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Leal CM, Geiger A, Molnár A, Váczy KZ, Kgobe G, Zsófi Z, Geml J. Disentangling the effects of terroir, season, and vintage on the grapevine fungal pathobiome. Front Microbiol 2024; 14:1322559. [PMID: 38298541 PMCID: PMC10829339 DOI: 10.3389/fmicb.2023.1322559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024] Open
Abstract
The composition, diversity and dynamics of microbial communities associated with grapevines may be influenced by various environmental factors, including terroir, vintage, and season. Among these factors, terroir stands out as a unique possible determinant of the pathobiome, the community of plant-associated pathogens. This study employed high-throughput molecular techniques, including metabarcoding and network analysis, to investigate the compositional dynamics of grapevine fungal pathobiome across three microhabitats (soil, woody tissue, and bark) using the Furmint cultivar. Samples were collected during late winter and late summer in 2020 and 2021, across three distinct terroirs in Hungary's Tokaj wine region. Of the 123 plant pathogenic genera found, Diplodia, Phaeomoniella, and Fusarium displayed the highest richness in bark, wood, and soil, respectively. Both richness and abundance exhibited significant disparities across microhabitats, with plant pathogenic fungi known to cause grapevine trunk diseases (GTDs) demonstrating highest richness and abundance in wood and bark samples, and non-GTD pathogens prevailed soil. Abundance and richness, however, followed distinct patterns Terroir accounted for a substantial portion of the variance in fungal community composition, ranging from 14.46 to 24.67%. Season and vintage also contributed to the variation, explaining 1.84 to 2.98% and 3.67 to 6.39% of the variance, respectively. Notably, significant compositional differences in fungi between healthy and diseased grapevines were only identified in wood and bark samples. Cooccurrence networks analysis, using both unweighted and weighted metrics, revealed intricate relationships among pathogenic fungal genera. This involved mostly positive associations, potentially suggesting synergism, and a few negative relationships, potentially suggesting antagonistic interactions. In essence, the observed differences among terroirs may stem from environmental filtering due to varied edaphic and mesoclimatic conditions. Temporal weather and vine management practices could explain seasonal and vintage fungal dynamics. This study provides insights into the compositional dynamics of grapevine fungal pathobiome across different microhabitats, terroirs, seasons, and health statuses. The findings emphasize the importance of considering network-based approaches in studying microbial communities and have implications for developing improved viticultural plant health strategies.
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Affiliation(s)
- Carla Mota Leal
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
| | - Adrienn Geiger
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Anna Molnár
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Kálmán Z. Váczy
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Glodia Kgobe
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
| | - Zsolt Zsófi
- Institute for Viticulture and Enology, Eszterházy Károly Catholic University, Eger, Hungary
| | - József Geml
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
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Moulíková Š, Kolařík M, Lorch J, Kolarczyková D, Hubka V, Čmoková A. Wild rodents harbour high diversity of Arthroderma. PERSOONIA 2023; 50:27-47. [PMID: 38567260 PMCID: PMC10983839 DOI: 10.3767/persoonia.2023.50.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/01/2022] [Indexed: 02/04/2023]
Abstract
Arthroderma is the most diverse genus of dermatophytes, and its natural reservoir is considered to be soil enriched by keratin sources. During a study on the diversity of dermatophytes in wild small rodents in the Czech Republic, we isolated several strains of Arthroderma. To explore the diversity and ecological significance of these isolates from rodents (n = 29), we characterised the strains genetically (i.e., sequenced ITS, tubb and tef1α), morphologically, physiologically, and by conducting mating experiments. We then compared the rodent-derived strains to existing ITS sequence data from GenBank and the GlobalFungi Database to further investigate biogeography and the association of Arthroderma species with different types of environments. In total, eight Arthroderma species were isolated from rodents, including four previously described species (A. crocatum, A. cuniculi, A. curreyi, A. quadrifidum) and four new species proposed herein, i.e., A. rodenticum, A. simile, A. zoogenum and A. psychrophilum. The geographical distribution of these newly described species was not restricted to the Czech Republic nor rodents. Additional isolates were obtained from bats and other mammals, reptiles, and soil from Europe, North America, and Asia. Data mining showed that the genus has a diverse ecology, with some lineages occurring relatively frequently in soil, whereas others appeared to be more closely associated with live animals, as we observed in A. rodenticum. Low numbers of sequence reads ascribed to Arthroderma in soil show that the genus is rare in this environment, which supports the hypothesis that Arthroderma spp. are not soil generalists but rather strongly associated with animals and keratin debris. This is the first study to utilise existing metabarcoding data to assess biogeographical, ecological, and diversity patterns in dermatophytes. Citation: Moulíková Š, Kolařík M, Lorch JM, et al. 2022. Wild rodents harbour high diversity of Arthroderma. Persoonia 50: 27- 47. https://doi.org/10.3767/persoonia.2023.50.02.
