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Probst M, Ascher-Jenull J, Insam H, Gómez-Brandón M. The Molecular Information About Deadwood Bacteriomes Partly Depends on the Targeted Environmental DNA. Front Microbiol 2021; 12:640386. [PMID: 33986733 PMCID: PMC8110828 DOI: 10.3389/fmicb.2021.640386] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Microbiome studies mostly rely on total DNA extracts obtained directly from environmental samples. The total DNA consists of both intra- and extracellular DNA, which differ in terms of their ecological interpretation. In the present study, we have investigated for the first time the differences among the three DNA types using microbiome sequencing of Picea abies deadwood logs (Hunter decay classes I, III, and V). While the bacterial compositions of all DNA types were comparable in terms of more abundant organisms and mainly depended on the decay class, we found substantial differences between DNA types with regard to less abundant amplicon sequence variants (ASVs). The analysis of the sequentially extracted intra- and extracellular DNA fraction, respectively, increased the ecological depth of analysis compared to the directly extracted total DNA pool. Both DNA fractions were comparable in proportions and the extracellular DNA appeared to persist in the P. abies deadwood logs, thereby causing its masking effect. Indeed, the extracellular DNA masked the compositional dynamics of intact cells in the total DNA pool. Our results provide evidence that the choice of DNA type for analysis might benefit a study’s answer to its respective ecological question. In the deadwood environment researched here, the differential analysis of the DNA types underlined the relevance of Burkholderiales, Rhizobiales and other taxa for P. abies deadwood decomposition and revealed that the role of Acidobacteriota under this scenario might be underestimated, especially compared to Actinobacteriota.
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Affiliation(s)
- Maraike Probst
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - María Gómez-Brandón
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria.,Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, Vigo, Spain
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Nagler M, Podmirseg SM, Mayr M, Ascher-Jenull J, Insam H. The masking effect of extracellular DNA and robustness of intracellular DNA in anaerobic digester NGS studies: A discriminatory study of the total DNA pool. Mol Ecol 2020; 30:438-450. [PMID: 33219564 PMCID: PMC7839673 DOI: 10.1111/mec.15740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 01/08/2023]
Abstract
Most commonly, next generation sequencing-based microbiome studies are performed on the total DNA (totDNA) pool; however, this consists of extracellular- (exDNA) and intracellular (iDNA) DNA fractions. By investigating the microbiomes of different anaerobic digesters over time, we found that totDNA suggested lower species richness considering all and/or only common species and yielded fewer unique reads as compared to iDNA. Additionally, exDNA-derived sequences were more similar to those from totDNA than from iDNA and, finally, iDNA showed the best performance in tracking temporal changes in microbial communities. We postulate that abundant sequences present within the exDNA fraction mask the overall results of totDNA and provide evidence that exDNA has the potential to qualitatively bias microbiome studies at least in the anaerobic digester environment as it contains information about cells that were lysed hours or days ago. iDNA, however, was found to be more appropriate in providing reliable genetic information about potentially alive as well as rare microbes within the target habitat.
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Affiliation(s)
- Magdalena Nagler
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Markus Mayr
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Heribert Insam
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
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Nagler M, Podmirseg SM, Mayr M, Ascher-Jenull J, Insam H. Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea. Front Microbiol 2020; 11:1894. [PMID: 32849470 PMCID: PMC7419480 DOI: 10.3389/fmicb.2020.01894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.
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Affiliation(s)
- Magdalena Nagler
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Markus Mayr
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Heribert Insam
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
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Gómez-Brandón M, Probst M, Siles JA, Peintner U, Bardelli T, Egli M, Insam H, Ascher-Jenull J. Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood. Sci Rep 2020; 10:8025. [PMID: 32415174 PMCID: PMC7228967 DOI: 10.1038/s41598-020-64808-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/20/2020] [Indexed: 11/22/2022] Open
Abstract
Deadwood decomposition is relevant in nature and wood inhabiting fungi (WIF) are its main decomposers. However, climate influence on WIF community and their interactions with bacteria are poorly understood. Therefore, we set up an in-field mesocosm experiment in the Italian Alps and monitored the effect of slope exposure (north- vs. south-facing slope) on the decomposition of Picea abies wood blocks and their microbiome over two years. Unlike fungal richness and diversity, we observed compositional and functional differences in the WIF communities as a function of exposure. Wood-degrading operational taxonomic units (OTUs) such as Mycena, and mycorrhizal and endophytic OTUs were characteristic of the south-facing slope. On the north-facing one, Mucoromycota, primarily Mucor, were abundant and mixotrophic basidiomycetes with limited lignin-degrading capacities had a higher prevalence compared to the southern slope. The colder, more humid conditions and prolonged snow-coverage at north exposure likely influenced the development of the wood-degrading microbial communities. Networks between WIF and N2-fixing bacteria were composed of higher numbers of interacting microbial units and showed denser connections at the south-facing slope. The association of WIF to N2-fixing Burkholderiales and Rhizobiales could have provided additional competitive advantages, especially for early wood colonization.
