata and Fungus Symbiotic Biology, Zhaotong, P.R. China
| | - Han-Bo Zhang
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan, Kunming, P.R. China
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Gundale MJ, Axelsson EP, Buness V, Callebaut T, DeLuca TH, Hupperts SF, Ibáñez TS, Metcalfe DB, Nilsson MC, Peichl M, Spitzer CM, Stangl ZR, Strengbom J, Sundqvist MK, Wardle DA, Lindahl BD. The biological controls of soil carbon accumulation following wildfire and harvest in boreal forests: A review. GLOBAL CHANGE BIOLOGY 2024; 30:e17276. [PMID: 38683126 DOI: 10.1111/gcb.17276] [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: 02/09/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 05/01/2024]
Abstract
Boreal forests are frequently subjected to disturbances, including wildfire and clear-cutting. While these disturbances can cause soil carbon (C) losses, the long-term accumulation dynamics of soil C stocks during subsequent stand development is controlled by biological processes related to the balance of net primary production (NPP) and outputs via heterotrophic respiration and leaching, many of which remain poorly understood. We review the biological processes suggested to influence soil C accumulation in boreal forests. Our review indicates that median C accumulation rates following wildfire and clear-cutting are similar (0.15 and 0.20 Mg ha-1 year-1, respectively), however, variation between studies is extremely high. Further, while many individual studies show linear increases in soil C stocks through time after disturbance, there are indications that C stock recovery is fastest early to mid-succession (e.g. 15-80 years) and then slows as forests mature (e.g. >100 years). We indicate that the rapid build-up of soil C in younger stands appears not only driven by higher plant production, but also by a high rate of mycorrhizal hyphal production, and mycorrhizal suppression of saprotrophs. As stands mature, the balance between reductions in plant and mycorrhizal production, increasing plant litter recalcitrance, and ectomycorrhizal decomposers and saprotrophs have been highlighted as key controls on soil C accumulation rates. While some of these controls appear well understood (e.g. temporal patterns in NPP, changes in aboveground litter quality), many others remain research frontiers. Notably, very little data exists describing and comparing successional patterns of root production, mycorrhizal functional traits, mycorrhizal-saprotroph interactions, or C outputs via heterotrophic respiration and dissolved organic C following different disturbances. We argue that these less frequently described controls require attention, as they will be key not only for understanding ecosystem C balances, but also for representing these dynamics more accurately in soil organic C and Earth system models.
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Affiliation(s)
- Michael J Gundale
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - E Petter Axelsson
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vincent Buness
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Timon Callebaut
- Department of Environmental Science and Ecology, Umeå University, Umeå, Sweden
| | - Thomas H DeLuca
- College of Forestry, Oregon State University, Corvallis, Oregon, USA
| | - Stefan F Hupperts
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Theresa S Ibáñez
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Daniel B Metcalfe
- Department of Environmental Science and Ecology, Umeå University, Umeå, Sweden
| | - Marie-Charlotte Nilsson
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Matthias Peichl
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Clydecia M Spitzer
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Zsofia R Stangl
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Joachim Strengbom
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maja K Sundqvist
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - David A Wardle
- Department of Environmental Science and Ecology, Umeå University, Umeå, Sweden
| | - Björn D Lindahl
- Department of Soil Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
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5
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Zhao P, Gao G, Ding G, Zhang Y, Ren Y. Fungal complexity and stability across afforestation areas in changing desert environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169398. [PMID: 38114026 DOI: 10.1016/j.scitotenv.2023.169398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
The great achievements in combating desertification are attributed to large-scale afforestation, yet we lack verification of how the stability of the fungal community changes in afforestation areas in desert environments. Here, we present the fungal network structure from different niches (root and bulk soil) of plantations of Mongolian pine, a crucial species for afforestation introduced widely in desertification regions. We assessed changes in community complexity and stability of root-associated fungi (RAF) and soil fungi (SF) among different introduction sites: the Hulunbuir Desert (HB), the Horqin Desert (HQ) and the Mu Us Desert (MU). To illuminate the complexity and stability of the fungal network, the differences in topological properties, fungal function, and vegetation and environmental factors between introduction sites were fully considered. We showed that (1) the SF networks had more nodes and edges than the RAF networks. There was a lower ratio of negative:positive cohesion of RAF networks in HB and MU. For SF but not for RAF, across the three introduction sites, a higher modularity and ratio of negative:positive cohesion indicated higher stability. (2) Ectomycorrhizal (EcM) fungi were the dominant functional group in the RAF network (especially in HQ), and were only significantly correlated with vegetation factor. There was a higher relative abundance and number of OTUs of saprophytic fungi in the SF network and they showed positive correlations with soil nutrients. (3) RAF and SF network complexity and stability showed different responses to environmental and vegetation variables. The key determinant of the complexity and stability of the SF networks in Mongolian pine plantations was soil nutrients, followed by climate conditions. The composition and structure of the RAF community was closely related to host plants. Therefore, clarifying the complexity and stability of fungal communities in afforestation areas in changing desert environments is helpful for understanding the interactions between the environment, plants and fungi.
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Affiliation(s)
- Peishan Zhao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Guanglei Gao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Guodong Ding
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Ying Zhang
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yue Ren
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
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Centenaro G, de-Miguel S, Bonet JA, Martínez Peña F, De Gomez REG, Ponce Á, Dashevskaya S, Alday JG. Spatially-explicit effects of small-scale clear-cutting on soil fungal communities in Pinus sylvestris stands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168628. [PMID: 37979846 DOI: 10.1016/j.scitotenv.2023.168628] [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: 06/26/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/20/2023]
Abstract
Clear-cutting is a common silvicultural practice. Although temporal changes in the soil fungal community after clear-cutting have been widely investigated, little is known about stand-level variations in the spatial distribution of soil fungi, particularly at the clear-cut edge. We performed spatial soil sampling in three clear-cuts (0.5 ha), edge habitats, and surrounding forests 8 years after clear-cutting to examine the impact of clear-cutting on the soil fungal community (diversity, composition, guilds, and biomass) and soil properties in a managed Pinus sylvestris forest in northern Spain. Our analyses showed small differences in the composition of the soil fungal community between edge, forest, and clear-cut zones, with <4 % of the species strictly associated with one or two zones. The richness, diversity, and evenness of the fungal community in the edge zone was not significantly different to that in the forest or clear-cut zones, although the clear-cut core had approximately a third fewer ectomycorrhizal species than the edge or the forest. Saprotrophic fungi were widespread across the clear-cut-forest gradient. Soil fungal biomass varied significantly between zones, ranging from 4 to 5 mg g-1 dry soil in the forest and at the forest edge to 1.7 mg g-1 dry soil in the clear-cut area. Soil organic matter, pH, nitrogen, and phosphorus did not differ significantly between edge, forest, and clear-cutting zones and were not significantly related to the fungal community composition. Overall, our study showed that small-scale clear-cut treatments are optimal to guarantee, in the medium-term, soil fungal communities within harvested areas and at the forest edge that are comparable to soil fungal communities in the forest, even though the amount of fungal biomass in the clear-cut zone is lower than at the forest edge or in the forest.
