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Mannaa M, Han G, Jung H, Park J, Kim JC, Park AR, Seo YS. Aureobasidium pullulans Treatment Mitigates Drought Stress in Abies koreana via Rhizosphere Microbiome Modulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:3653. [PMID: 37896116 PMCID: PMC10610362 DOI: 10.3390/plants12203653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023]
Abstract
The Korean fir tree Abies koreana, an endangered species in Korea, faces threats primarily from climate change-induced stress and drought. This study proposed a sustainable method to enhance A. koreana drought tolerance using a black yeast-like fungus identified as Aureobasidium pullulans (AK10). The 16S/ITS metabarcoding analysis assessed the impact of drought and AK10 treatment on the seedlings' rhizosphere microbiome. Results revealed a profound drought influence on the microbiome, particularly affecting fungal mycobiota. Drought-stressed seedlings exhibited elevated Agaricaceae levels, opportunistic fungi generally associated with decomposition. AK10 treatment significantly mitigated this proliferation and increased the relative abundance of beneficial fungi like Cystofilobasidium and Mortierella, known biocontrol agents and phosphate solubilizers. A notable reduction in the phytopathogenic Fusarium levels was observed with AK10, alongside an increase in beneficial bacteria, including Azospirillum and Nitrospirillum. Furthermore, the conducted correlation analysis shed light on microbial interrelationships within the rhizosphere, elucidating potential co-associations and antagonisms. Taken together, the isolated A. pullulans AK10 identified in this study serves as a potential biostimulant, enhancing the drought tolerance in A. koreana through beneficial alterations in the rhizosphere microbiome. This approach presents a promising strategy for the conservation of this endangered species.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
| | - Jungwook Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea;
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea; (J.-C.K.); (A.R.P.)
| | - Ae Ran Park
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea; (J.-C.K.); (A.R.P.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (M.M.); (G.H.); (H.J.)
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Liu H, Jacquemyn H, Yu S, Chen W, He X, Huang Y. Mycorrhizal diversity and community composition in co-occurring Cypripedium species. MYCORRHIZA 2023; 33:107-118. [PMID: 36396734 DOI: 10.1007/s00572-022-01095-0] [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: 05/29/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Orchids commonly rely on mycorrhizal fungi to obtain the necessary resources for seed germination and growth. Whereas most photosynthetic orchids typically associate with so-called rhizoctonia fungi to complete their life cycle, there is increasing evidence that other fungi may be involved as well and that the mycorrhizal communities associated with orchids may be more diverse. Coexisting orchid species also tend to associate with different fungi to reduce competition for similar resources and to increase long-term population viability. However, few studies have related the mycorrhizal communities in the rhizosphere to communities found in the roots of closely related coexisting orchid species. In this study, we used high-throughput sequencing to investigate the diversity and community composition of orchid mycorrhizal fungi in the roots and the rhizosphere of four Cypripedium species growing in forests in Northeast China. The results showed that the investigated Cypripedium species associated with a wide variety of fungi including members of Tulasnellaceae, Psathyrellaceae, and Herpotrichiellaceae, whereas members of Russulaceae, Cortinariaceae, Thelephoraceae, and Herpotrichiellaceae showed high abundance in rhizosphere soils. The diversity of fungi detected in the rhizosphere soil was much higher than that in the roots. The observed variation in fungal communities in Cypripedium roots was not related to forest site or orchid species. On the other hand, variation in mycorrhizal communities of rhizosphere soil was significantly related to sampling site. These results indicate that orchid mycorrhizal communities in the rhizosphere display considerable variation among sites and that orchids use only a subset of the locally available fungi. Future studies focusing on the fine-scale spatial distribution of orchid mycorrhizal fungi and more detailed assessments of local environmental conditions will provide novel insights into the mechanisms explaining variation of fungal communities in both orchid roots and the rhizosphere.
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Affiliation(s)
- Huanchu Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiangxi, 332900, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Shuai Yu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Wei Chen
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China.
- Key Laboratory of Forest Ecology and Management, Chinese Academy of Sciences, Shenyang, 110016, China.
| | - Xingyuan He
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
- Key Laboratory of Forest Ecology and Management, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yanqing Huang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Shenyang Arboretum, Chinese Academy of Sciences, Shenyang, 110016, China
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Dueñas JF, Hempel S, Homeier J, Suárez JP, Rillig MC, Camenzind T. Root associated fungal lineages of a tropical montane forest show contrasting sensitivities to the long-term addition of nitrogen and phosphorus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:775-784. [PMID: 36085412 DOI: 10.1111/1758-2229.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Root associated fungal (RAF) communities can exert strong effects on plant communities and are potentially sensitive to shifts in soil fertility. As increased atmospheric nitrogen (N) and phosphorus (P) deposition can alter the nutrient balance in natural ecosystems, we assessed the response of RAF communities to a fertilization experiment deployed on a highly diverse Andean forest. The stand level fine root fraction was sampled after 7 years of systematic N and P additions and RAF communities were characterized by a deep sequencing approach. We expected that fertilization will enhance competition of fungal taxa for limiting nutrients, thus eliciting diversity reductions and alterations in the structure of RAF communities. Fertilization treatments did not reduce RAF richness but affected community composition. At the phylum level fertilization reduced richness exclusively among Glomeromycota. In contrast, N and P additions (alone or in combination) altered the composition of several fungal phyla. The lack of a generalized response to long-term fertilization among RAF lineages suggests that most of these lineages will not be directly and immediately affected by the increasing rates of atmospheric N and P deposition expected for this region by 2050.