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Affiliation(s)
- María Gómez-Brandón
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, E-36310, Vigo, Spain.
- Department of Microbiology, University of Innsbruck, Technikerstraβe 25, A-6020, Innsbruck, Austria.
| | - Maraike Probst
- Department of Microbiology, University of Innsbruck, Technikerstraβe 25, A-6020, Innsbruck, Austria
| | - José A Siles
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Technikerstraβe 25, A-6020, Innsbruck, Austria
| | - Tommaso Bardelli
- Department of Microbiology, University of Innsbruck, Technikerstraβe 25, A-6020, Innsbruck, Austria
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Piazzale delle Cascine 18, I-50144, Florence, Italy
- Council for Research and Experimentation in Agriculture (CREA-ZA), Via A. Lombardo 11, I-26900, Lodi, Italy
| | - Markus Egli
- Department of Geography, University of Zürich, Winterthurerstraße 190, CH-8057, Zürich, Switzerland
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstraβe 25, A-6020, Innsbruck, Austria
| | - Judith Ascher-Jenull
- Department of Microbiology, University of Innsbruck, Technikerstraβe 25, A-6020, Innsbruck, Austria
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Pathan SI, Arfaioli P, Ceccherini MT, Ascher-Jenull J, Pietramellara G. Preliminary evidences of the presence of extracellular DNA single stranded forms in soil. PLoS One 2020; 15:e0227296. [PMID: 31910237 PMCID: PMC6946138 DOI: 10.1371/journal.pone.0227296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.
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Affiliation(s)
- Shamina Imran Pathan
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
| | - Paola Arfaioli
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
| | - Maria Teresa Ceccherini
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
| | | | - Giacomo Pietramellara
- Department of Agri-food, Environmental, Forestry Science and Technology (DAGRI), University of Florence, Piazzale delle Cascine, Florence, Italy
- * E-mail:
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Probst M, Gómez-Brandón M, Bardelli T, Egli M, Insam H, Ascher-Jenull J. Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories. Environ Microbiol 2018; 20:3657-3670. [DOI: 10.1111/1462-2920.14359] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/26/2018] [Accepted: 07/08/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Maraike Probst
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
| | - María Gómez-Brandón
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Departamento de Ecología y Biología Animal; Universidad de Vigo; Vigo Spain
| | - Tommaso Bardelli
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Department of Agrifood and Environmental Science; University of Florence; Florence Italy
| | - Markus Egli
- Department of Geography; University of Zürich; Zürich Switzerland
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
| | - Judith Ascher-Jenull
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Department of Agrifood and Environmental Science; University of Florence; Florence Italy
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Nagler M, Insam H, Pietramellara G, Ascher-Jenull J. Extracellular DNA in natural environments: features, relevance and applications. Appl Microbiol Biotechnol 2018; 102:6343-6356. [PMID: 29858957 PMCID: PMC6061472 DOI: 10.1007/s00253-018-9120-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 01/13/2023]
Abstract
Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.
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Affiliation(s)
- Magdalena Nagler
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria.
| | - Heribert Insam
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
| | - Giacomo Pietramellara
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
| | - Judith Ascher-Jenull
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
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Bardelli T, Gómez-Brandón M, Ascher-Jenull J, Fornasier F, Arfaioli P, Francioli D, Egli M, Sartori G, Insam H, Pietramellara G. Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps. Sci Total Environ 2017; 575:1041-1055. [PMID: 27692937 DOI: 10.1016/j.scitotenv.2016.09.176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Due to their sensitivity to changing environmental conditions sub- and alpine soils are often monitored in the context of climate change, usually, however, neglecting slope exposure. Therefore, we set up a climosequence-approach to study the effect of exposure and, in general, climate, on the microbial biomass and microbial diversity and activity, comprising five pairs of north (N)- and south (S)-facing sites along an altitudinal gradient ranging from 1200 to 2400m a.s.l. in the Italian Alps (Trentino Alto Adige, Italy). Soil physico-chemical properties were related to microbiological properties (microbial biomass: double strand DNA yield vs. substrate-induced respiration; diversity of bacterial, fungal and archaeal communities: genetic fingerprinting DGGE vs. real-time PCR; microbial activity: basal respiration vs. multiple hydrolytic enzyme assays) to monitor shifts in the diversity and activity of microbial communities as a function of slope exposure and to evaluate the most determinant chemical parameters shaping the soil microbiota. The exposure-effect on several hydrolytic key-enzymes was enzyme-specific: e.g. acid phosphomonoesterase potential activity was more pronounced at the N-facing slope while the activities of alkaline phosphomonoesterase, pyrophosphate-phosphodiesterase and arylsulfatase were higher at the S-facing slope. Furthermore, this exposure-effect was domain-specific: bacteria (S>N, altitude-independent); fungi (N~S); and archaea (N>S; altitude-dependent). Additionally, the abiotic parameters shaping the community composition were in general depending on soil depth. Our multidisciplinary approach allowed us to survey the exposure and altitudinal effects on soil physico-chemical and microbiological properties and thus unravel the complex multiple edaphic factor-effects on soil microbiota in mountain ecosystems.
