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Mugnai G, Pinchuk I, Borruso L, Tiziani R, Sannino C, Canini F, Turchetti B, Mimmo T, Zucconi L, Buzzini P. The hidden network of biocrust successional stages in the High Arctic: Revealing abiotic and biotic factors shaping microbial and metazoan communities. Sci Total Environ 2024; 926:171786. [PMID: 38508248 DOI: 10.1016/j.scitotenv.2024.171786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
Despite the important role that biocrust communities play in maintaining ecosystem structure and functioning in deglaciated barren soil, few studies have been conducted on the dynamics of biotic communities and the impact of physicochemical characteristics in shaping the different successional stages. In this study an integrated approach encompassing physicochemical parameters and molecular taxonomy was used for identifying the indicator taxa and the presence of intra- and inter-kingdom interactions in five different crust/biocrust successional stages: i) physical crust, ii) cyanobacteria-dominated biocrust, iii) cyanobacteria/moss-dominated biocrust, iv) moss-dominated biocrust and v) bryophyte carpet. The phylum Gemmatimonadota was the bacterial indicator taxon in the early stage, promoting both inter- and intra-kingdom interactions, while Cyanobacteria and Nematoda phyla played a pivotal role in formation and dynamics of cyanobacteria-dominated biocrusts. A multitrophic community, characterized by a shift from oligotrophic to copiotrophic bacteria and the presence of saproxylic arthropod and herbivore insects was found in the cyanobacteria/moss-dominated biocrust, while a more complex biota, characterized by an increased fungal abundance (classes Sordariomycetes, Leotiomycetes, and Dothideomycetes, phylum Ascomycota), associated with highly trophic consumer invertebrates (phyla Arthropoda, Rotifera, Tardigrada), was observed in moss-dominated biocrusts. The class Bdelloidea and the family Hypsibiidae (phyla Rotifera and Tardigrada, respectively) were metazoan indicator taxon in bryophyte carpet, suggesting their potential role in shaping structure and function of this late successional stage. Nitrogen and phosphorus were the main physicochemical limiting factors driving the shift among different crust/biocrust successional stages. Identification and characterization of indicator taxa, biological intra- and inter-kingdom interactions and abiotic factors driving the shift among different crust/biocrust successional stages provide a detailed picture on crust/biocrust dynamics, revealing a strong interconnection among micro- and macrobiota systems. These findings enhance our understanding of biocrust ecosystems in High Arctic, providing valuable insights for their conservation and management in response to environmental shifts due to climate change.
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Affiliation(s)
- Gianmarco Mugnai
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, Perugia 06121, Italy.
| | - Irina Pinchuk
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, Perugia 06121, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Science, Free University of Bolzano-Bozen, Bozen-Bolzano, 39100, Italy
| | - Raphael Tiziani
- Faculty of Agricultural, Environmental and Food Science, Free University of Bolzano-Bozen, Bozen-Bolzano, 39100, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, Perugia 06121, Italy
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, Perugia 06121, Italy
| | - Tanja Mimmo
- Faculty of Agricultural, Environmental and Food Science, Free University of Bolzano-Bozen, Bozen-Bolzano, 39100, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, Perugia 06121, Italy
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Fracasso I, Zaccone C, Oskolkov N, Da Ros L, Dinella A, Belelli Marchesini L, Buzzini P, Sannino C, Turchetti B, Cesco S, Le Roux G, Tonon G, Vernesi C, Mimmo T, Ventura M, Borruso L. Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA. Sci Total Environ 2024; 908:168159. [PMID: 37923262 DOI: 10.1016/j.scitotenv.2023.168159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.
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Affiliation(s)
- Ilaria Fracasso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
| | - Claudio Zaccone
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 221 00 Lund, Sweden
| | - Luca Da Ros
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Anna Dinella
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luca Belelli Marchesini
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Stefano Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Gael Le Roux
- Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245 CNRS/UPS/INPT), Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giustino Tonon
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Tanja Mimmo
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Maurizio Ventura
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
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Leo P, Onofri S, Zucconi L, Selbmann L, Turchetti B, Buzzini P, Chander AM, Simpson A, Singh N, Vellone D, Tighe S, Venkateswaran K. Draft genome sequencing of Naganishia species isolated from the polar environments. Microbiol Resour Announc 2023; 12:e0038823. [PMID: 37754785 PMCID: PMC10586123 DOI: 10.1128/mra.00388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/28/2023] [Indexed: 09/28/2023] Open
Abstract
The draft genomes of five Naganishia strains were sequenced using MinION and annotated using Funannotate pipeline. Phylogenetic and genomic analyses were performed to provide their genetic relationships, diversity, and potential functional capabilities. This approach will aid in understanding their potential to survive under microgravity and their resilience to extreme environments.