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Affiliation(s)
- Juan F Dueñas
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefan Hempel
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jürgen Homeier
- Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Chuang S, Yang H, Wang X, Xue C, Jiang J, Hong Q. Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125496. [PMID: 33667802 DOI: 10.1016/j.jhazmat.2021.125496] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to reveal the effects of high and low dose of carbendazim and its degrading strain, Rhodococcus qingshengii strain djl-6, on the composition, diversity, and interrelationship of soil bacterial and fungal communities in short- and medium-term under laboratory conditions. The results showed that carbendazim exhibited an increased negative impact on bacterial communities and reduced the proportion of dominant fungal phylum Ascomycota during a 14-day incubation period. Only the impacts of low-dose carbendazim (2 mg·kg-1 dry soil) on fungal community were weakened. Network analysis showed that carbendazim increased the connectivity and modularity of microbial co-occurrence networks. Strain djl-6 exhibited good potential for bioremediation of carbendazim-contaminated soils. Moreover, it driven the assembly of potential carbendazim-degrading consortia from indigenous microbial communities; and members of the genera Arthrobacter, Bacillus, Brevundimonas, Lysinibacillus, Massilia, Mycobacterium, Paenibacillus, and Pseudarthrobacter might be participated in the degradation of carbendazim. Taken together, our study provides a relatively comprehensive understanding of the effects of carbendazim and its degrading strain djl-6 on soil microbial communities.
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Affiliation(s)
- Shaochuang Chuang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongxing Yang
- College of Resource and Environment, Anhui Science and Technology University, Fengyang 233100, China
| | - Xiang Wang
- College of Resource and Environment, Anhui Science and Technology University, Fengyang 233100, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Hong
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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5
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Tienda S, Vida C, Lagendijk E, de Weert S, Linares I, González-Fernández J, Guirado E, de Vicente A, Cazorla FM. Soil Application of a Formulated Biocontrol Rhizobacterium, Pseudomonas chlororaphis PCL1606, Induces Soil Suppressiveness by Impacting Specific Microbial Communities. Front Microbiol 2020; 11:1874. [PMID: 32849458 PMCID: PMC7426498 DOI: 10.3389/fmicb.2020.01874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Biocontrol bacteria can be used for plant protection against some plant diseases. Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a model bacterium isolated from the avocado rhizosphere with strong antifungal antagonism mediated by the production of 2-hexyl, 5-propil resorcinol (HPR). Additionally, PcPCL1606 has biological control against different soil-borne fungal pathogens, including the causal agent of the white root rot of many woody crops and avocado in the Mediterranean area, Rosellinia necatrix. The objective of this study was to assess whether the semicommercial application of PcPCL1606 to soil can potentially affect avocado soil and rhizosphere microbial communities and their activities in natural conditions and under R. necatrix infection. To test the putative effects of PcPCL1606 on soil eukaryotic and prokaryotic communities, a formulated PcPCL1606 was prepared and applied to the soil of avocado plants growing in mesocosm experiments, and the communities were analyzed by using 16S/ITS metagenomics. PcPCL1606 survived until the end of the experiments. The effect of PcPCL1606 application on prokaryotic communities in soil and rhizosphere samples from natural soil was not detectable, and very minor changes were observed in eukaryotic communities. In the infested soils, the presence of R. necatrix strongly impacted the soil and rhizosphere microbial communities. However, after PcPCL1606 was applied to soil infested with R. necatrix, the prokaryotic community reacted by increasing the relative abundance of few families with protective features against fungal soilborne pathogens and organic matter decomposition (Chitinophagaceae, Cytophagaceae), but no new prokaryotic families were detected. The treatment of PcPCL1606 impacted the fungal profile, which strongly reduced the presence of R. necatrix in avocado soil and rhizosphere, minimizing its effect on the rest of the microbial communities. The bacterial treatment of formulated PcPCL1606 on avocado soils infested with R. necatrix resulted in biological control of the pathogen. This suppressiveness phenotype was analyzed, and PcPCL1606 has a key role in suppressiveness induction; in addition, this phenotype was strongly dependent on the production of HPR.