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Affiliation(s)
- Š. Moulíková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - J.M. Lorch
- U.S. Geological Survey — National Wildlife Health Center, Madison, Wisconsin, USA
| | - D. Kolarczyková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - A. Čmoková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
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3
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Martín-Pinto P, Fernández C, Santos M, Fontúrbel T, Oria-de-Rueda JA, Vázquez-Veloso A, Stadler T, Mediavilla O, Sanz-Benito I. Unaltered fungal community after fire prevention treatments over widespread Mediterranean rockroses (Halimium lasianthum). Sci Rep 2023; 13:608. [PMID: 36635464 PMCID: PMC9837117 DOI: 10.1038/s41598-023-27945-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Mediterranean ecosystems are frequently invaded by pyrophytic scrubs such as Halimium lasianthum that colonize areas traditionally used by livestock. A diverse fungal community is associated with this kind of vegetation, playing an important ecological role in these ecosystems. However, uncontrolled expansion of these shrubs considerably increases the risk of wildfires in these stands and, hence, fire-prevention treatments are needed. To investigate the long-term effects of two different forest-fire-prevention treatments on the soil fungal community, we analyzed these communities 9 years after prescribed burning or mechanical shredding were carried out in scrubland dominated by H. lasianthum. Neither of the fire-prevention treatments had a negative long-term effect on the abundance or richness of ectomycorrhizal fungi. However, saprotrophs and lichenized fungi experienced negative effects. Soil fertility significantly affected the distribution of fungi according to their functional groups, and pH was the most influential variable in terms of the distribution of edible species. Our findings indicate that forest management practices to prevent forest fires does not negatively affect the fungal community in the long-term, but for lichens and decomposers. Moreover, prescribed burning is suggested as a more economical way of reducing the risk of wildfires without affecting the ecology of the fungal community.
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Affiliation(s)
- Pablo Martín-Pinto
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, S/N, 34004, Palencia, Spain. .,Department of Vegetal Production and Natural Resources, University of Valladolid, Avenida Madrid, S/N, 34004, Palencia, Spain.
| | - Cristina Fernández
- Centro de Investigación Forestal-Lourizán, Xunta de Galicia, P.O. Box. 127, 36080 Pontevedra, Spain
| | - María Santos
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, S/N, 34004 Palencia, Spain
| | - Teresa Fontúrbel
- Centro de Investigación Forestal-Lourizán, Xunta de Galicia, P.O. Box. 127, 36080 Pontevedra, Spain
| | - Juan Andrés Oria-de-Rueda
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, S/N, 34004 Palencia, Spain
| | - Aitor Vázquez-Veloso
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, S/N, 34004 Palencia, Spain
| | - Tim Stadler
- University for Sustainable Development Eberswalde, Schickler Street 5, 16225 Eberswalde, Germany
| | - Olaya Mediavilla
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, S/N, 34004 Palencia, Spain
| | - Ignacio Sanz-Benito
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, S/N, 34004 Palencia, Spain
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Geml J, Leal CM, Nagy R, Sulyok J. Abiotic environmental factors drive the diversity, compositional dynamics and habitat preference of ectomycorrhizal fungi in Pannonian forest types. Front Microbiol 2022; 13:1007935. [PMID: 36312934 PMCID: PMC9597314 DOI: 10.3389/fmicb.2022.1007935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
Ectomycorrhizal (ECM) fungi are among the most diverse and dominant fungal groups in temperate forests and are crucial for ecosystem functioning of forests and their resilience toward disturbance. We carried out DNA metabarcoding of ECM fungi from soil samples taken at 62 sites in the Bükk Mountains in northern Hungary. The selected sampling sites represent the characteristic Pannonian forest types distributed along elevation (i.e., temperature), pH and slope aspect gradients. We compared richness and community composition of ECM fungi among forest types and explored relationships among environmental variables and ECM fungal alpha and beta diversity. The DNA sequence data generated in this study indicated strong correlations between fungal community composition and environmental variables, particularly with pH and soil moisture, with many ECM fungi showing preference for specific zonal, topographic or edaphic forest types. Several ECM fungal genera showed significant differences in richness among forest types and exhibited strong compositional differences mostly driven by differences in environmental factors. Despite the relatively high proportions of compositional variance explained by the tested environmental variables, a large proportion of the compositional variance remained unexplained, indicating that both niche (environmental filtering) and neutral (stochastic) processes shape ECM fungal community composition at landscape level. Our work provides unprecedented insights into the diversity, landscape-level distribution, and habitat preferences of ECM fungi in the Pannonian forests of Northern Hungary.