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Affiliation(s)
- Giada Centenaro
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain.
| | - Sergio de-Miguel
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - José Antonio Bonet
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - Fernando Martínez Peña
- Agrifood Research and Technology Centre of Aragon CITA, Avda Montañana 930, E-50059 Zaragoza, Spain; European Mycological Institute EGTC-EMI, E-42003 Soria, Spain
| | | | - Ángel Ponce
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - Svetlana Dashevskaya
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - Josu G Alday
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
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7
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Harder CB, Hesling E, Botnen SS, Lorberau KE, Dima B, von Bonsdorff-Salminen T, Niskanen T, Jarvis SG, Ouimette A, Hester A, Hobbie EA, Taylor AFS, Kauserud H. Mycena species can be opportunist-generalist plant root invaders. Environ Microbiol 2023; 25:1875-1893. [PMID: 37188366 DOI: 10.1111/1462-2920.16398] [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: 02/13/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of 13 C/15 N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published 13 C/15 N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Microbial Ecology, Lund University, Lund, Sweden
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - Emily Hesling
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Synnøve S Botnen
- Department of Biosciences, University of Oslo, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | - Kelsey E Lorberau
- Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Arctic and Marine Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Bálint Dima
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
| | | | - Tuula Niskanen
- Botany Unit, Finnish Museum of Natural History LUOMUS, University of Helsinki, Helsinki, Finland
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey, UK
| | | | - Andrew Ouimette
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | | | - Erik A Hobbie
- Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire, USA
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- The James Hutton Institute, Aberdeen, UK
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8
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Osburn ED, Moon C, Stephenson T, Kittipalawattanapol K, Jones M, Strickland MS, Lynch LM. Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities. FEMS Microbiol Ecol 2023; 99:fiad085. [PMID: 37481693 DOI: 10.1093/femsec/fiad085] [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: 05/08/2023] [Revised: 07/06/2023] [Accepted: 07/21/2023] [Indexed: 07/24/2023] Open
Abstract
Forest disturbance has well-characterized effects on soil microbial communities in tropical and northern hemisphere ecosystems, but little is known regarding effects of disturbance in temperate forests of the southern hemisphere. To address this question, we collected soils from intact and degraded Eucalyptus forests along an east-west transect across Tasmania, Australia, and characterized prokaryotic and fungal communities using amplicon sequencing. Forest degradation altered soil microbial community composition and function, with consistent patterns across soil horizons and regions of Tasmania. Responses of prokaryotic communities included decreased relative abundance of Acidobacteriota, nitrifying archaea, and methane-oxidizing prokaryotes in the degraded forest sites, while fungal responses included decreased relative abundance of some saprotrophic taxa (e.g. litter saprotrophs). Forest degradation also reduced network connectivity in prokaryotic communities and increased the importance of dispersal limitation in assembling both prokaryotic and fungal communities, suggesting recolonization dynamics drive microbial composition following disturbance. Further, changes in microbial functional groups reflected changes in soil chemical properties-reductions in nitrifying microorganisms corresponded with reduced NO3-N pools in the degraded soils. Overall, our results show that soil microbiota are highly responsive to forest degradation in eucalypt forests and demonstrate that microbial responses to degradation will drive changes in key forest ecosystem functions.
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Affiliation(s)
- Ernest D Osburn
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
| | - Cooper Moon
- Department of Environmental Science, University of Idaho, 875 Perimeter Dr. MS 1139, Moscow, ID 83844, USA
| | - Torrey Stephenson
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
| | - Kawinwit Kittipalawattanapol
- School of Natural Sciences, University of Tasmania, Life Sciences Building, Biological Sciences, Hobart, Tasmania 7001, Australia
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Life Sciences Building, Biological Sciences, Hobart, Tasmania 7001, Australia
| | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
| | - Laurel M Lynch
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
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9
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Behnke-Borowczyk J, Korzeniewicz R, Łukowski A, Baranowska M, Jagiełło R, Bułaj B, Hauke-Kowalska M, Szmyt J, Behnke JM, Robakowski P, Kowalkowski W. Variability of Functional Groups of Rhizosphere Fungi of Norway Spruce ( Picea abies (L.) H.Karst.) in the Boreal Range: The Wigry National Park, Poland. Int J Mol Sci 2023; 24:12628. [PMID: 37628809 PMCID: PMC10454689 DOI: 10.3390/ijms241612628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Rhizosphere microbial communities can influence plant growth and development. Natural regeneration processes take place in the tree stands of protected areas, which makes it possible to observe the natural changes taking place in the rhizosphere along with the development of the plants. This study aimed to determine the diversity (taxonomic and functional) of the rhizosphere fungal communities of Norway spruce growing in one of four developmental stages. Our research was based on the ITS region using Illumina system sequencing. Saprotrophs dominated in the studied rhizospheres, but their percentage share decreased with the age of the development group (for 51.91 from 43.13%). However, in the case of mycorrhizal fungi, an opposite trend was observed (16.96-26.75%). The most numerous genera were: saprotrophic Aspergillus (2.54-3.83%), Penicillium (6.47-12.86%), Pyrenochaeta (1.39-11.78%), pathogenic Curvularia (0.53-4.39%), and mycorrhizal Cortinarius (1.80-5.46%), Pseudotomentella (2.94-5.64%) and Tomentella (4.54-15.94%). The species composition of rhizosphere fungal communities was favorable for the regeneration of natural spruce and the development of multi-generational Norway spruce stands. The ratio of the abundance of saprotrophic and mycorrhizal fungi to the abundance of pathogens was high and promising for the durability of the large proportion of spruce in the Wigry National Park and for forest ecosystems in general.
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Affiliation(s)
- Jolanta Behnke-Borowczyk
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Robert Korzeniewicz
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Adrian Łukowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Marlena Baranowska
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Radosław Jagiełło
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Bartosz Bułaj
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Maria Hauke-Kowalska
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Janusz Szmyt
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Jerzy M. Behnke
- School of Life Sciences, University Park Nottingham, Nottingham NG7 2RD, UK;
| | - Piotr Robakowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
| | - Wojciech Kowalkowski
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625 Poznań, Poland; (R.K.); (A.Ł.); (M.B.); (R.J.); (B.B.); (M.H.-K.); (J.S.); (P.R.); (W.K.)
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10
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Semerád J, Lhotský O, Filipová A, Urban O, Šírová K, Boháčková J, Komárek M, Cajthaml T. Remedial trial of sequential anoxic/oxic chemico-biological treatment for decontamination of extreme hexachlorocyclohexane concentrations in polluted soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130199. [PMID: 36279651 DOI: 10.1016/j.jhazmat.2022.130199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
During production of γ-hexachlorocyclohexane (γ-HCH), thousands of tons of other isomers were synthesized as byproducts, and after dumping represent sources of contamination for the environment. Several microbes have the potential for aerobic and anaerobic degradation of HCHs, and zero-valent iron is an effective remediation agent for abiotic dechlorination of HCHs, whereas the combination of the processes has not yet been explored. In this study, a sequence of anoxic/oxic chemico-biological treatments for the degradation of HCHs in a real extremely contaminated soil (10-30 g/kg) was applied. Approximately 1500 kg of the soil was employed, and various combinations of reducing and oxygen-releasing chemicals were used for setting up the aerobic and anaerobic phases. The best results were obtained with mZVI/nZVI, grass cuttings, and oxygen-releasing compounds. In this case, 80 % removal of HCHs was achieved in 129 days, and 98 % degradation was achieved after 1106 days. The analysis of HCHs and their transformation products proved active degradation when slight accumulation of the transformation product during the anaerobic phase was followed by aerobic degradation. The results document that switching between aerobic and anaerobic phases, together with the addition of grass, also created suitable conditions for the biodegradation of HCHs and monochlorobenzene/benzene by microbes.
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Affiliation(s)
- Jaroslav Semerád
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic
| | - Ondřej Lhotský
- Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic; Dekonta a.s., Dřetovice 109, CZ-27342 Stehelčeves, Czech Republic
| | - Alena Filipová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic
| | - Ondřej Urban
- Dekonta a.s., Dřetovice 109, CZ-27342 Stehelčeves, Czech Republic
| | - Kateřina Šírová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic
| | - Jana Boháčková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic
| | - Michael Komárek
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague - Suchdol, CZ-165 00, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic.
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11
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Tanunchai B, Ji L, Schroeter SA, Wahdan SFM, Hossen S, Delelegn Y, Buscot F, Lehnert AS, Alves EG, Hilke I, Gleixner G, Schulze ED, Noll M, Purahong W. FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species. MICROBIAL ECOLOGY 2023; 85:411-428. [PMID: 35124727 PMCID: PMC9958157 DOI: 10.1007/s00248-022-01973-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/16/2023]
Abstract
Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.