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Affiliation(s)
- Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Carmen Vida
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Ellen Lagendijk
- Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Sandra de Weert
- Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Irene Linares
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Jorge González-Fernández
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Estación Experimental “La Mayora”, Algarrobo, Spain
| | - Emilio Guirado
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Estación Experimental “La Mayora”, Algarrobo, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Francisco M. Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
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6
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Juvigny-Khenafou NPD, Zhang Y, Piggott JJ, Atkinson D, Matthaei CD, Van Bael SA, Wu N. Anthropogenic stressors affect fungal more than bacterial communities in decaying leaf litter: A stream mesocosm experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:135053. [PMID: 31859062 DOI: 10.1016/j.scitotenv.2019.135053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Despite the progress made in environmental microbiology techniques and knowledge, the succession and functional changes of the microbial community under multiple stressors are still poorly understood. This is a substantial knowledge gap as microbial communities regulate the biogeochemistry of stream ecosystems. Our study assessed the structural and temporal changes in stream fungal and bacterial communities associated with decomposing leaf litter under a multiple-stressor scenario. We conducted a fully crossed 4-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 days of colonisation, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S and 18S rRNA genes) to identify changes in microbial community composition. Our results indicate that (1) shifts in relative abundances of the pre-existing terrestrial microbial community, rather than changes in community identity, drove the observed responses to stressors; (2) changes in relative abundances within the microbial community paralleled decomposition rate patterns with time; (3) both fungal and bacterial communities had a certain resistance to stressors, as indicated by relatively minor changes in alpha diversity or multivariate community structure; (4) overall, stressor interactions were more common than stressor main effects when affecting microbial diversity metrics or abundant individual genera; and (5) stressor effects on microbes often changed from 2 weeks to 3 weeks of stressor exposure, with several response patterns being reversed. Our study suggests that future research should focus more on understanding the temporal dynamics of fungal and bacterial communities and how they relate to ecosystem processes to advance our understanding of the mechanisms associated with multiple-stressor interactions.
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Affiliation(s)
- Noël P D Juvigny-Khenafou
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK; Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Yixin Zhang
- Department of Landscape Architecture, Gold Mantis School of Architecture, Soochow University, Suzhou, China.
| | - Jeremy J Piggott
- Trinity Centre for the Environment & Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - David Atkinson
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Christoph D Matthaei
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St. Charles Avenue, Boggs 400, New Orleans, LA 70118, USA
| | - Naicheng Wu
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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7
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Kirker GT, Bishell A, Cappellazzi J, Palmer J, Bechle N, Lebow P, Lebow S. Role of Leaf Litter in Above-Ground Wood Decay. Microorganisms 2020; 8:microorganisms8050696. [PMID: 32397554 PMCID: PMC7286020 DOI: 10.3390/microorganisms8050696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023] Open
Abstract
The effects of leaf litter on moisture content and fungal decay development in above-ground wood specimens were assessed. Untreated southern pine specimens were exposed with or without leaf litter contact. Two types of leaf litter were evaluated; aged (decomposed) and young (early stages of decomposition). The moisture content of specimens was monitored, and specimens were periodically removed for visual evaluation of decay development. In addition, amplicon-based sequencing analysis of specimens and associated leaf litter was conducted at two time points. Contact with either type of leaf litter resulted in consistently higher moisture contents than those not in contact with leaf litter. Visually, evident decay developed most rapidly in specimens in contact with the aged leaf litter. Analysis of amplicon-based sequencing revealed that leaf litter contributes a significant amount of the available wood decay fungal community with similar communities found in the litter exposed wood and litter itself, but dissimilar community profiles from unexposed wood. Dominant species and guild composition shifted over time, beginning initially with more leaf saprophytes (ascomycetes) and over time shifting to more wood rotting fungi (basidiomycetes). These results highlight the importance of the contributions of leaf litter to fungal colonization and subsequent decay hazard for above-ground wood.