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Affiliation(s)
- Patrick Leo
- Biotechnology and Planetary Protection Group, NASA‐Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Environmental Sciences, Informatics, and Statistics, University Ca’ Foscari of Venice, Mestre, Italy
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, Viterbo, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, Viterbo, Italy
- Institute of Polar Sciences, National Research Council of Italy (CNR‐ISP), Messina, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, Viterbo, Italy
- Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Atul M. Chander
- Biotechnology and Planetary Protection Group, NASA‐Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Anna Simpson
- Biotechnology and Planetary Protection Group, NASA‐Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nitin Singh
- Biotechnology and Planetary Protection Group, NASA‐Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Daniel Vellone
- Vermont Integrative Genomics Lab, University of Vermont Cancer Center, Health Science Research Facility, Burlington, Vermont, USA
| | - Scott Tighe
- Vermont Integrative Genomics Lab, University of Vermont Cancer Center, Health Science Research Facility, Burlington, Vermont, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, NASA‐Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Turchetti B, De Francesco G, Mugnai G, Sileoni V, Alfeo V, Buzzini P, Yurkov A, Marconi O. Species and temperature-dependent fermentative aptitudes of Mrakia genus for innovative brewing. Food Res Int 2023; 170:113004. [PMID: 37316073 DOI: 10.1016/j.foodres.2023.113004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
The use of non-conventional brewing yeasts as alternative starters is a very promising approach which received increasing attention from worldwide scientists and brewers. Despite the feasible application of non-conventional yeasts in brewing processes, their regulations and safety assessment by the European Food Safety Authority still represent a bottlenecked hampering their commercial release, at least into EU market. Thus, research on yeast physiology, accurate taxonomic species identification and safety concerns associated with the use of non-conventional yeasts in food chains is needed to develop novel healthier and safer beers. Currently, most of the documented brewing applications catalysed by non-conventional yeasts are associated to ascomycetous yeasts, while little is known about analogous uses of basidiomycetous taxa. Therefore, in order to extend the phenotypic diversity of basidiomycetous brewing yeasts the aim of this investigation is to check the fermentation aptitudes of thirteen Mrakia species in relation to their taxonomic position within the genus Mrakia. The volatile profile, ethanol content and sugar consumption were compared with that produced by a commercial starter for low alcohol beers, namely Saccharomycodes ludwigii WSL 17. The phylogeny of Mrakia genus showed three clusters that clearly exhibited different fermentation aptitudes. Members of M. gelida cluster showed a superior aptitude to produce ethanol, higher alcohols, esters and sugars conversion compared to the members of M. cryoconiti and M. aquatica clusters. Among M. gelida cluster, the strain M. blollopis DBVPG 4974 exhibited a medium flocculation profile, a high tolerance to ethanol and to iso-α-acids, and a considerable production of lactic and acetic acids, and glycerol. In addition, an inverse relationship between fermentative performances and incubation temperature is also displayed by this strain. Possible speculations on the association between the cold adaptation exhibited by M. blollopis DBVPG 4974 and the release of ethanol in the intracellular matrix and in the bordering environment are presented.
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Affiliation(s)
- Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - Giovanni De Francesco
- Italian Brewing Research Centre, University of Perugia, Via San Costanzo, 06126 Perugia, Italy; Department of Agriculture, Food and Environmental Science, University of Perugia, Via San Costanzo, 06126 Perugia, Italy
| | - Gianmarco Mugnai
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy.