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Affiliation(s)
- Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, 150040 Harbin, People’s Republic of China
| | - Simon Andreas Schroeter
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522 Egypt
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Yoseph Delelegn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ann-Sophie Lehnert
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Eliane Gomes Alves
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Gerd Gleixner
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
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12
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Fang FZ, Chen SL, Gui HY, Li ZJ, Zhang XF. Long-Read Sequencing Analysis Revealed the Impact of Forest Conversion on Soil Fungal Diversity in Limu Mountain, Hainan. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02129-y. [PMID: 36329282 DOI: 10.1007/s00248-022-02129-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Soil fungi are essential to soil microorganisms that play an important role in the ecosystem's soil carbon cycle and mineral nutrient transformation. Understanding the structural characteristics and diversity of soil fungal communities helps understand the health of forest ecosystems. The transition from tropical rainforest to artificial forest greatly impacts the composition and diversity of fungal communities. Hainan Limushan tropical rainforest National Park has a large area of artificial forests. Ecologists have conducted in-depth studies on the succession of animals and plants to regenerate tropical rainforests. There are few reports on the diversity of soil fungi and its influencing factors in the succession of tropical rainforests in Limu Mountain. In this study, 44 soil samples from five different stands were collected in the tropical rainforest of Limushan, Hainan. High-throughput sequencing of rDNA in its region was used to analyze fungal communities and study their α and β diversity. Analysis of variance and multiple regression models was used to analyze soil variables and fungal functional groups to determine the effects of interaction between fungi and environmental factors. A total of 273,996 reads and 1290 operational taxonomic units (OTUs) were obtained, belonging to 418 species, 325 genera, 159 families, eight phyla, 30 classes, and 73 orders. The results showed that the composition of soil fungal communities in the five stands was similar, with ascomycetes accounting for 70.5% and basidiomycetes accounting for 14.7%. α and β diversity analysis showed that soil fungi in Limushan tropical rainforest had high abundance and diversity. Multiple regression analysis between soil variables and functional groups showed that organic matter, TN, TP, TK, and AK were excellent predictors for soil fungi. TP was the strongest predictor in all functional groups except soil saprotroph. Organic matter and total nitrogen were the strongest predictors of soil rot. The transformation from tropical rainforest to artificial forest in Limushan did not change the soil fungal community structure, but the richness and diversity of soil fungi changed. The forest transformation did not lead to decreased soil fungal abundance and diversity. Different vegetation types and soil properties affect the diversity of soil fungal communities. We found that Caribbean pine plantations can improve soil fungal diversity, while long-term Eucalyptus spp. plantations may reduce soil fungal diversity.
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Affiliation(s)
- Fa-Zhi Fang
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Su-Ling Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Hui-Ying Gui
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Zhao-Jia Li
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Xiao-Feng Zhang
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China.
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13
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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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14
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Marčiulynienė D, Marčiulynas A, Mishcherikova V, Lynikienė J, Gedminas A, Franic I, Menkis A. Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris. J Fungi (Basel) 2022; 8:1112. [PMID: 36294677 PMCID: PMC9604598 DOI: 10.3390/jof8101112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023] Open
Abstract
The plant- and soil-associated microbial communities are critical to plant health and their resilience to stressors, such as drought, pathogens, and pest outbreaks. A better understanding of the structure of microbial communities and how they are affected by different environmental factors is needed to predict and manage ecosystem responses to climate change. In this study, we carried out a country-wide analysis of fungal communities associated with Pinus sylvestris growing under different environmental conditions. Needle, shoot, root, mineral, and organic soil samples were collected at 30 sites. By interconnecting the high-throughput sequencing data, environmental variables, and soil chemical properties, we were able to identify key factors that drive the diversity and composition of fungal communities associated with P. sylvestris. The fungal species richness and community composition were also found to be highly dependent on the site and the substrate they colonize. The results demonstrated that different functional tissues and the rhizosphere soil of P. sylvestris are associated with diverse fungal communities, which are driven by a combination of climatic (temperature and precipitation) and edaphic factors (soil pH), and stand characteristics.
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Affiliation(s)
- Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Valeriia Mishcherikova
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Iva Franic
- Department of Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden;
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007 Uppsala, Sweden;
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15
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Zuo YL, Hu QN, Qin L, Liu JQ, He XL. Species identity and combinations differ in their overall benefits to Astragalus adsurgens plants inoculated with single or multiple endophytic fungi under drought conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:933738. [PMID: 36160950 PMCID: PMC9490189 DOI: 10.3389/fpls.2022.933738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Although desert plants often establish multiple simultaneous symbiotic associations with various endophytic fungi in their roots, most studies focus on single fungus inoculation. Therefore, combined inoculation of multiple fungi should be applied to simulate natural habitats with the presence of a local microbiome. Here, a pot experiment was conducted to test the synergistic effects between three extremely arid habitat-adapted root endophytes (Alternaria chlamydospora, Sarocladium kiliense, and Monosporascus sp.). For that, we compared the effects of single fungus vs. combined fungi inoculation, on plant morphology and rhizospheric soil microhabitat of desert plant Astragalus adsurgens grown under drought and non-sterile soil conditions. The results indicated that fungal inoculation mainly influenced root biomass of A. adsurgens, but did not affect the shoot biomass. Both single fungus and combined inoculation decreased plant height (7-17%), but increased stem branching numbers (13-34%). However, fungal inoculation influenced the root length and surface area depending on their species and combinations, with the greatest benefits occurring on S. kiliense inoculation alone and its co-inoculation with Monosporascus sp. (109% and 61%; 54% and 42%). Although A. chlamydospora and co-inoculations with S. kiliense and Monosporascus sp. also appeared to promote root growth, these inoculations resulted in obvious soil acidification. Despite no observed root growth promotion, Monosporascus sp. associated with its combined inoculations maximally facilitated soil organic carbon accumulation. However, noticeably, combined inoculation of the three species had no significant effects on root length, surface area, and biomass, but promoted rhizospheric fungal diversity and abundance most, with Sordariomycetes being the dominant fungal group. This indicates the response of plant growth to fungal inoculation may be different from that of the rhizospheric fungal community. Structural equation modeling also demonstrated that fungal inoculation significantly influenced the interactions among the growth of A. adsurgens, soil factors, and rhizospheric fungal groups. Our findings suggest that, based on species-specific and combinatorial effects, endophytic fungi enhanced the plant root growth, altered soil nutrients, and facilitated rhizospheric fungal community, possibly contributing to desert plant performance and ecological adaptability. These results will provide the basis for evaluating the potential application of fungal inoculants for developing sustainable management for desert ecosystems.
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Affiliation(s)
- Yi-Ling Zuo
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Qian-Nan Hu
- School of Life Sciences, Hebei University, Baoding, China
| | - Le Qin
- School of Life Sciences, Hebei University, Baoding, China
| | - Jia-Qiang Liu
- School of Life Sciences, Hebei University, Baoding, China
| | - Xue-Li He
- School of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
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16
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Adnan M, Islam W, Gang L, Chen HYH. Advanced research tools for fungal diversity and its impact on forest ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45044-45062. [PMID: 35460003 DOI: 10.1007/s11356-022-20317-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Fungi are dominant ecological participants in the forest ecosystems, which play a major role in recycling organic matter and channeling nutrients across trophic levels. Fungal populations are shaped by plant communities and environmental parameters, and in turn, fungal communities also impact the forest ecosystem through intrinsic participation of different fungal guilds. Mycorrhizal fungi result in conservation and stability of forest ecosystem, while pathogenic fungi can bring change in forest ecosystem, by replacing the dominant plant species with new or exotic plant species. Saprotrophic fungi, being ecological regulators in the forest ecosystem, convert dead tree logs into reusable constituents and complete the ecological cycles of nitrogen and carbon. However, fungal communities have not been studied in-depth with respect to functional, spatiotemporal, or environmental parameters. Previously, fungal diversity and its role in shaping the forest ecosystem were studied by traditional and laborious cultural methods, which were unable to achieve real-time results and draw a conclusive picture of fungal communities. This review highlights the latest advances in biological methods such as next-generation sequencing and meta'omics for observing fungal diversity in the forest ecosystem, the role of different fungal groups in shaping forest ecosystem, forest productivity, and nutrient cycling at global scales.
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Affiliation(s)
- Muhammad Adnan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu Gang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Han Y H Chen
- Faculty of Forestry and the Forest Environment, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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17
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Home-Field Advantage of Litter Decomposition Faded 8 Years after Spruce Forest Clearcutting in Western Germany. SOIL SYSTEMS 2022. [DOI: 10.3390/soilsystems6010026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Home-field advantage (HFA) encompasses all the processes leading to faster litter decomposition in the ‘home’ environment compared to that of ‘away’ environments. To determine the occurrence of HFA in a forest and adjacent clear-cut, we set up a reciprocal litter decomposition experiment within the forest and clear-cut for two soil types (Cambisols and Gleysols) in temperate Germany. The forest was dominated by Norway spruce (Picea abies), whereas forest regeneration of European Beech (Fagus sylvatica) after clearcutting was encouraged. Our observation that Norway spruce decomposed faster than European beech in 70-yr-old spruce forest was most likely related to specialized litter-soil interaction under existing spruce, leading to an HFA. Elevated soil moisture and temperature, and promoted litter N release, indicated the rapid change of soil-litter affinity of the original spruce forest even after a short-term regeneration following clearcutting, resulting in faster beech decomposition, particularly in moisture- and nutrient-deficient Cambisols. The divergence between forest and clear-cut in the Cambisol of their litter δ15N values beyond nine months implied litter N decomposition was only initially independent of soil and residual C status. We conclude that clearcutting modifies the litter-field affinity and helps promote the establishment or regeneration of European beech in this and similar forest mountain upland areas.