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Affiliation(s)
- Grant T. Kirker
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
- Correspondence: ; Tel.: +1-608-231-9256
| | - Amy Bishell
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
| | - Jed Cappellazzi
- Dept. of Wood Science and Engineering, Oregon State University, Corvallis, OR 97731, USA;
| | - Jonathan Palmer
- Northern Research Station, USDA Forest Service, Madison, WI 53726, USA;
| | - Nathan Bechle
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
| | - Patricia Lebow
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
| | - Stan Lebow
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
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Schimann H, Vleminckx J, Baraloto C, Engel J, Jaouen G, Louisanna E, Manzi S, Sagne A, Roy M. Tree communities and soil properties influence fungal community assembly in neotropical forests. Biotropica 2020. [DOI: 10.1111/btp.12747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heidy Schimann
- INRA EcoFoG (AgroParisTech, CNRS, CIRAD, INRA, Université des Antilles, Université de Guyane) Kourou France
| | - Jason Vleminckx
- Department of Biological Science Florida International University Miami FL USA
| | | | - Julien Engel
- AMAP (Université de Montpellier, CIRAD, CNRS, INRA, IRD) Montpellier France
| | - Gaelle Jaouen
- AgroParisTech EcoFoG (AgroParisTech, CNRS, CIRAD, INRA, Université des Antilles, Université de Guyane) Kourou France
| | - Eliane Louisanna
- INRA EcoFoG (AgroParisTech, CNRS, CIRAD, INRA, Université des Antilles, Université de Guyane) Kourou France
| | - Sophie Manzi
- Laboratoire Évolution et Diversité Biologique CNRS, UMR 5174 UPS CNRS ENFA IRD Université Toulouse 3 Paul Sabatier Toulouse France
| | - Audrey Sagne
- INRA EcoFoG (AgroParisTech, CNRS, CIRAD, INRA, Université des Antilles, Université de Guyane) Kourou France
| | - Mélanie Roy
- Laboratoire Évolution et Diversité Biologique CNRS, UMR 5174 UPS CNRS ENFA IRD Université Toulouse 3 Paul Sabatier Toulouse France
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9
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Harkes P, van Steenbrugge JJM, van den Elsen SJJ, Suleiman AKA, de Haan JJ, Holterman MHM, Helder J. Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management. FRONTIERS IN PLANT SCIENCE 2020; 10:1697. [PMID: 31998352 PMCID: PMC6965313 DOI: 10.3389/fpls.2019.01697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/02/2019] [Indexed: 06/10/2023]
Abstract
Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.
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Affiliation(s)
- Paula Harkes
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | | | | | - Afnan Khalil Ahmad Suleiman
- Department of Microbial Ecology, NIOO-KNAW, Wageningen, Netherlands
- Department of Microbiological Water Quality and Health, KWR Watercycle Research Institute, PE Nieuwegein, Netherlands
| | - Johannes Jan de Haan
- Open Teelten, Department of Wageningen Plant Research, Wageningen University & Research, Lelystad, Netherlands
| | | | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
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10
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Lumibao CY, Borer ET, Condon B, Kinkel L, May G, Seabloom EW. Site-specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales. Ecol Evol 2019; 9:12231-12244. [PMID: 31832156 PMCID: PMC6854330 DOI: 10.1002/ece3.5711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/14/2022] Open
Abstract
The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within-host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.
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Affiliation(s)
- Candice Y. Lumibao
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Elizabeth T. Borer
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Bradford Condon
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Linda Kinkel
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMinnesota
| | - Georgiana May
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Eric W. Seabloom
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
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11
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Zhang QG, Lu HS, Buckling A. Temperature drives diversification in a model adaptive radiation. Proc Biol Sci 2018; 285:rspb.2018.1515. [PMID: 30185639 DOI: 10.1098/rspb.2018.1515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/15/2018] [Indexed: 01/10/2023] Open
Abstract
The warmer regions harbour more species, attributable to accelerated speciation and increased ecological opportunities for coexistence. While correlations between temperature and energy availability and habitat area have been suggested as major drivers of these biodiversity patterns, temperature can theoretically also have direct effects on the evolution of diversity. Here, we experimentally studied the evolution of diversity in a model adaptive radiation of the bacterium Pseudomonas fluorescens across a temperature gradient. Diversification increased at higher temperatures, driven by both faster generation of genetic variation and stronger diversifying selection. Specifically, low temperatures could limit the generation of diversity, suggested by the observation that supply of genetic variation through immigration increased diversity at low, but not high temperatures. The two major determinants of mutation supply, population size and mutation rate, both showed a positive temperature dependence. Stronger diversifying selection in warmer environments was suggested by promoted coexistence, and further explicitly inferred by the ability of evolved phenotypes to invade the ancestral type from rare. We discuss possible physiological and environmental mechanisms underlying the findings, most of which are likely to be general.
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Affiliation(s)
- Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Han-Shu Lu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Angus Buckling
- ESI and CEC, Biosciences, University of Exeter, Penryn, Cornwall TR10 9EZ, UK
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12
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Chen H, Xia Q, Yang T, Shi W. Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa. Front Microbiol 2018; 9:1776. [PMID: 30116234 PMCID: PMC6083213 DOI: 10.3389/fmicb.2018.01776] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/16/2018] [Indexed: 01/25/2023] Open
Abstract
Soil microbes have critical influence on the productivity and sustainability of agricultural ecosystems, yet the magnitude and direction to which management practices affect the soil microbial community remain unclear. This work aimed to examine the impacts of three farming systems, conventional grain cropping (CON), organic grain cropping (ORG), and grain cropping-pasture rotation (ICL), on the soil microbial community structure and putative gene abundances of N transformations using high-throughput 16S rRNA gene and ITS sequencing approaches. Two additional systems, a forest plantation (PF) and an abandoned agricultural field subject to natural succession (SUC), were also included for better assessment of the soil microbial community in terms of variation scale and regulatory importance of management intensity vs. plant type. Farming systems significantly affected the biodiversity of soil fungi but not bacteria, with Shannon index being the lowest in ORG. Bacterial and fungal communities in three cropping systems clustered and separated from those in PF and SUC, suggesting that management practices as such played minor roles in shaping the soil microbial community compared to plant type (i.e., woody vs. herbaceous plants). However, management practices prominently regulated habitat-specific taxa. Lecanoromycetes, a class of Ascomycota accounted for ∼10% of total fungal population in ORG, but almost nil in the other four systems. ORG also enriched bacteria belonging to the phyla, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes. Further, PICRUSt predicted that N-cycle community compositions varied with farming systems; compared to CON, ORG and ICL were more divergent from PF and SUC. Soil pH, together with inorganic N, extractable organic C, and soil organic C:N ratio explained < 50% of the total variations in both bacterial and fungal communities. Our data indicates that while moderately affecting the overall structure of the soil microbial community, management practices, particularly fertilization and the source of N (synthetic vs. organic), were important in regulating the presence and abundance of habitat-specific taxa.