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Affiliation(s)
- Tommaso Bardelli
- Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy; Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - María Gómez-Brandón
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - Judith Ascher-Jenull
- Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy; Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - Flavio Fornasier
- Council for Research and Experimentation in Agriculture, Via Trieste 23, 34170 Gorizia, Italy.
| | - Paola Arfaioli
- Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy.
| | - Davide Francioli
- Helmholtz Centre for Environmental Research-UFZ, 06120, Halle (Saale), Germany.
| | - Markus Egli
- Department of Geography, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Giacomo Sartori
- Museo delle Scienze (MUSE), Corso del Lavoro e della Scienza 3, 38122 Trento, Italy.
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - Giacomo Pietramellara
- Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy.
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Fravolini G, Egli M, Derungs C, Cherubini P, Ascher-Jenull J, Gómez-Brandón M, Bardelli T, Tognetti R, Lombardi F, Marchetti M. Soil attributes and microclimate are important drivers of initial deadwood decay in sub-alpine Norway spruce forests. Sci Total Environ 2016; 569-570:1064-1076. [PMID: 27373380 DOI: 10.1016/j.scitotenv.2016.06.167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/20/2016] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
Deadwood is known to significantly contribute to global terrestrial carbon stocks and carbon cycling, but its decay dynamics are still not thoroughly understood. Although the chemistry of deadwood has been studied as a function of decay stage in temperate to subalpine environments, it has generally not been related to time. We therefore studied the decay (mass of deadwood, cellulose and lignin) of equal-sized blocks of Picea abies wood in soil-mesocosms over two years in the Italian Alps. The 8 sites selected were along an altitudinal sequence, reflecting different climate zones. In addition, the effect of exposure (north- and south-facing slopes) was taken into account. The decay dynamics of the mass of deadwood, cellulose and lignin were related to soil parameters (pH, soil texture, moisture, temperature) and climatic data. The decay rate constants of Picea abies deadwood were low (on average between 0.039 and 0.040y(-1)) and of lignin close to zero (or not detectable), while cellulose reacted much faster with average decay rate constants between 0.110 and 0.117y(-1). Our field experiments showed that local scale factors, such as soil parameters and topographic properties, influenced the decay process: higher soil moisture and clay content along with a lower pH seemed to accelerate wood decay. Interestingly, air temperature negatively correlated with decay rates or positively with the amount of wood components on south-facing sites. It exerted its influence rather on moisture availability, i.e. the lower the temperature the higher the moisture availability. Topographic features were also relevant with generally slower decay processes on south-facing sites than on north-facing sites owing to the drier conditions, the higher pH and the lower weathering state of the soils (less clay minerals). This study highlights the importance of a multifactorial consideration of edaphic parameters to unravel the complex dynamics of initial wood decay.
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Affiliation(s)
- Giulia Fravolini
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone snc, 86090 Pesche (IS), Italy.
| | - Markus Egli
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Curdin Derungs
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Paolo Cherubini
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research, Zürcherstrasse 111, 8903 Birmensdorf, ZH, Switzerland.
| | - Judith Ascher-Jenull
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25d, 6020 Innsbruck, Austria; Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 28, I-50144 Florence, Italy.
| | - María Gómez-Brandón
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25d, 6020 Innsbruck, Austria.
| | - Tommaso Bardelli
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25d, 6020 Innsbruck, Austria; Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 28, I-50144 Florence, Italy.
| | - Roberto Tognetti
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone snc, 86090 Pesche (IS), Italy; The EFI Project Centre on Mountain Forests (MOUNTFOR), Edmund Mach Foundation, San Michele all'Adige, Italy.
| | - Fabio Lombardi
- Department of AGRARIA, Mediterranean University of Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria (RC), Italy.
| | - Marco Marchetti
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone snc, 86090 Pesche (IS), Italy.
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