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Yang S, Poorter L, Kuramae EE, Sass-Klaassen U, Leite MFA, Costa OYA, Kowalchuk GA, Cornelissen JHC, van Hal J, Goudzwaard L, Hefting MM, van Logtestijn RSP, Sterck FJ. Stem traits, compartments, and tree species affect fungal communities on decaying wood. Environ Microbiol 2022; 24:3625-3639. [PMID: 35229433 PMCID: PMC9544286 DOI: 10.1111/1462-2920.15953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/12/2022] [Accepted: 02/23/2022] [Indexed: 12/01/2022]
Abstract
Dead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.
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Affiliation(s)
- Shanshan Yang
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ute Sass-Klaassen
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Johannes H C Cornelissen
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Jurgen van Hal
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Leo Goudzwaard
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Richard S P van Logtestijn
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Frank J Sterck
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
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19
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Bail J, Gomez JAM, de Oliveira Vaz GC, de Castro WAC, Bonugli-Santos RC. Structural and functional changes in the fungal community of plant detritus in an invaded Atlantic Forest. BMC Microbiol 2022; 22:10. [PMID: 34986801 PMCID: PMC8729104 DOI: 10.1186/s12866-021-02431-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Changes in the fungal community in the litter decomposition by invasive plants can negatively impact nutrient cycling in natural ecosystems. One still does not know the dimension of this hypothesis, but apparently, it is not despicable. This study evaluated the assemblage composition of fungi during litter decomposition in areas of Atlantic Forest invaded or not invaded by Tradescantia zebrina using Illumina MiSeq and metabarcoding analysis. RESULTS The invaded sample showed significantly higher richness and a difference in the species dominance than the invaded litter. Ascomycota was the first most abundant phylum in both areas. Even so, the dissimilarity between areas can be evidenced. The fungal from Basidiomycota were very representative in the non-invaded areas (ranged from an abundance of 43.29% in the non-invaded to 2.35% in the invaded sample). The genus Lepiota can indicate the primary functional group related to biomass degradation and showed the might difference about the invaded areas due to its essential reduction by the invader. In the invaded sample, there was a total absence of the endophyte-undefined saprotroph guild. Also, some genera not taxonomically characterized were eliminated in the invaded sample, revealing that the fungal biodiversity of areas has not yet been thoroughly characterized. CONCLUSIONS Hence, makes impossible the real interpretation of the invasive plant impact, showing the importance of continuing research on fungal biodiversity. It is important to emphasize that the replacement of the native species by T. zebrina may be responsible for the elimination of fungal groups that have not yet been identified.
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Affiliation(s)
- Jaqueline Bail
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Jose Alejandro Morales Gomez
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Giselle Cristina de Oliveira Vaz
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Wagner Antonio Chiba de Castro
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Rafaella Costa Bonugli-Santos
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil.
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20
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Bail J, Gomez JAM, de Oliveira Vaz GC, de Castro WAC, Bonugli-Santos RC. Structural and functional changes in the fungal community of plant detritus in an invaded Atlantic Forest. BMC Microbiol 2022. [PMID: 34986801 DOI: 10.1186/s12866-021-02431-859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Changes in the fungal community in the litter decomposition by invasive plants can negatively impact nutrient cycling in natural ecosystems. One still does not know the dimension of this hypothesis, but apparently, it is not despicable. This study evaluated the assemblage composition of fungi during litter decomposition in areas of Atlantic Forest invaded or not invaded by Tradescantia zebrina using Illumina MiSeq and metabarcoding analysis. RESULTS The invaded sample showed significantly higher richness and a difference in the species dominance than the invaded litter. Ascomycota was the first most abundant phylum in both areas. Even so, the dissimilarity between areas can be evidenced. The fungal from Basidiomycota were very representative in the non-invaded areas (ranged from an abundance of 43.29% in the non-invaded to 2.35% in the invaded sample). The genus Lepiota can indicate the primary functional group related to biomass degradation and showed the might difference about the invaded areas due to its essential reduction by the invader. In the invaded sample, there was a total absence of the endophyte-undefined saprotroph guild. Also, some genera not taxonomically characterized were eliminated in the invaded sample, revealing that the fungal biodiversity of areas has not yet been thoroughly characterized. CONCLUSIONS Hence, makes impossible the real interpretation of the invasive plant impact, showing the importance of continuing research on fungal biodiversity. It is important to emphasize that the replacement of the native species by T. zebrina may be responsible for the elimination of fungal groups that have not yet been identified.
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Affiliation(s)
- Jaqueline Bail
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Jose Alejandro Morales Gomez
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Giselle Cristina de Oliveira Vaz
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Wagner Antonio Chiba de Castro
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Rafaella Costa Bonugli-Santos
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil.
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21
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Jörgensen K, Granath G, Strengbom J, Lindahl BD. Links between boreal forest management, soil fungal communities and below‐ground carbon sequestration. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karolina Jörgensen
- Department of Soil and Environment Swedish University of Agricultural Sciences Uppsala Sweden
| | - Gustaf Granath
- Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Joachim Strengbom
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Uppsala Sweden
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22
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Effects of Early, Small-Scale Nitrogen Addition on Germination and Early Growth of Scots Pine (Pinus sylvestris) Seedlings and on the Recruitment of the Root-Associated Fungal Community. FORESTS 2021. [DOI: 10.3390/f12111589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.
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23
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Argiroff WA, Zak DR, Pellitier PT, Upchurch RA, Belke JP. Decay by ectomycorrhizal fungi couples soil organic matter to nitrogen availability. Ecol Lett 2021; 25:391-404. [PMID: 34787356 DOI: 10.1111/ele.13923] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/21/2021] [Accepted: 10/30/2021] [Indexed: 01/04/2023]
Abstract
Interactions between soil nitrogen (N) availability, fungal community composition, and soil organic matter (SOM) regulate soil carbon (C) dynamics in many forest ecosystems, but context dependency in these relationships has precluded general predictive theory. We found that ectomycorrhizal (ECM) fungi with peroxidases decreased with increasing inorganic N availability across a natural inorganic N gradient in northern temperate forests, whereas ligninolytic fungal saprotrophs exhibited no response. Lignin-derived SOM and soil C were negatively correlated with ECM fungi with peroxidases and were positively correlated with inorganic N availability, suggesting decay of lignin-derived SOM by these ECM fungi reduced soil C storage. The correlations we observed link SOM decay in temperate forests to tradeoffs in tree N nutrition and ECM composition, and we propose SOM varies along a single continuum across temperate and boreal ecosystems depending upon how tree allocation to functionally distinct ECM taxa and environmental stress covary with soil N availability.