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Affiliation(s)
- Huaihai Chen
- Department of Crop and Soil Sciences, NC State University, Raleigh, NC, United States
| | - Qing Xia
- Department of Crop and Soil Sciences, NC State University, Raleigh, NC, United States
| | - Tianyou Yang
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Wei Shi
- Department of Crop and Soil Sciences, NC State University, Raleigh, NC, United States
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13
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Purahong W, Wubet T, Kahl T, Arnstadt T, Hoppe B, Lentendu G, Baber K, Rose T, Kellner H, Hofrichter M, Bauhus J, Krüger D, Buscot F. Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy ensure ecosystem function. Environ Microbiol 2018; 20:1693-1710. [PMID: 29473288 DOI: 10.1111/1462-2920.14081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/13/2018] [Accepted: 02/20/2018] [Indexed: 01/07/2023]
Abstract
Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions and processes are still unclear. Here, we investigated the impacts of N deposition on wood-inhabiting fungi (WIF) and their related ecological functions and processes in a highly N-limited deadwood habitat. Based on high-throughput sequencing, enzymatic activity assay and measurements of wood decomposition rates, we show that N addition has no significant effect on the overall WIF community composition or on related ecosystem functions and processes in this habitat. Nevertheless, we detected several switches in presence/absence (gain/loss) of wood-inhabiting fungal OTUs due to the effect of N addition. The responses of WIF differed from previous studies carried out with fungi living in soil and leaf-litter, which represent less N-limited fungal habitats. Our results suggest that adaptation at different levels of organization and functional redundancy may explain this buffered response and the resistant microbial-mediated ecosystem function and processes against N deposition in highly N-limited habitats.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
| | - Tiemo Kahl
- University of Freiburg, Faculty of Environment and Natural Resources, Chair of Silviculture, Tennenbacherstr. 4, Freiburg im Breisgau, D-79085, Germany.,Biosphere Reserve Vessertal-Thuringian Forest, Brunnenstr. 1, Schmiedefeld am Rennsteig, D-98711, Germany
| | - Tobias Arnstadt
- Technische Universität Dresden - International Institute (IHI) Zittau, Department of Bio- and Environmental Sciences, Markt 23, Zittau, D-02763, Germany
| | - Björn Hoppe
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Messeweg 11/12, Braunschweig, D-38104, Germany
| | - Guillaume Lentendu
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern, 67663, Germany
| | - Kristin Baber
- Department of Systematic Botany and Functional Biodiversity, University of Leipzig, Institute of Biology Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Tyler Rose
- University of Freiburg, Faculty of Environment and Natural Resources, Chair of Silviculture, Tennenbacherstr. 4, Freiburg im Breisgau, D-79085, Germany
| | - Harald Kellner
- Technische Universität Dresden - International Institute (IHI) Zittau, Department of Bio- and Environmental Sciences, Markt 23, Zittau, D-02763, Germany
| | - Martin Hofrichter
- Technische Universität Dresden - International Institute (IHI) Zittau, Department of Bio- and Environmental Sciences, Markt 23, Zittau, D-02763, Germany
| | - Jürgen Bauhus
- University of Freiburg, Faculty of Environment and Natural Resources, Chair of Silviculture, Tennenbacherstr. 4, Freiburg im Breisgau, D-79085, Germany
| | - Dirk Krüger
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
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14
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Characterization of fungi from different ecosystems of tropical peat in Sarawak, Malaysia. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2018. [DOI: 10.1007/s12210-018-0685-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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15
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Kaspari M, Bujan J, Weiser MD, Ning D, Michaletz ST, Zhili H, Enquist BJ, Waide RB, Zhou J, Turner BL, Wright SJ. Biogeochemistry drives diversity in the prokaryotes, fungi, and invertebrates of a Panama forest. Ecology 2017; 98:2019-2028. [PMID: 28500769 DOI: 10.1002/ecy.1895] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/26/2017] [Accepted: 05/05/2017] [Indexed: 01/13/2023]
Abstract