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Affiliation(s)
- József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Research and Development Centre, Eszterházy Károly Catholic University, Eger, Hungary
- *Correspondence: József Geml,
| | - Carla Mota Leal
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
| | - Richárd Nagy
- Research and Development Centre, Eszterházy Károly Catholic University, Eger, Hungary
| | - József Sulyok
- Biodiversity Protection Group, Bükk National Park Directorate, Eger, Hungary
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5
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Molnár A, Geml J, Geiger A, Leal CM, Kgobe G, Tóth AM, Villangó S, Mézes L, Czeglédi M, Lőrincz G, Zsófi Z. Exploring Relationships among Grapevine Chemical and Physiological Parameters and Leaf and Berry Mycobiome Composition. PLANTS 2022; 11:plants11151924. [PMID: 35893628 PMCID: PMC9331551 DOI: 10.3390/plants11151924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022]
Abstract
Improving our knowledge on biotic and abiotic factors that influence the composition of the grapevine mycobiome is of great agricultural significance, due to potential effects on plant health, productivity, and wine characteristics. Here, we assessed the influence of scion cultivar on the diversity and composition of fungal communities in the berries and leaves of three different cultivars. We generated DNA metabarcoding data, and statistically compared the richness, relative abundance, and composition of several functional groups of fungi among cultivars, which are partly explained by measured differences in chemical composition of leaves and berries and physiological traits of leaves. Fungal communities in leaves and berries show contrasting patterns among cultivars. The richness and relative abundance of fungal functional groups statistically differ among berry and leaf samples, but less so among cultivars. Community composition of the dominant functional groups of fungi, i.e., plant pathogens in leaves and saprotrophs in berries, differs significantly among cultivars. We also detect cultivar-level differences in the macro- and microelement content of the leaves, and in acidity and sugar concentration of berries. Our findings suggest that there appears to be a relatively diverse set of fungi that make up the grapevine mycobiome at the sampled terroir that spans several cultivars, and that both berry and leaf mycobiomes are likely influenced by the chemical characteristics of berries and leaves, e.g., pH and the availability of nutrients and simple carbohydrates. Finally, the correlation between fungal community composition and physiological variables in leaves is noteworthy, and merits further research to explore causality. Our findings offer novel insights into the microbial dynamics of grapevine considering plant chemistry and physiology, with implications for viticulture.
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Affiliation(s)
- Anna Molnár
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
| | - József Geml
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
- ELKH–EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary;
- Correspondence: ; Tel.: +36-365204004406
| | - Adrienn Geiger
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Páter K. u. 1, 2100 Gödöllő, Hungary;
| | - Carla Mota Leal
- ELKH–EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary;
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Páter K. u. 1, 2100 Gödöllő, Hungary;
| | - Glodia Kgobe
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Páter K. u. 1, 2100 Gödöllő, Hungary;
| | - Adrienn Mária Tóth
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
| | - Szabolcs Villangó
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
| | - Lili Mézes
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
| | - Márk Czeglédi
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
| | - György Lőrincz
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
| | - Zsolt Zsófi
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
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6
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Geml J, Arnold AE, Semenova-Nelsen TA, Nouhra ER, Drechsler-Santos ER, Góes-Neto A, Morgado LN, Ódor P, Hegyi B, Grau O, Ibáñez A, Tedersoo L, Lutzoni F. Community dynamics of soil-borne fungal communities along elevation gradients in neotropical and paleotropical forests. Mol Ecol 2022; 31:2044-2060. [PMID: 35080063 DOI: 10.1111/mec.16368] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 12/28/2021] [Accepted: 01/18/2022] [Indexed: 11/29/2022]
Abstract
Because of their steep gradients in abiotic and biotic factors, mountains offer an ideal setting to illuminate the mechanisms that underlie patterns of species distributions and community assembly. We compared the composition of taxonomically and functionally diverse fungal communities in soils along five elevational gradients in mountains of the Neo- and Paleotropics (northern Argentina, southern Brazil, Panama, Malaysian Borneo, and Papua New Guinea). Both richness and composition of soil fungal communities reflect environmental factors, particularly temperature and soil pH, with some shared patterns among neotropical and paleotropical regions. Community dynamics are characterized by replacement of species along elevation gradients, implying a relatively narrow elevation range for most fungi, which appears to be driven by contrasting environmental preferences among both functional and taxonomic groups. For functional groups dependent on symbioses with plants (especially ectomycorrhizal fungi), the distribution of host plants drives richness and community composition, resulting in important differences in elevational patterns between neotropical and paleotropical montane communities. The pronounced compositional and functional turnover along elevation gradients implies that tropical montane forest fungi will be sensitive to climate change, resulting in shifts in composition and functionality over time.