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Affiliation(s)
- William A Argiroff
- School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter T Pellitier
- School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
| | - Rima A Upchurch
- School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
| | - Julia P Belke
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
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24
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska‐Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon‐Cochard C, Rose L, Ryser P, Scherer‐Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde‐Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021; 232:973-1122. [PMID: 34608637 PMCID: PMC8518129 DOI: 10.1111/nph.17572] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T. Freschet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
| | - Loïc Pagès
- UR 1115 PSHCentre PACA, site AgroparcINRAE84914Avignon cedex 9France
| | - Colleen M. Iversen
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Louise H. Comas
- USDA‐ARS Water Management Research Unit2150 Centre Avenue, Bldg D, Suite 320Fort CollinsCO80526USA
| | - Boris Rewald
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesVienna1190Austria
| | - Catherine Roumet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Jitka Klimešová
- Department of Functional EcologyInstitute of Botany CASDukelska 13537901TrebonCzech Republic
| | - Marcin Zadworny
- Institute of DendrologyPolish Academy of SciencesParkowa 562‐035KórnikPoland
| | - Hendrik Poorter
- Plant Sciences (IBG‐2)Forschungszentrum Jülich GmbHD‐52425JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | | | - Thomas S. Adams
- Department of Plant SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Agnieszka Bagniewska‐Zadworna
- Department of General BotanyInstitute of Experimental BiologyFaculty of BiologyAdam Mickiewicz UniversityUniwersytetu Poznańskiego 661-614PoznańPoland
| | - A. Glyn Bengough
- The James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundee,DD1 4HNUK
| | | | - Ivano Brunner
- Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
| | - Johannes H. C. Cornelissen
- Department of Ecological ScienceFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 1085Amsterdam1081 HVthe Netherlands
| | - Eric Garnier
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Arthur Gessler
- Forest DynamicsSwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH Zurich8092ZurichSwitzerland
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt PaulMN55108USA
| | - Ina C. Meier
- Functional Forest EcologyUniversity of HamburgHaidkrugsweg 122885BarsbütelGermany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupDepartment of Environmental SciencesWageningen University and ResearchPO Box 476700 AAWageningenthe Netherlands
| | | | - Laura Rose
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
- Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Peter Ryser
- Laurentian University935 Ramsey Lake RoadSudburyONP3E 2C6Canada
| | | | - Nadejda A. Soudzilovskaia
- Environmental Biology DepartmentInstitute of Environmental SciencesCMLLeiden UniversityLeiden2300 RAthe Netherlands
| | - Alexia Stokes
- INRAEAMAPCIRAD, IRDCNRSUniversity of MontpellierMontpellier34000France
| | - Tao Sun
- Institute of Applied EcologyChinese Academy of SciencesShenyang110016China
| | - Oscar J. Valverde‐Barrantes
- International Center for Tropical BotanyDepartment of Biological SciencesFlorida International UniversityMiamiFL33199USA
| | - Monique Weemstra
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Alexandra Weigelt
- Systematic Botany and Functional BiodiversityInstitute of BiologyLeipzig UniversityJohannisallee 21-23Leipzig04103Germany
| | - Nina Wurzburger
- Odum School of EcologyUniversity of Georgia140 E. Green StreetAthensGA30602USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sarah A. Batterman
- School of Geography and Priestley International Centre for ClimateUniversity of LeedsLeedsLS2 9JTUK
- Cary Institute of Ecosystem StudiesMillbrookNY12545USA
| | - Moemy Gomes de Moraes
- Department of BotanyInstitute of Biological SciencesFederal University of Goiás1974690-900Goiânia, GoiásBrazil
| | - Štěpán Janeček
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawley (Perth)WA 6009Australia
| | - Hans Lambers
- School of Biological SciencesThe University of Western AustraliaCrawley (Perth)WAAustralia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Nishanth Tharayil
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - M. Luke McCormack
- Center for Tree ScienceMorton Arboretum, 4100 Illinois Rt. 53LisleIL60532USA
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska-Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon-Cochard C, Rose L, Ryser P, Scherer-Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde-Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021. [PMID: 34608637 DOI: 10.1111/nph.17572.hal-03379708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T Freschet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
| | - Loïc Pagès
- UR 1115 PSH, Centre PACA, site Agroparc, INRAE, 84914, Avignon cedex 9, France
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Louise H Comas
- USDA-ARS Water Management Research Unit, 2150 Centre Avenue, Bldg D, Suite 320, Fort Collins, CO, 80526, USA
| | - Boris Rewald
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Catherine Roumet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Jitka Klimešová
- Department of Functional Ecology, Institute of Botany CAS, Dukelska 135, 37901, Trebon, Czech Republic
| | - Marcin Zadworny
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Johannes A Postma
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Thomas S Adams
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - A Glyn Bengough
- The James Hutton Institute, Invergowrie, Dundee,, DD2 5DA, UK
- School of Science and Engineering, University of Dundee, Dundee,, DD1 4HN, UK
| | - Elison B Blancaflor
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
| | - Johannes H C Cornelissen
- Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Eric Garnier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Arthur Gessler
- Forest Dynamics, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zurich, 8092, Zurich, Switzerland
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | - Ina C Meier
- Functional Forest Ecology, University of Hamburg, Haidkrugsweg 1, 22885, Barsbütel, Germany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University and Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | | | - Laura Rose
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Peter Ryser
- Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | | | - Nadejda A Soudzilovskaia
- Environmental Biology Department, Institute of Environmental Sciences, CML, Leiden University, Leiden, 2300 RA, the Netherlands
| | - Alexia Stokes
- INRAE, AMAP, CIRAD, IRD, CNRS, University of Montpellier, Montpellier, 34000, France
| | - Tao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, Leipzig, 04103, Germany
| | - Nina Wurzburger
- Odum School of Ecology, University of Georgia, 140 E. Green Street, Athens, GA, 30602, USA
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sarah A Batterman
- School of Geography and Priestley International Centre for Climate, University of Leeds, Leeds, LS2 9JT, UK
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
| | - Moemy Gomes de Moraes
- Department of Botany, Institute of Biological Sciences, Federal University of Goiás, 19, 74690-900, Goiânia, Goiás, Brazil
| | - Štěpán Janeček
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley (Perth), WA 6009, Australia
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Crawley (Perth), WA, Australia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nishanth Tharayil
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - M Luke McCormack
- Center for Tree Science, Morton Arboretum, 4100 Illinois Rt. 53, Lisle, IL, 60532, USA
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Differential Responses of Soil Bacterial and Fungal Community to Short-Term Crop Tree Management in a Larix gmelinii Plantation. FORESTS 2021. [DOI: 10.3390/f12101411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Crop tree management (CTM) is a widely applicable silviculture technology that is used to improve the performance of individual trees. However, only little information is available about the effects of the CTM regime on the soil microbial community structure. We conducted a study to explore the effects of short-term (five years) CTM on the soil bacterial and fungal diversity, community composition, and structure in the 0–10 cm soil layer in a Larix gmelinii (Rupr.) Kuzen. plantation. We set out to investigate the differential response of bacterial and fungal communities to variations in soil properties mediated by short-term CTM. Compared with the control plots, the soil microbial biomass carbon and microbial biomass nitrogen in CTM increased significantly by 64.2% and 32.3%, respectively. CTM significantly promoted the content of soil organic carbon, dissolved organic carbon, and nitrate nitrogen, and reduced the content of dissolved organic nitrogen. CTM changed the Shannon and Simpson indices of soil fungi to a remarkable extent but had little effect on the α diversity of bacterial communities. The bacterial β diversity was more sensitive to CTM than fungi. The relative abundance of Verrucomicrobiae (the dominant class of soil bacteria) in CTM was significantly increased by 78.2%, while the relative abundance of Agaricomycetes (dominant class for soil fungi) was reduced by 43.3%. We observed a significantly increased number of unique OTUs for soil fungi in the CTM plots. Redundancy analysis showed that dissolved organic carbon, soil moisture, and total phosphorus content significantly affected the composition of bacterial communities, while soil dissolved organic nitrogen, C/N, and total phosphorus drove the high variation in fungal community composition. Overall, our results emphasize the divergent response of soil bacterial and fungal communities in Larix gmelinii plantations to short-term CTM. We must pay more attention to the functional role of soil microbiota in future forest management.
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Osburn ED, Badgley BD, Strahm BD, Aylward FO, Barrett JE. Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests. Ecology 2021; 102:e03553. [PMID: 34622940 DOI: 10.1002/ecy.3553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/31/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023]
Abstract
Despite ever-increasing availability of detailed information about microbial community structure, relationships of microbial diversity with ecosystem functioning remain unclear. We investigated these relationships at the Coweeta Hydrologic Laboratory, where past forest disturbances (e.g., clear-cut) have altered both ecosystem processes (e.g., increased N export) and microbial communities (e.g., increased bacterial diversity). We sampled soils from disturbed and adjacent reference forests, characterized resident microbial communities, and measured several microbial C-cycle and N-cycle process rates. Microbial communities from historically disturbed soils exhibited altered ecosystem functioning, including generally higher rates of C- and N-cycle processes. Disturbed soil microbial communities also exhibited altered ecosystem multifunctionality, a composite variable consisting of all measured process rates as well as extracellular enzyme activities. Although we found few relationships between ecosystem functions and microbial alpha diversity, all functions were correlated with microbial community composition metrics, particularly r:K strategist ratios of bacterial phyla. Additionally, for both ecosystem multifunctionality and specific processes (i.e., C- and N-mineralization), microbial metrics significantly improved models seeking to explain variation in process rates. Our work sheds light on the links between microbial communities and ecosystem functioning and identifies specific microbial metrics important for modeling ecosystem responses to environmental change.