| | - Valeria Sileoni
- Universitas Mercatorum, Piazza Mattei, 10, Rome 00186, Italy
| | - Vincenzo Alfeo
- Italian Brewing Research Centre, University of Perugia, Via San Costanzo, 06126 Perugia, Italy
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - Andrey Yurkov
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Brunswick, Germany
| | - Ombretta Marconi
- Italian Brewing Research Centre, University of Perugia, Via San Costanzo, 06126 Perugia, Italy; Department of Agriculture, Food and Environmental Science, University of Perugia, Via San Costanzo, 06126 Perugia, Italy
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Barili S, Bernetti A, Sannino C, Montegiove N, Calzoni E, Cesaretti A, Pinchuk I, Pezzolla D, Turchetti B, Buzzini P, Emiliani C, Gigliotti G. Impact of PVC microplastics on soil chemical and microbiological parameters. Environ Res 2023; 229:115891. [PMID: 37059323 DOI: 10.1016/j.envres.2023.115891] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/15/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
Microplastics (MPs) are emerging pollutants whose occurrence is a global problem in natural ecosystems including soil. Among MPs, polyvinyl chloride (PVC) is a well-known polymer with remarkable resistance to degradation, and because its recalcitrant nature serious environmental concerns are created during manufacturing and waste disposal. The effect of PVC (0.021% w/w) on chemical and microbial parameters of an agricultural soil was tested by a microcosm experiment at different incubation times (from 3 to 360 days). Among chemical parameters, soil CO2 emission, fluorescein diacetate (FDA) activity, total organic C (TOC), total N, water extractable organic C (WEOC), water extractable N (WEN) and SUVA254 were considered, while the structure of soil microbial communities was studied at different taxonomic levels (phylum and genus) by sequencing bacterial 16S and fungal ITS2 rDNA (Illumina MiSeq). Although some fluctuations were found, chemical and microbiological parameters exhibited some significant trends. Significant (p < 0.05) variations of soil CO2 emission, FDA hydrolysis, TOC, WEOC and WEN were found in PVC-treated soils over different incubation times. Considering the structure of soil microbial communities, the presence of PVC significantly (p < 0.05) affected the abundances of specific bacterial and fungal taxa: Candidatus_Saccharibacteria, Proteobacteria, Actinobacteria, Acidobacteria and Bacteroides among bacteria, and Basidiomycota, Mortierellomycota and Ascomycota among fungi. After one year of experiment, a reduction of the number and the dimensions of PVC was detected supposing a possible role of microorganisms on PVC degradation. The abundance of both bacterial and fungal taxa at phylum and genus level was also affected by PVC, suggesting that the impact of this polymer could be taxa-dependent.
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Affiliation(s)
- Sofia Barili
- Department of Civil and Environmental Engineering, University of Perugia, Italy
| | - Alessandro Bernetti
- Department of Agricultural, Food and Environmental Science, University of Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Science, University of Perugia, Italy.
| | - Nicolò Montegiove
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Italy
| | - Eleonora Calzoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Italy
| | - Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Italy
| | - Irina Pinchuk
- Department of Agricultural, Food and Environmental Science, University of Perugia, Italy
| | - Daniela Pezzolla
- Department of Civil and Environmental Engineering, University of Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, University of Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Science, University of Perugia, Italy
| | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Italy
| | - Giovanni Gigliotti
- Department of Civil and Environmental Engineering, University of Perugia, Italy
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Biagioli F, Coleine C, Buzzini P, Turchetti B, Sannino C, Selbmann L. Positive fungal interactions are key drivers in Antarctic endolithic microcosms at the boundaries for life sustainability. FEMS Microbiol Ecol 2023:7158681. [PMID: 37160346 DOI: 10.1093/femsec/fiad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
In the ice-free areas of Victoria Land in continental Antarctica, where the conditions reach the limits for life sustainability, highly adapted and extreme-tolerant microbial communities exploit the last habitable niches inside porous rocks (i.e. cryptoendolithic communities). These guilds host the main standing biomass and principal, if not sole, contributors to environmental/biogeochemical cycles, driving ecosystem processes and functionality in these otherwise dead lands. Although knowledge advances on their composition, ecology, genomic and metabolic features, a large-scale perspective of occurring interactions and interconnections within and between endolithic fungal assemblages is still lacking to date. Unravelling the tight relational network among functional guilds in the Antarctic cryptoendolithic communities may represent a main task. Aiming to fill this knowledge gap, we performed a correlation-network analysis based on amplicon-sequencing data of 74 endolithic microbiomes collected throughout Victoria Land. Endolithic communities' compositional pattern was largely dominated by Lichenized fungi group (83.5%), mainly represented by Lecanorales and Lecideales, followed by Saprotrophs (14.2%) and RIF+BY (2.4%) guilds led by Tremellales and Capnodiales respectively. Our findings highlighted that fungal functional guilds' relational spectrum was dominated by cooperative interactions led by lichenised and black fungi, deeply engaged in community trophic sustain and protection, respectively. On the other hand, a few negative correlations found may help in preserving niche boundaries between microbes living in such strict spatial association.