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Affiliation(s)
- József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, H-3300, Eger, Hungary.,Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, 2300 RA, Leiden, The Netherlands
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, U.S.A
| | - Tatiana A Semenova-Nelsen
- Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, 2300 RA, Leiden, The Netherlands
| | - Eduardo R Nouhra
- Multidisciplinary Institute of Plant Biology (IMBIV), CONICET, FCEFyN, National University of Córdoba, Córdoba, Córdoba, Argentina
| | | | - Aristóteles Góes-Neto
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luis N Morgado
- Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, 2300 RA, Leiden, The Netherlands.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Péter Ódor
- Institute of Ecology and Botany, Centre for Ecological Research, 2163, Vácrátót, Hungary
| | - Balázs Hegyi
- Research and Development Centre, Eszterházy Károly Catholic University, H-3300, Eger, Hungary.,Doctoral School of Earth Science and Department for Landscape Protection and Environmental Geography, University of Debrecen, H-4002, Debrecen, Hungary
| | - Oriol Grau
- CREAF, Global Ecology Unit, 08193, Cerdanyola del Vallès, Catalonia, Spain.,Cirad, UMR EcoFoG (AgroParisTech, CNRS, Inra, Univ. Antilles, Univ. Guyane), Campus Agronomique, Kourou, French Guiana.,Spanish National Research Council (CSIC), Global Ecology Unit, CREAF-CSIC-UAB, Cerdanyola del Vallès, Catalonia, Spain
| | - Alicia Ibáñez
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, U.S.A
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, 50411, Tartu, Estonia
| | - François Lutzoni
- Department of Biology, Duke University, Durham, NC, 27708, U.S.A
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7
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Pan J, Liu Y, Yang Y, Cheng Z, Lan X, Hu W, Shi G, Zhang Q, Feng H. Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem. Environ Microbiol 2022; 24:3598-3611. [PMID: 35048487 DOI: 10.1111/1462-2920.15900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongjun Liu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.,State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730000, China
| | - Yue Yang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhongxia Cheng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaomei Lan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Weigang Hu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guoxi Shi
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741000, China
| | - Qi Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China
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8
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Yamauchi DH, Garcia Garces H, Teixeira MDM, Rodrigues GFB, Ullmann LS, Garcia Garces A, Hebeler-Barbosa F, Bagagli E. Soil Mycobiome Is Shaped by Vegetation and Microhabitats: A Regional-Scale Study in Southeastern Brazil. J Fungi (Basel) 2021; 7:587. [PMID: 34436126 PMCID: PMC8396882 DOI: 10.3390/jof7080587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 11/20/2022] Open
Abstract
Soil is the principal habitat and reservoir of fungi that act on ecological processes vital for life on Earth. Understanding soil fungal community structures and the patterns of species distribution is crucial, considering climatic change and the increasing anthropic impacts affecting nature. We evaluated the soil fungal diversity in southeastern Brazil, in a transitional region that harbors patches of distinct biomes and ecoregions. The samples originated from eight habitats, namely: semi-deciduous forest, Brazilian savanna, pasture, coffee and sugarcane plantation, abandoned buildings, owls' and armadillos' burrows. Forty-four soil samples collected in two periods were evaluated by metagenomic approaches, focusing on the high-throughput DNA sequencing of the ITS2 rDNA region in the Illumina platform. Normalized difference vegetation index (NDVI) was used for vegetation cover analysis. NDVI values showed a linear relationship with both diversity and richness, reinforcing the importance of a healthy vegetation for the establishment of a diverse and complex fungal community. The owls' burrows presented a peculiar fungal composition, including high rates of Onygenales, commonly associated with keratinous animal wastes, and Trichosporonales, a group of basidiomycetous yeasts. Levels of organic matter and copper influenced all guild communities analyzed, supporting them as important drivers in shaping the fungal communities' structures.