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Affiliation(s)
- Ernest D Osburn
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Brian D Badgley
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Brian D Strahm
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - J E Barrett
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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28
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D'Alò F, Odriozola I, Baldrian P, Zucconi L, Ripa C, Cannone N, Malfasi F, Brancaleoni L, Onofri S. Microbial activity in alpine soils under climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147012. [PMID: 33872894 DOI: 10.1016/j.scitotenv.2021.147012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/05/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
Soil enzymatic activity was assessed in the Stelvio Pass area (Italian Central Alps) aiming to define the possible effects of climate change on microbial functioning. Two sites at two different elevations were chosen, a subalpine (2239 m) and an alpine belt (2604-2624 m), with mean annual air temperature differing by almost 3 °C, coherent with the worst future warming scenario (RCP 8.5) by 2100. The lower altitude site may represent a proxy of the potential future situation at higher altitude after the upward shift of subalpine vegetation due to climate change. Additionally, hexagonal open top chambers (OTCs) were installed at the upper site, to passively increase by about 2 °C the summer inner temperature to simulate short term effects of warming before the vegetation shift takes place. Soil physicochemical properties and the bacterial and fungal abundances of the above samples were also considered. The subalpine soils showed a higher microbial activity, especially for hydrolytic enzymes, higher carbon, ammonium and hydrogen (p < 0.001) contents, and a slightly higher PO4 content (p < 0.05) than alpine soils. Bacterial abundance was higher than fungal abundance, both for alpine and subalpine soils. On the other hand, the short term effect, which increased the mean soil temperature during the peak of the growing season in the OTC, showed to induce scarcely significant differences for edaphic parameters and microbial biomass content among the warmed and control plots. Using the manipulative warming experiments, we demonstrated that warming is able to change the enzyme activity starting from colder and higher altitude sites, known to be more vulnerable to the rising temperatures associated with climate change. Although five-years of experimental warming does not allow us to make bold conclusions, it appeared that warming-induced upwards vegetation shift might induce more substantial changes in enzymatic activities than the short-term effects, in the present vegetation context.
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Affiliation(s)
- Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic.
| | - Petr Baldrian
- 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.
| | - Lisa Brancaleoni
- Botanical Garden, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, 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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Osburn ED, Badgley BD, Aylward FO, Barrett JE. Historical forest disturbance mediates soil microbial community responses to drought. Environ Microbiol 2021; 23:6405-6419. [PMID: 34347364 DOI: 10.1111/1462-2920.15706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/11/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Despite the abundance of studies demonstrating the effects of drought on soil microbial communities, the role of land use legacies in mediating these drought effects is unclear. To assess historical land use influences on microbial drought responses, we conducted a drought-rewetting experiment in soils from two adjacent and currently forested watersheds with distinct land use histories: an undisturbed 'reference' site and a 'disturbed' site that was clear-cut and converted to agriculture ~60 years prior. We incubated intact soil cores at either constant moisture or under a drought-rewet treatment and characterized bacterial and fungal communities using amplicon sequencing throughout the experiment. Bacterial alpha diversity decreased following drought-rewetting while fungal diversity increased. Bacterial beta diversity also changed markedly following drought-rewetting, especially in historically disturbed soils, while fungal beta diversity exhibited little response. Additionally, bacterial beta diversity in disturbed soils recovered less from drought-rewetting compared with reference soils. Disturbed soil communities also exhibited notable reductions in nitrifying taxa, increases in putative r-selected bacteria, and reductions in network connectivity following drought-rewetting. Overall, our study reveals historical land use to be important in mediating responses of soil bacterial communities to drought, which will influence the ecosystem-scale trajectories of these environments under ongoing and future climate change.
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Affiliation(s)
- Ernest D Osburn
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Brian D Badgley
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - J E Barrett
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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30
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Gorfer M, Mayer M, Berger H, Rewald B, Tallian C, Matthews B, Sandén H, Katzensteiner K, Godbold DL. High Fungal Diversity but Low Seasonal Dynamics and Ectomycorrhizal Abundance in a Mountain Beech Forest. MICROBIAL ECOLOGY 2021; 82:243-256. [PMID: 33755773 PMCID: PMC8282586 DOI: 10.1007/s00248-021-01736-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/10/2021] [Indexed: 05/05/2023]
Abstract
Forests on steep slopes constitute a significant proportion of European mountain areas and are important as production and protection forests. This study describes the soil fungal community structure in a European beech-dominated mountain forest stands in the Northern Calcareous Alps and investigates how it is determined by season and soil properties. Samples were collected at high spatial resolution in an area of ca. 100 m × 700 m in May (spring) and August (summer). Illumina MiSeq high-throughput sequencing of the ITS2-region revealed distinct patterns for the soil fungal communities. In contrast to other studies from temperate European beech forest stands, Ascomycota dominated the highly diverse fungal community, while ectomycorrhizal fungi were of lower abundance. Russulaceae, which are often among the dominant ectomycorrhizal fungi associated with European beech, were absent from all samples. Potentially plant pathogenic fungi were more prevalent than previously reported. Only subtle seasonal differences were found between fungal communities in spring and summer. Especially, dominant saprotrophic taxa were largely unaffected by season, while slightly stronger effects were observed for ectomycorrhizal fungi. Soil characteristics like pH and organic carbon content, on the other hand, strongly shaped abundant taxa among the saprotrophic fungal community.
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Affiliation(s)
- Markus Gorfer
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Mathias Mayer
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | | | - Boris Rewald
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria.
| | - Claudia Tallian
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Bradley Matthews
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
- Environment Agency Austria, Vienna, Austria
| | - Hans Sandén
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Klaus Katzensteiner
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Douglas L Godbold
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
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31
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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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32
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Roy BA, Thomas DC, Soukup HC, Peterson IAB. Mycena citrinomarginata is associated with roots of the perennial grass Festuca roemeri in Pacific Northwest prairies. Mycologia 2021; 113:693-702. [PMID: 33956585 DOI: 10.1080/00275514.2021.1884814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Prairies in the Pacific Northwest are dominated by perennial bunchgrasses. A Mycena in the citrinomarginata complex was observed to tightly co-occur with bunchgrasses at several prairie study sites. Mapping and spatial statistics showed that it was strongly and significantly associated with Festuca roemeri tussocks. We further found that this fungus is attached to F. roemeri roots (17/17 examined) and both specific primers and next-generation DNA sequencing established that the fungus is in the roots, suggesting that M. citrinomarginata may be endophytic or biotrophic in some contexts, and not simply saprotrophic. These results combined with a literature review indicate that Mycena species are often found as endophytes in grass roots. Given the importance of grasses and grasslands for humans, this ecological association deserves further study.
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Affiliation(s)
- Bitty A Roy
- Institute of Ecology and Evolution, University of Oregon, Eugene, 5289, Oregon 97403
| | - Daniel C Thomas
- Institute of Ecology and Evolution, University of Oregon, Eugene, 5289, Oregon 97403.,Biology Department, Whitman College, Walla Walla, Washington 99362
| | - Hannah C Soukup
- Institute of Ecology and Evolution, University of Oregon, Eugene, 5289, Oregon 97403.,Horticultural Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, 3420 NW Orchard Avenue, Corvallis, Oregon 97331
| | - Ian A B Peterson
- Institute of Ecology and Evolution, University of Oregon, Eugene, 5289, Oregon 97403
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33
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Marupakula S, Mahmood S, Clemmensen KE, Jacobson S, Högbom L, Finlay RD. Root associated fungi respond more strongly than rhizosphere soil fungi to N fertilization in a boreal forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:142597. [PMID: 33077205 DOI: 10.1016/j.scitotenv.2020.142597] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen (N) fertilization is a routine practice in boreal forests but its effects on fungal functional guilds in Pinus sylvestris forests are still incompletely understood. Sampling is often restricted to the upper organic horizons and based on DNA extracted from mixtures of soil and roots without explicitly analysing different spatial niches. Fungal community structure in soil and roots of an 85-y-old Pinus sylvestris forest was investigated using high throughput sequencing. Fertilized plots had been treated with a single dose of N fertilizer, 15 months prior to sampling. Species richness of fungi colonizing roots was reduced in all horizons by N fertilization. In contrast, species richness of soil fungi in the organic horizon was increased by N fertilization, but unaffected in the mineral horizons. Community composition of fungi colonizing roots differed from that of soil fungi, and both communities were significantly influenced by soil horizon and N. The ectomycorrhizal community composition in both roots and soil was significantly affected by N fertilization but no significant effect was found on saprotrophic fungi. The results highlight the importance of analysing the rhizosphere soil and root compartments separately since the fungal communities in these two niches appear to respond differently to environmental perturbations involving the addition of nitrogen.