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Affiliation(s)
- Federico Biagioli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, 06121 Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, 06121 Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, 06121 Perugia, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy
- Italian National Antarctic Museum (MNA), Mycological Section, 16121 Genoa, Italy
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Troiano E, Larini I, Binati RL, Gatto V, Torriani S, Buzzini P, Turchetti B, Salvetti E, Felis GE. Finding a correct species assignment for a Metschnikowia strain: insights from the genome sequencing of strain DBT012. FEMS Yeast Res 2023; 23:7109264. [PMID: 37019825 DOI: 10.1093/femsyr/foad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/07/2023] Open
Abstract
Metschnikowia pulcherrima is an important yeast species that is attracting increased interest thanks to its biotechnological potential, especially in agri-food applications. Phylogenetically related species of the so-called 'pulcherrima clade' were first described and then reclassified in one single species, which makes the identification an intriguing issue. Starting from the whole-genome sequencing of the pro-technological strain Metschnikowia sp. DBT012, this study applied comparative genomics to calculate similarity with the M. pulcherrima clade publicly available genomes with the aim to verify if novel single-copy putative phylogenetic markers could be selected, in comparison with the commonly used primary and secondary barcodes. The genome-based bioinformatic analysis allowed the identification of 85 consensus single-copy orthologs, which were reduced to three after split decomposition analysis. However, wet-lab amplification of these three genes in non-sequenced type strains revealed the presence of multiple copies, which made them unsuitable as phylogenetic markers. Finally, Average Nucleotide Identity (ANI) was calculated between strain DBT012 and available genome sequences of the M. pulcherrima clade, although the genome dataset is still rather limited. Presence of multiple copies of phylogenetic markers as well as ANI values were compatible with the recent reclassification of the clade, allowing the identification of strain DBT012 as M. pulcherrima.
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Affiliation(s)
- Eleonora Troiano
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Ilaria Larini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Renato L Binati
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Veronica Gatto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & DBVPG Industrial Yeasts Collection, University of Perugia, Borgo XX Giugno 74, 06121 Perugia (PG), Italy
| | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & DBVPG Industrial Yeasts Collection, University of Perugia, Borgo XX Giugno 74, 06121 Perugia (PG), Italy
| | - Elisa Salvetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
- VUCC-DBT, Verona University Culture Collection - Department of Biotechnology; University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
- VUCC-DBT, Verona University Culture Collection - Department of Biotechnology; University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
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Sannino C, Borruso L, Mezzasoma A, Turchetti B, Ponti S, Buzzini P, Mimmo T, Guglielmin M. The Unusual Dominance of the Yeast Genus Glaciozyma in the Deeper Layer in an Antarctic Permafrost Core (Adélie Cove, Northern Victoria Land) Is Driven by Elemental Composition. J Fungi (Basel) 2023; 9:jof9040435. [PMID: 37108890 PMCID: PMC10145851 DOI: 10.3390/jof9040435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Rock glaciers are relatively common in Antarctic permafrost areas and could be considered postglacial cryogenic landforms. Although the extensive presence of rock glaciers, their chemical–physical and biotic composition remain scarce. Chemical–physical parameters and fungal community (by sequencing the ITS2 rDNA, Illumina MiSeq) parameters of a permafrost core were studied. The permafrost core, reaching a depth of 6.10 m, was divided into five units based on ice content. The five units (U1–U5) of the permafrost core exhibited several significant (p < 0.05) differences in terms of chemical and physical characteristics, and significant (p < 0.05) higher values of Ca, K, Li, Mg, Mn, S, and Sr were found in U5. Yeasts dominated on filamentous fungi in all the units of the permafrost core; additionally, Ascomycota was the prevalent phylum among filamentous forms, while Basidiomycota was the dominant phylum among yeasts. Surprisingly, in U5 the amplicon sequence variants (ASVs) assigned to the yeast genus Glaciozyma represented about two-thirds of the total reads. This result may be considered extremely rare in Antarctic yeast diversity, especially in permafrost habitats. Based on of the chemical–physical composition of the units, the dominance of Glaciozyma in the deepest unit was correlated with the elemental composition of the core.