Humans are both fertilizing the world and depleting its soils, decreasing the diversity of aquatic ecosystems and terrestrial plants in the process. We know less about how nutrients shape the abundance and diversity of the prokaryotes, fungi, and invertebrates of Earth's soils. Here we explore this question in the soils of a Panama forest subject to a 13-yr fertilization with factorial combinations of nitrogen (N), phosphorus (P), and potassium (K) and a separate micronutrient cocktail. We contrast three hypotheses linking biogeochemistry to abundance and diversity. Consistent with the Stress Hypothesis, adding N suppressed the abundance of invertebrates and the richness of all three groups of organisms by ca. 1 SD or more below controls. Nitrogen addition plots were 0.8 pH units more acidic with 18% more exchangeable aluminum, which is toxic to both prokaryotes and eukaryotes. These stress effects were frequently reversed, however, when N was added with P (for prokaryotes and invertebrates) and with added K (for fungi). Consistent with the Abundance Hypothesis, adding P generally increased prokaryote and invertebrate diversity, and adding K enhanced invertebrate diversity. Also consistent with the Abundance Hypothesis, increases in invertebrate abundance generated increases in richness. We found little evidence for the Competition Hypothesis: that single nutrients suppressed diversity by favoring a subset of high nutrient specialists, and that nutrient combinations suppressed diversity even more. Instead, combinations of nutrients, and especially the cation/micronutrient treatment, yielded the largest increases in richness in the two eukaryote groups. In sum, changes in soil biogeochemistry revealed a diversity of responses among the three dominant soil groups, positive synergies among nutrients, and-in contrast with terrestrial plants-the frequent enhancement of soil biodiversity.
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Affiliation(s)
- Michael Kaspari
- Department of Biology, Graduate Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, 73019, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Jelena Bujan
- Department of Biology, Graduate Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, 73019, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Michael D Weiser
- Department of Biology, Graduate Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Daliang Ning
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Sean T Michaletz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA.,Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, Los Alamos, New Mexico, 87545, USA
| | - He Zhili
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA.,Santa Fe Institute, Santa Fe, New Mexico, 87501, USA
| | - Robert B Waide
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131, USA.,LTER Network Office, University of New Mexico, Albuquerque, New Mexico, 87131, USA
| | - Jizhong Zhou
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA.,CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
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16
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Fernandez RD, Bulacio N, Álvarez A, Pajot H, Aragón R. Fungal decomposers of leaf litter from an invaded and native mountain forest of NW Argentina. Antonie van Leeuwenhoek 2017; 110:1207-1218. [PMID: 28553697 DOI: 10.1007/s10482-017-0893-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/22/2017] [Indexed: 11/27/2022]
Abstract
The impact of plant species invasions on the abundance, composition and activity of fungal decomposers of leaf litter is poorly understood. In this study, we isolated and compared the relative abundance of ligninocellulolytic fungi of leaf litter mixtures from a native forest and a forest invaded by Ligustrum lucidum in a lower mountain forest of Tucuman, Argentina. In addition, we evaluated the relationship between the relative abundance of ligninocellulolytic fungi and properties of the soil of both forest types. Finally, we identified lignin degrading fungi and characterized their polyphenol oxidase activities. The relative abundance of ligninocellulolytic fungi was higher in leaf litter mixtures from the native forest. The abundance of cellulolytic fungi was negatively related with soil pH while the abundance of ligninolytic fungi was positively related with soil humidity. We identified fifteen genera of ligninolytic fungi; four strains were isolated from both forest types, six strains only from the invaded forest and five strains were isolated only from the native forest. The results found in this study suggest that L. Lucidum invasion could alter the abundance and composition of fungal decomposers. Long-term studies that include an analysis of the nutritional quality of litter are needed, for a more complete overview of the influence of L. Lucidum invasion on fungal decomposers and on leaf litter decomposition.
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Affiliation(s)
- Romina Daiana Fernandez
- Instituto de Ecología Regional (IER, UNT- CONICET), Casilla de Correo 34(4107), Yerba Buena, Tucumán, Argentina.