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Affiliation(s)
- Srisailam Marupakula
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Shahid Mahmood
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
| | - Karina E Clemmensen
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
| | | | - Lars Högbom
- Skogforsk, Uppsala Science Park, SE-751 83 Uppsala, Sweden.
| | - Roger D Finlay
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
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Oh SY, Park KH, Baldrian P, Fong JJ, Kwon HJ, Kim SY, Lim YW. Fungal diversity living in the root and sporophore of the endemic Korean fern Mankyua chejuense. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2020.101038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Soil Microbiome Composition along the Natural Norway Spruce Forest Life Cycle. FORESTS 2021. [DOI: 10.3390/f12040410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Stand-replacing disturbances are a key element of the Norway spruce (Picea abies) forest life cycle. While the effect of a natural disturbance regime on forest physiognomy, spatial structure and pedocomplexity was well described in the literature, its impact on the microbiome, a crucial soil component that mediates nutrient cycling and stand productivity, remains largely unknown. For this purpose, we conducted research on a chronosequence of sites representing the post-disturbance development of a primeval Norway spruce forest in the Calimani Mts., Romania. The sites were selected along a gradient of duration from 16 to 160 years that ranges from ecosystem regeneration phases of recently disturbed open gaps to old-growth forest stands. Based on DNA amplicon sequencing, we followed bacterial and fungal community composition separately in organic, upper mineral and spodic horizons of present Podzol soils. We observed that the canopy opening and subsequent expansion of the grass-dominated understorey increased soil N availability and soil pH, which was reflected in enlarged bacterial abundance and diversity, namely due to the contribution of copiotrophic bacteria that prefer nutrient-richer conditions. The fungal community composition was affected by the disturbance as well but, contrary to our expectations, with no obvious effect on the relative abundance of ectomycorrhizal fungi. Once the mature stand was re-established, the N availability was reduced, the pH gradually decreased and the original old-growth forest microbial community dominated by acidotolerant oligotrophs recovered. The effect of the disturbance and forest regeneration was most evident in organic horizons, while the manifestation of these events was weaker and delayed in deeper soil horizons.
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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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Kohout P, Sudová R, Brabcová V, Vosolsobě S, Baldrian P, Albrechtová J. Forest Microhabitat Affects Succession of Fungal Communities on Decomposing Fine Tree Roots. Front Microbiol 2021; 12:541583. [PMID: 33584602 PMCID: PMC7876299 DOI: 10.3389/fmicb.2021.541583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
Belowground litter derived from tree roots has been shown as a principal source of soil organic matter in coniferous forests. Fate of tree root necromass depends on fungal communities developing on the decaying roots. Local environmental conditions which affect composition of tree root mycobiome may also influence fungal communities developing on decaying tree roots. Here, we assessed fungal communities associated with decaying roots of Picea abies decomposing in three microhabitats: soil with no vegetation, soil with ericoid shrubs cover, and P. abies deadwood, for a 2-year period. Forest microhabitat showed stronger effect on structuring fungal communities associated with decaying roots compared to living roots. Some ericoid mycorrhizal fungi showed higher relative abundance on decaying roots in soils under ericoid shrub cover, while saprotrophic fungi had higher relative abundance in roots decomposing inside deadwood. Regardless of the studied microhabitat, we observed decline of ectomycorrhizal fungi and increase of endophytic fungi during root decomposition. Interestingly, we found substantially more fungal taxa with unknown ecology in late stages of root decomposition, indicating that highly decomposed roots may represent so far overlooked niche for soil fungi. Our study shows the importance of microhabitats on the fate of the decomposing spruce roots.
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Affiliation(s)
- Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Radka Sudová
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Stanislav Vosolsobě
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Albrechtová
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
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Rodriguez-Ramos JC, Cale JA, Cahill JF, Simard SW, Karst J, Erbilgin N. Changes in soil fungal community composition depend on functional group and forest disturbance type. THE NEW PHYTOLOGIST 2021; 229:1105-1117. [PMID: 32557647 DOI: 10.1111/nph.16749] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Disturbances have altered community dynamics in boreal forests with unknown consequences for belowground ecological processes. Soil fungi are particularly sensitive to such disturbances; however, the individual response of fungal guilds to different disturbance types is poorly understood. Here, we profiled soil fungal communities in lodgepole pine forests following a bark beetle outbreak, wildfire, clear-cut logging, and salvage-logging. Using Illumina MiSeq to sequence ITS1 and SSU rDNA, we characterized communities of ectomycorrhizal, arbuscular mycorrhizal, saprotrophic, and pathogenic fungi in sites representing each disturbance type paired with intact forests. We also quantified soil fungal biomass by measuring ergosterol. Abiotic disturbances changed the community composition of ectomycorrhizal fungi and shifted the dominance from ectomycorrhizal to saprotrophic fungi compared to intact forests. The disruption of the soil organic layer with disturbances correlated with the decline of ectomycorrhizal and the increase of arbuscular mycorrhizal fungi. Wildfire changed the community composition of pathogenic fungi but did not affect their proportion and diversity. Fungal biomass declined with disturbances that disrupted the forest floor. Our results suggest that the disruption of the forest floor with disturbances, and the changes in C and nutrient dynamics it may promote, structure the fungal community with implications for fungal biomass-C.
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Affiliation(s)
| | - Jonathan A Cale
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Suzanne W Simard
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justine Karst
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
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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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Van Nuland ME, Smith DP, Bhatnagar JM, Stefanski A, Hobbie SE, Reich PB, Peay KG. Warming and disturbance alter soil microbiome diversity and function in a northern forest ecotone. FEMS Microbiol Ecol 2020; 96:5849001. [PMID: 32472932 DOI: 10.1093/femsec/fiaa108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
The response to global change by soil microbes is set to affect important ecosystem processes. These impacts could be most immediate in transitional zones, such as the temperate-boreal forest ecotone, yet previous work in these forests has primarily focused on specific subsets of microbial taxa. Here, we examined how bacterial and fungal communities respond to simulated above- and below-ground warming under realistic field conditions in closed and open canopy treatments in Minnesota, USA. Our results show that warming and canopy disturbance shifted bacterial and fungal community structure as dominant bacterial and fungal groups differed in the direction and intensity of their responses. Ectomycorrhizal and saprotrophic fungal communities with greater connectivity (higher prevalence of strongly interconnected taxa based on pairwise co-occurrence relationships) were more resistant to compositional change. Warming effects on soil enzymes involved in the hydrolytic and oxidative liberation of carbon from plant cell walls and nutrients from organic matter were most strongly linked to fungal community responses, although community structure-function relationships differed between fungal guilds. Collectively, these findings indicate that warming and disturbance will influence the composition and function of microbial communities in the temperate-boreal ecotone, and fungal responses are particularly important to understand for predicting future ecosystem functioning.