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Affiliation(s)
- Ciro Sannino
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Ambra Mezzasoma
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Benedetta Turchetti
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Stefano Ponti
- Department of Theoretical and Applied Sciences, Insubria University, 21100 Varese, Italy
| | - Pietro Buzzini
- Industrial Yeasts Collection DBVPG, Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, Insubria University, 21100 Varese, Italy
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9
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Coleine C, Delgado-Baquerizo M, Zerboni A, Turchetti B, Buzzini P, Franceschi P, Selbmann L. Rock Traits Drive Complex Microbial Communities at the Edge of Life. Astrobiology 2023; 23:395-406. [PMID: 36812458 DOI: 10.1089/ast.2022.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Antarctic deserts are among the driest and coldest ecosystems of the planet; there, some microbes survive under these extreme conditions inside porous rocks, forming the so-called endolithic communities. Yet the contribution of distinct rock traits to support complex microbial assemblies remains poorly determined. Here, we combined an extensive Antarctic rock survey with rock microbiome sequencing and ecological networks and found that contrasting combinations of microclimatic and rock traits such as thermal inertia, porosity, iron concentration, and quartz cement can help explain the multiple complex microbial assemblies found in Antarctic rocks. Our work highlights the pivotal role of rocky substrate heterogeneity in sustaining contrasting groups of microorganisms, which is essential to understand life at the edge on Earth and for the search for life on other rocky planets such as Mars.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, Milano, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Franceschi
- Research and Innovation Center, Fondazione Edmund Mach, Trento, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
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10
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Marozzi G, Benucci GMN, Turchetti B, Massaccesi L, Baciarelli Falini L, Bonito G, Buzzini P, Agnelli A, Donnini D, Albertini E. Correction to: Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome. Microb Ecol 2023; 85:522. [PMID: 35403892 DOI: 10.1007/s00248-022-02010-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- G Marozzi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - G M N Benucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
| | - B Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - L Massaccesi
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100, Viterbo, Italy
| | - L Baciarelli Falini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - G Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - P Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - A Agnelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - D Donnini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - E Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
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11
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Guglielmin M, Azzaro M, Buzzini P, Battistel D, Roman M, Ponti S, Turchetti B, Sannino C, Borruso L, Papale M, Lo Giudice A. A possible unique ecosystem in the endoglacial hypersaline brines in Antarctica. Sci Rep 2023; 13:177. [PMID: 36604573 PMCID: PMC9814585 DOI: 10.1038/s41598-022-27219-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Here, we present the results related to a new unique terrestrial ecosystem found in an englacial hypersaline brine found in Northern Victoria Land (Antarctica). Both the geochemistry and microbial (prokaryotic and fungal) diversity revealed an unicity with respect to all the other known Antarctic brines and suggested a probable ancient origin mainly due a progressive cryoconcentration of seawater. The prokaryotic community presented some peculiarities, such as the occurrence of sequences of Patescibacteria (which can thrive in nutrient-limited water environments) or few Spirochaeta, and the presence of archaeal sequences of Methanomicrobia closely related to Methanoculleus, a methanogen commonly detected in marine and estuarine environments. The high percentage (35%) of unassigned fungal taxa suggested the presence of a high degree of undiscovered diversity within a structured fungal community (including both yeast and filamentous life forms) and reinforce the hypothesis of a high degree of biological uniqueness of the habitat under study.