| | - Natalia Bulacio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Avenida Belgrano y Pasaje Caseros(4000), San Miguel De Tucumán, Tucumán, Argentina
| | - Analía Álvarez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Avenida Belgrano y Pasaje Caseros(4000), San Miguel De Tucumán, Tucumán, Argentina
- Facultad de Ciencias Naturales e IML (UNT), Miguel Lillo 205(4000), San Miguel De Tucumán, Tucumán, Argentina
| | - Hipólito Pajot
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Avenida Belgrano y Pasaje Caseros(4000), San Miguel De Tucumán, Tucumán, Argentina
| | - Roxana Aragón
- Instituto de Ecología Regional (IER, UNT- CONICET), Casilla de Correo 34(4107), Yerba Buena, Tucumán, Argentina
- Facultad de Ciencias Naturales e IML (UNT), Miguel Lillo 205(4000), San Miguel De Tucumán, Tucumán, Argentina
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17
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Gao C, Shi NN, Chen L, Ji NN, Wu BW, Wang YL, Xu Y, Zheng Y, Mi XC, Ma KP, Guo LD. Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest. THE NEW PHYTOLOGIST 2017; 213:1874-1885. [PMID: 28164340 DOI: 10.1111/nph.14287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Elucidating interactions of above-ground and below-ground communities in different habitat types is essential for understanding biodiversity maintenance and ecosystem functioning. Using 454 pyrosequencing of ITS2 sequences we examined the relationship between subtropical mountain forest soil fungal communities, abiotic conditions, and plant communities using correlation and partial models. Ridge and valley habitats with differing fungal communities were delineated. Total, saprotrophic and pathogenic fungal richness were significantly correlated with plant species richness and/or soil nutrients and moisture in the ridge habitat, but with habitat convexity or basal area of Castanopsis eyrei in the valley habitat. Ectomycorrhizal (EM) fungal richness was significantly correlated with basal area of C. eyrei and total EM plants in the ridge and valley habitats, respectively. Total, saprotrophic, pathogenic and EM fungal compositions were significantly correlated with plant species composition and geographic distance in the ridge habitat, but with various combinations of plant species composition, plant species richness, soil C : N ratio and pH or no variables in the valley habitat. Our findings suggest that mechanisms influencing soil fungal diversity and community composition differ between ridge and valley habitats, and relationships between fungal and woody plant assemblages depend on habitat types in the subtropical forest ecosystem.
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Affiliation(s)
- Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Nan-Nan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Niu-Niu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin-Wei Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Zheng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ke-Ping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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18
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Schimann H, Bach C, Lengelle J, Louisanna E, Barantal S, Murat C, Buée M. Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence. MICROBIAL ECOLOGY 2017; 73:310-320. [PMID: 27645139 DOI: 10.1007/s00248-016-0839-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.
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Affiliation(s)
- Heidy Schimann
- INRA, UMR Ecology of Guiana Forests (AgroParisTech, CNRS, CIRAD, Université des Antilles, Université de Guyane), 97310, Kourou, France.
| | - Cyrille Bach
- INRA, UMR Interactions Arbres-Microorganisms, Université de Lorraine, 54280, Champenoux, France
| | - Juliette Lengelle
- INRA, UMR Interactions Arbres-Microorganisms, Université de Lorraine, 54280, Champenoux, France
| | - Eliane Louisanna
- INRA, UMR Ecology of Guiana Forests (AgroParisTech, CNRS, CIRAD, Université des Antilles, Université de Guyane), 97310, Kourou, France
| | - Sandra Barantal
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et Pays de l'Adour, 64000, Pau, France
| | - Claude Murat
- INRA, UMR Interactions Arbres-Microorganisms, Université de Lorraine, 54280, Champenoux, France
| | - Marc Buée
- INRA, UMR Interactions Arbres-Microorganisms, Université de Lorraine, 54280, Champenoux, France
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19
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Monkai J, Hyde KD, Xu J, Mortimer PE. Diversity and ecology of soil fungal communities in rubber plantations. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2016.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Kivlin SN, Hawkes CV. Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests. Environ Microbiol 2016; 18:4662-4673. [PMID: 27130750 DOI: 10.1111/1462-2920.13342] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/13/2016] [Indexed: 11/29/2022]
Abstract
Tropical ecosystems remain poorly understood and this is particularly true for belowground soil fungi. Soil fungi may respond to plant identity when, for example, plants differentially allocate resources belowground. However, spatial and temporal heterogeneity in factors such as plant inputs, moisture, or nutrients can also affect fungal communities and obscure our ability to detect plant effects in single time point studies or within diverse forests. To address this, we sampled replicated monocultures of four tree species and secondary forest controls sampled in the drier and wetter seasons over 2 years. Fungal community composition was primarily related to vegetation type and spatial heterogeneity in the effects of vegetation type, with increasing divergence partly reflecting greater differences in soil pH and soil moisture. Across wetter versus drier dates, fungi were 7% less diverse, but up to four-fold more abundant. The combined effects of tree species and seasonality suggest that predicted losses of tropical tree diversity and intensification of drought have the potential to cascade belowground to affect both diversity and abundance of tropical soil fungi.