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Affiliation(s)
| | - Dylan P Smith
- University of California, California Institute for Quantitative Biosciences, Berkeley, CA 94720 USA
| | | | - Artur Stefanski
- Department of Forest Resources, University of Minnesota, St. Paul, MN 55108 USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108 USA
| | - Peter B Reich
- Department of Forest Resources, University of Minnesota, St. Paul, MN 55108 USA.,Hawkesbury Institute for the Environment, Western Sydney University, Richmond, 2753, NSW Australia
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA 94305 USA
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Modi D, Simard S, Bérubé J, Lavkulich L, Hamelin R, Grayston SJ. Long-term effects of stump removal and tree species composition on the diversity and structure of soil fungal communities. FEMS Microbiol Ecol 2020; 96:5818759. [PMID: 32275308 DOI: 10.1093/femsec/fiaa061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 04/07/2020] [Indexed: 11/12/2022] Open
Abstract
Stump removal is a common forest management practice used to reduce the mortality of trees affected by the fungal pathogen-mediated root disease, Armillaria root rot, but the impact of stumping on soil fungal community structure is not well understood. This study analyzed the long-term impact of stumping and tree species composition on the abundance, diversity and taxonomic composition of soil fungal communities using internal transcribed spacer (ITS) marker-based DNA metabarcoding in a 48-year-old trial at Skimikin, British Columbia. A total of 108 samples were collected from FH (fermented and humus layers), and soil mineral horizons (A and B) from stumped and unstumped plots of six tree species treatments (pure stands and admixtures of Douglas-fir, western red-cedar and paper birch). Fungal α-diversity in the A horizon significantly increased with stumping regardless of tree species composition, while β-diversity was significantly affected by stumping in all the horizons. We also observed that the relative abundance of the saprotrophic fungal community declined while that of the ectomycorrhizal fungal community increased with stumping. In conclusion, increase in ectomycorrhizal fungal associations, which are positively associated with tree productivity, suggests that stumping can be considered a good management practice for mitigating root disease and promoting tree regeneration.
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Affiliation(s)
- Dixi Modi
- Department of Soil Science, Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Suzanne Simard
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bérubé
- Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, QC G1V 4C7, Canada
| | - Les Lavkulich
- Department of Soil Science, Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Richard Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sue J Grayston
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Long-term decomposition of litter in the montane forest and the definition of fungal traits in the successional space. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100913] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Thoen E, Harder CB, Kauserud H, Botnen SS, Vik U, Taylor AFS, Menkis A, Skrede I. In vitro evidence of root colonization suggests ecological versatility in the genus Mycena. THE NEW PHYTOLOGIST 2020; 227:601-612. [PMID: 32171021 DOI: 10.1111/nph.16545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
The root-associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root-associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula. In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14 C and 32 P to show potential transfer between symbionts. All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle-like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32 P to the seedlings. Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.
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Affiliation(s)
- Ella Thoen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
- Department of Plant and Soil Science, Texas Tech University, PO Box 42122, Lubbock, TX, 79409, USA
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Synnøve S Botnen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Unni Vik
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
| | - Andy F S Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, SE-75007, Uppsala, Sweden
| | - Inger Skrede
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway
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Beck JL, Cale JA, Rodriguez‐Ramos JC, Kanekar SS, Karst J, Cahill JF, Simard SW, Erbilgin N. Changes in soil fungal communities following anthropogenic disturbance are linked to decreased lodgepole pine seedling performance. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jackson L. Beck
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | - Jonathan A. Cale
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | | | - Sanat S. Kanekar
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | - Justine Karst
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | - James F. Cahill
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Suzanne W. Simard
- Department of Forest & Conservation Sciences University of British Columbia Vancouver BC Canada
| | - Nadir Erbilgin
- Department of Renewable Resources University of Alberta Edmonton AB Canada
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Gray L, Kernaghan G. Fungal Succession During the Decomposition of Ectomycorrhizal Fine Roots. MICROBIAL ECOLOGY 2020; 79:271-284. [PMID: 31392355 DOI: 10.1007/s00248-019-01418-3] [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: 03/30/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Ectomycorrhizal (ECM) fine roots account for a substantial proportion of forest production and their decomposition releases large amounts of nutrients to the soil ecosystem. However, little is known about the fungi involved in ECM decomposition, including assemblages of fungal saprotrophs, endophytes, and the ECM fungi themselves. To follow fungal succession during the degradation of senescing fine roots, understory seedlings of Abies balsamea and Picea rubens at two sites in the Acadian forest of Nova Scotia were either severed at the root collar or left as controls. Root systems were collected sequentially over two growing seasons and assessed for fine root loss and ECM mantle integrity. ECM were identified by ITS-PCR and grouped into broad morphological categories. Fungal communities colonizing the senescing fine roots were also monitored by systematically constructing clone libraries over the course of the experiment. ECM with cottony, weakly pigmented mantles (e.g., Cortinarius) degraded within the first year. Those with cottony, but intensely pigmented mantles (Piloderma), and smooth mantles with weak pigmentation (Russulaceae) degraded more slowly. Smooth, melanized ECM (Cenococcum and Tomentella) generally maintained integrity over the course of the experiment. Rates of fine root loss and changes in ECM mantle integrity were positively correlated with soil temperature. ECM DNA was detected throughout the experiment, and was not replaced by that of saprotrophic species during the two seasons sampled. However, fungal root endophytes (e.g., Helotiaceae) initially increased in abundance and then decreased as mantles degraded, suggesting a possible role in ECM decomposition.
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Affiliation(s)
- Logan Gray
- Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3, Canada
| | - Gavin Kernaghan
- Department of Biology, Mount Saint Vincent University, Halifax, NS, B3M 2J6, Canada.
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 403] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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Osburn ED, McBride SG, Aylward FO, Badgley BD, Strahm BD, Knoepp JD, Barrett JE. Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests. Front Microbiol 2019; 10:2872. [PMID: 31921050 PMCID: PMC6917579 DOI: 10.3389/fmicb.2019.02872] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/28/2019] [Indexed: 11/24/2022] Open
Abstract
In Appalachian ecosystems, forest disturbance has long-term effects on microbially driven biogeochemical processes such as nitrogen (N) cycling. However, little is known regarding long-term responses of forest soil microbial communities to disturbance in the region. We used 16S and ITS sequencing to characterize soil bacterial (16S) and fungal (ITS) communities across forested watersheds with a range of past disturbance regimes and adjacent reference forests at the Coweeta Hydrologic Laboratory in the Appalachian mountains of North Carolina. Bacterial communities in previously disturbed forests exhibited consistent responses, including increased alpha diversity and increased abundance of copiotrophic (e.g., Proteobacteria) and N-cycling (e.g., Nitrospirae) bacterial phyla. Fungal community composition also showed disturbance effects, particularly in mycorrhizal taxa. However, disturbance did not affect fungal alpha diversity, and disturbance effects were not consistent at the fungal class level. Co-occurrence networks constructed for bacteria and fungi showed that disturbed communities were characterized by more connected and tightly clustered network topologies, indicating that disturbance alters not only community composition but also potential ecological interactions among taxa. Although bacteria and fungi displayed different long-term responses to forest disturbance, our results demonstrate clear responses of important bacterial and fungal functional groups (e.g., nitrifying bacteria and mycorrhizal fungi), and suggest that both microbial groups play key roles in the long-term alterations to biogeochemical processes observed following forest disturbance in the region.
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Affiliation(s)
- Ernest D. Osburn
- Department of Biological Sciences, College of Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Steven G. McBride
- Department of Biological Sciences, College of Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Frank O. Aylward
- Department of Biological Sciences, College of Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Brian D. Badgley
- School of Plant and Environmental Sciences, College of Agriculture and Life Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Brian D. Strahm
- Department of Forest Resources and Environmental Conservation, College of Natural Resources and Environment, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jennifer D. Knoepp
- Coweeta Hydrologic Laboratory, USDA Forest Service Southern Research Station, Otto, NC, United States
| | - J. E. Barrett
- Department of Biological Sciences, College of Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Argiroff WA, Zak DR, Upchurch RA, Salley SO, Grandy AS. Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots. GLOBAL CHANGE BIOLOGY 2019; 25:4369-4382. [PMID: 31314956 DOI: 10.1111/gcb.14770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (-31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin-derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin-derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin-derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.
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Affiliation(s)
- William A Argiroff
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rima A Upchurch
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Sydney O Salley
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - A Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
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50
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Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev Camb Philos Soc 2019; 95:409-433. [PMID: 31763752 DOI: 10.1111/brv.12570] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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Affiliation(s)
- Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, U.S.A
| | - Carlos A Aguilar-Trigueros
- Freie Universität-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Scott Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, U.S.A
| | | | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, U.S.A
| | - Natalie Christian
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Habacuc Flores-Moreno
- Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Dimitrios Floudas
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Romina Gazis
- Department of Plant Pathology, Tropical Research & Education Center, University of Florida, Homestead, FL, 33031, U.S.A
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, 01610, U.S.A
| | - Peter Kennedy
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, WI, 53726, U.S.A
| | - Daniel S Maynard
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Amy M Milo
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Rolf Henrik Nilsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA, 93101, U.S.A
| | - Jonathan Schilling
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, U.S.A
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