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Affiliation(s)
- M. Guglielmin
- grid.18147.3b0000000121724807Department of Theoretical and Applied Sciences, Insubria University, Via Dunant, 3, 21100 Varese, Italy ,grid.18147.3b0000000121724807Climate Change Research Center, Insubria University, Via Regina Teodolinda, 37, 22100 Como, Italy
| | - M. Azzaro
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy
| | - P. Buzzini
- grid.9027.c0000 0004 1757 3630Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - D. Battistel
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy ,grid.7240.10000 0004 1763 0578Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino, 155, 30172 Mestre, VE Italy
| | - M. Roman
- grid.7240.10000 0004 1763 0578Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino, 155, 30172 Mestre, VE Italy
| | - S. Ponti
- grid.18147.3b0000000121724807Department of Theoretical and Applied Sciences, Insubria University, Via Dunant, 3, 21100 Varese, Italy
| | - B. Turchetti
- grid.9027.c0000 0004 1757 3630Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - C. Sannino
- grid.9027.c0000 0004 1757 3630Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - L. Borruso
- grid.34988.3e0000 0001 1482 2038Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, 9100 Bozen-Bolzano, Italy
| | - M. Papale
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy
| | - A. Lo Giudice
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy
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12
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Turchetti B, Buzzini P, Baeza M. A genomic approach to analyze the cold adaptation of yeasts isolated from Italian Alps. Front Microbiol 2022; 13:1026102. [DOI: 10.3389/fmicb.2022.1026102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Microorganisms including yeasts are responsible for mineralization of organic matter in cold regions, and their characterization is critical to elucidate the ecology of such environments on Earth. Strategies developed by yeasts to survive in cold environments have been increasingly studied in the last years and applied to different biotechnological applications, but their knowledge is still limited. Microbial adaptations to cold include the synthesis of cryoprotective compounds, as well as the presence of a high number of genes encoding the synthesis of proteins/enzymes characterized by a reduced proline content and highly flexible and large catalytic active sites. This study is a comparative genomic study on the adaptations of yeasts isolated from the Italian Alps, considering their growth kinetics. The optimal temperature for growth (OTG), growth rate (Gr), and draft genome sizes considerably varied (OTG, 10°C–20°C; Gr, 0.071–0.0726; genomes, 20.7–21.5 Mpb; %GC, 50.9–61.5). A direct relationship was observed between calculated protein flexibilities and OTG, but not for Gr. Putative genes encoding for cold stress response were found, as well as high numbers of genes encoding for general, oxidative, and osmotic stresses. The cold response genes found in the studied yeasts play roles in cell membrane adaptation, compatible solute accumulation, RNA structure changes, and protein folding, i.e., dihydrolipoamide dehydrogenase, glycogen synthase, omega-6 fatty acid, stearoyl-CoA desaturase, ATP-dependent RNA helicase, and elongation of very-long-chain fatty acids. A redundancy for several putative genes was found, higher for P-loop containing nucleoside triphosphate hydrolase, alpha/beta hydrolase, armadillo repeat-containing proteins, and the major facilitator superfamily protein. Hundreds of thousands of small open reading frames (SmORFs) were found in all studied yeasts, especially in Phenoliferia glacialis. Gene clusters encoding for the synthesis of secondary metabolites such as terpene, non-ribosomal peptide, and type III polyketide were predicted in four, three, and two studied yeasts, respectively.
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13
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Isola D, Prigione VP, Zucconi L, Varese GC, Poli A, Turchetti B, Canini F. Knufia obscura sp. nov. and Knufia victoriae sp. nov., two new species from extreme environments. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Six strains of black meristematic fungi were isolated from Antarctic soils, gasoline car tanks and from the marine alga Flabellia petiolata. These fungi were characterized by morphological, physiological and phylogenetic analyses. According to the maximum-likelihood analysis reconstructed with ITS and LSU sequences, these strains belonged to the genus Knufia. Knufia obscura sp. nov. (holotype CBS 148926) and Knufia victoriae sp. nov. (holotype CBS 149015) are proposed as two novel species and descriptions of their morphological, physiological and phylogenetic features are presented. Based on the maximum-likelihood analyses, K. obscura was closely related to Knufia hypolithi (99 % bootstrap support), while K. victoriae clustered in the clade of Knufia cryptophialidica and Knufia perfecta (93 % bootstrap support). Knufia victoriae, recorded in Antarctic soil samples, had a psychrophilic behaviour, with optimal growth between 10 and 15 °C and no growth recorded at 20 °C. Knufia obscura, from a gasoline car tank and algae, displayed optimal growth between 20 and 25 °C and was more tolerant to salinity than K. victoriae.