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Affiliation(s)
- Stephanie N Kivlin
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78701, USA
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78701, USA
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21
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Mueller RC, Rodrigues JLM, Nüsslein K, Bohannan BJM. Land use change in the Amazon rain forest favours generalist fungi. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12651] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rebecca C. Mueller
- Institute of Ecology and Evolution University of Oregon Eugene Oregon 97403 USA
| | - Jorge L. M. Rodrigues
- Department of Land Air and Water Resources University of California Davis Davis California 95616 USA
| | - Klaus Nüsslein
- Department of Microbiology University of Massachusetts Amherst Amherst Massachusetts 01003 USA
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22
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Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, Schilling JS, Kennedy PG. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.06.006] [Citation(s) in RCA: 1783] [Impact Index Per Article: 222.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Fernandes I, Pereira A, Trabulo J, Pascoal C, Cássio F, Duarte S. Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity? FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Langarica-Fuentes A, Fox G, Robson GD. Metabarcoding analysis of home composts reveals distinctive fungal communities with a high number of unassigned sequences. Microbiology (Reading) 2015; 161:1921-1932. [DOI: 10.1099/mic.0.000153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Adrian Langarica-Fuentes
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Graeme Fox
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Geoffrey D. Robson
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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25
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26
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Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH. METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol Ecol Resour 2015; 15:1403-14. [PMID: 25732605 DOI: 10.1111/1755-0998.12399] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 11/29/2022]
Abstract
The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The METAXA software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to METAXA - METAXA2 - that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short-read (100 bp) and paired-end sequences, among other changes. The performance of METAXA2 was compared to other commonly used taxonomic classifiers, showing that METAXA2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. METAXA2 is freely available from http://microbiology.se/software/metaxa2/.
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Affiliation(s)
- Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46, Gothenburg, Sweden
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland.,Molecular Ecology, Institute for Sustainability Sciences, Agroscope, CH-8046 Zurich, Switzerland
| | - Karl Martin Eriksson
- Department of Shipping and Marine Technology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Chandan Pal
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46, Gothenburg, Sweden
| | - Kaisa Thorell
- Department of Microbiology and Immunology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Box 435, 40530 Gothenburg, Sweden.,Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels Väg 16, 171 77 Stockholm, Sweden
| | - Dan Göran Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 413 46, Gothenburg, Sweden
| | - Rolf Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
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Amend AS, Matulich KL, Martiny JBH. Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities. Front Microbiol 2015; 6:109. [PMID: 25741330 PMCID: PMC4332350 DOI: 10.3389/fmicb.2015.00109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/28/2015] [Indexed: 11/15/2022] Open
Abstract
Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity (PD). This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between PD and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial PD, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of 66 days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial PD failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which PD predicts ecosystem function will depend on environmental context.
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Affiliation(s)
- Anthony S Amend
- Department of Botany, University of Hawaii at Manoa Honolulu, HI, USA
| | - Kristin L Matulich
- Department of Ecology and Evolutionary Biology, University of California at Irvine Irvine, CA USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California at Irvine Irvine, CA USA
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28
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An investigation of the biodiversity of thermophilic and thermotolerant fungal species in composts using culture-based and molecular techniques. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2014.05.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0300-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Brown SP, Rigdon-Huss AR, Jumpponen A. Analyses of ITS and LSU gene regions provide congruent results on fungal community responses. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2014.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Branco S, Bruns TD, Singleton I. Fungi at a small scale: spatial zonation of fungal assemblages around single trees. PLoS One 2013; 8:e78295. [PMID: 24147130 PMCID: PMC3797779 DOI: 10.1371/journal.pone.0078295] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/13/2013] [Indexed: 01/25/2023] Open
Abstract
Biological communities are often structured by environmental factors even at small spatial scales. Fungi are no exception, though the patterns and mechanisms underlying their community structure are usually unknown. Previous work documented zonation in fungi under tree canopies primarily through their fruiting patterns. Here we investigate the existence of zonation patterns in fungal communities around isolated Pinus muricata trees of different ages in northern coastal California. Using a combination of ingrowth bags and pyrosequencing to target underground mycelium we found highly diverse soil fungal communities associated with single trees. Both ectomycorrhizal and non-ectomycorrhizal fungi were present in all samples, but the latter were more species rich, dominated the samples by sequence read abundance, and showed partitioning by canopy-defined zones and tree age. Soil chemistry was correlated with fungal zonation, but host root density was not. Our results indicate different guilds of fungi partition space differently and are driven by distinct environmental parameters.
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Affiliation(s)
- Sara Branco
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Ian Singleton
- School of Biology and Newcastle Institute for Research on Sustainability, Newcastle University, Newcastle upon Tyne, United Kingdom
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Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H. Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide. THE NEW PHYTOLOGIST 2013; 199:288-299. [PMID: 23534863 PMCID: PMC3712477 DOI: 10.1111/nph.12243] [Citation(s) in RCA: 510] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/18/2013] [Indexed: 05/17/2023]
Abstract
Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
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Affiliation(s)
- Björn D Lindahl
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Kessy Abarenkov
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Tor Carlsen
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Taina Pennanen
- The Finnish Forest Research Institute, PL 18, FI-01301, Vantaa, Finland
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Håvard Kauserud
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
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