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Affiliation(s)
- Danielle Hamae Yamauchi
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
| | - Hans Garcia Garces
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
| | - Marcus de Melo Teixeira
- Center for Tropical Medicine, Faculty of Medicine, University of Brasília (UnB), Brasília 70910-900, DF, Brazil;
| | - Gabriel Fellipe Barros Rodrigues
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil;
| | - Leila Sabrina Ullmann
- Institute for Biotechnology, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18607-440, SP, Brazil;
| | - Adalberto Garcia Garces
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
| | - Flavia Hebeler-Barbosa
- Laboratory of Molecular Biology, Medical School, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-687, SP, Brazil;
| | - Eduardo Bagagli
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University ‘Júlio de Mesquita Filho’, Botucatu 18618-689, SP, Brazil; (H.G.G.); (A.G.G.)
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9
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Adamo I, Piñuela Y, Bonet JA, Castaño C, Martínez de Aragón J, Parladé J, Pera J, Alday JG. Sampling forest soils to describe fungal diversity and composition. Which is the optimal sampling size in mediterranean pure and mixed pine oak forests? Fungal Biol 2021; 125:469-476. [PMID: 34024594 DOI: 10.1016/j.funbio.2021.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 01/19/2023]
Abstract
Soil sampling is a critical step affecting perceived fungal diversity, however sampling optimization for high-throughput-DNA sequencing studies have never been tested in Mediterranean forest ecosystems. We identified the minimum number of pooled samples needed to obtain a reliable description of fungal communities in terms of diversity and composition in three different Mediterranean forests (pine, oak, and mixed-pine-oak). Twenty soil samples were randomly selected in each of the three plots per type. Samples obtained in 100 m2 plots were pooled to obtain mixtures of 3, 6, 10, 15, 20 samples, and sequenced using Illumina MiSeq of fungal ITS2 amplicons. Pooling three soil samples in Pinus and Quercus stands provided consistent richness estimations, while at least six samples were needed in mixed-stands. β-diversity decreased with increasing sample pools in monospecific-stands, while there was no effect of sample pool size on mixed-stands. Soil sample pooling had no effect over species composition. We estimate that three samples would be already optimal to describe fungal richness and composition in Mediterranean pure stands, while at least six samples would be needed in mixed stands.
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Affiliation(s)
- Irene Adamo
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain; Dep. Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain.
| | - Yasmine Piñuela
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain; Dep. Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain; Forest Science and Technology Centre of Catalonia, Ctra, Sant Llorenç de Morunys Km 2, E25280, Solsona, Spain
| | - José Antonio Bonet
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain; Dep. Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain
| | - Carles Castaño
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, SE, 75007, Uppsala, Sweden
| | - Juan Martínez de Aragón
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain; Forest Science and Technology Centre of Catalonia, Ctra, Sant Llorenç de Morunys Km 2, E25280, Solsona, Spain
| | - Javier Parladé
- Sustainable Plant Protection, IRTA, Centre de Cabrils, Ctra Cabrils Km 2, E08348, Cabrils, Barcelona, Spain
| | - Joan Pera
- Sustainable Plant Protection, IRTA, Centre de Cabrils, Ctra Cabrils Km 2, E08348, Cabrils, Barcelona, Spain
| | - Josu G Alday
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain; Dep. Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198, Lleida, Spain
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10
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Canini F, Geml J, D'Acqui LP, Selbmann L, Onofri S, Ventura S, Zucconi L. Exchangeable cations and pH drive diversity and functionality of fungal communities in biological soil crusts from coastal sites of Victoria Land, Antarctica. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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11
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Grau O, Saravesi K, Ninot JM, Geml J, Markkola A, Ahonen SHK, Peñuelas J. Encroachment of shrubs into subalpine grasslands in the Pyrenees modifies the structure of soil fungal communities and soil properties. FEMS Microbiol Ecol 2019; 95:5370081. [DOI: 10.1093/femsec/fiz028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/05/2019] [Indexed: 01/21/2023] Open
Affiliation(s)
- Oriol Grau
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, 08193, Cerdanyola del Vallès, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Karita Saravesi
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014, University of Oulu, Oulu, Finland
| | - Josep M Ninot
- Institute for Research in Biodiversity (IRBio) and Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - József Geml
- Naturalis Biodiversity Center, Vondellaan 55, P.O. Box 9517, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Annamari Markkola
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014, University of Oulu, Oulu, Finland
| | - Saija HK Ahonen
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014, University of Oulu, Oulu, Finland
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, 08193, Cerdanyola del Vallès, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
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