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Affiliation(s)
- Daniela Isola
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo 01100, Italy
| | - Valeria Paola Prigione
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Torino, Viale Mattioli 25, 10125, Torino, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo 01100, Italy
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Torino, Viale Mattioli 25, 10125, Torino, Italy
| | - Anna Poli
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Torino, Viale Mattioli 25, 10125, Torino, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo 01100, Italy
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14
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Sannino C, Cannone N, D'Alò F, Franzetti A, Gandolfi I, Pittino F, Turchetti B, Mezzasoma A, Zucconi L, Buzzini P, Guglielmin M, Onofri S. Fungal communities in European alpine soils are not affected by short-term in situ simulated warming than bacterial communities. Environ Microbiol 2022; 24:4178-4192. [PMID: 35691701 DOI: 10.1111/1462-2920.16090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022]
Abstract
The impact of global warming on biological communities colonizing European alpine ecosystems was recently studied. Hexagonal open top chambers (OTCs) were used for simulating a short-term in situ warming (estimated around 1°C) in some alpine soils to predict the impact of ongoing climate change on resident microbial communities. Total microbial DNA was extracted from soils collected either inside or outside the OTCs over 3 years of study. Bacterial and fungal rRNA copies were quantified by qPCR. Metabarcoding sequencing of taxonomy target genes was performed (Illumina MiSeq) and processed by bioinformatic tools. Alpha- and beta-diversity were used to evaluate the structure of bacterial and fungal communities. qPCR suggests that, although fluctuations have been observed between soils collected either inside and outside the OTCs, the simulated warming induced a significant (p < 0.05) shift only for bacterial abundance. Likewise, significant (p < 0.05) changes in bacterial community structure were detected in soils collected inside the OTCs, with a clear increase of oligotrophic taxa. On the contrary, fungal diversity of soils collected either inside and outside the OTCs did not exhibit significant (p < 0.05) differences, suggesting that the temperature increase in OTCs compared to ambient conditions was not sufficient to change fungal communities.
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Affiliation(s)
- Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Nicoletta Cannone
- Department of Theoretical and Applied Sciences, Insubria University, Varese, Italy
| | - Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Isabella Gandolfi
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Ambra Mezzasoma
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, Insubria University, Varese, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
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15
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Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Riffo FC, Dashko S, Dimitrov R, Fisher KJ, Gibson BR, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. Yeasts from temperate forests. Yeast 2022; 39:4-24. [PMID: 35146791 DOI: 10.1002/yea.3699] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.
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Affiliation(s)
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Graham Bell
- Biology Department and Redpath Museum, McGill University, Québec, Canada
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Neža Čadež
- Biotechnical Faculty, Food Science and Technology Department, University of Ljubljana, Ljubljana, Slovenia
| | - Francisco Cubillos Riffo
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sofia Dashko
- DSM Food Specialties, Center for Food Innovation, AX, Delft, The Netherlands
| | - Roumen Dimitrov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kaitlin J Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian R Gibson
- Technische Universität Berlin, Institute of Food Technology and Food Chemistry, Chair of Brewing and Beverage Technology, Berlin, Germany
| | - Dilnora Gouliamova
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Duncan Greig
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Lina Heistinger
- ETH Zurich, Department of Biology, Institute of Biochemistry, Switzerland
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian R Landry
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Canada.,PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Canada.,Centre de Recherche sur les Données Massives, Université Laval, Canada.,Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Canada
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dana Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, USA
| | | | - Uroš Petrovič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia.,Jožef Stefan Institute, Department of Molecular and Biomedical Sciences, Ljubljana, Slovenia
| | | | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Pablo Villarreal
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
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16
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Yurkov A, Alves A, Bai FY, Boundy-Mills K, Buzzini P, Čadež N, Cardinali G, Casaregola S, Chaturvedi V, Collin V, Fell JW, Girard V, Groenewald M, Hagen F, Hittinger CT, Kachalkin AV, Kostrzewa M, Kouvelis V, Libkind D, Liu X, Maier T, Meyer W, Péter G, Piątek M, Robert V, Rosa CA, Sampaio JP, Sipiczki M, Stadler M, Sugita T, Sugiyama J, Takagi H, Takashima M, Turchetti B, Wang QM, Boekhout T. Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes. IMA Fungus 2021; 12:18. [PMID: 34256869 PMCID: PMC8278710 DOI: 10.1186/s43008-021-00067-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/18/2021] [Indexed: 01/25/2023] Open
Abstract
The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.
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Affiliation(s)
- Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Artur Alves
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, Phaff Yeast Culture Collection, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Neža Čadež
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ul. 101, 1000, Ljubljana, Slovenia
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
| | - Valérie Collin
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France
| | - Jack W Fell
- Emeritus Professor, Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Key Biscayne, FL, 33149, USA
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | - Aleksey V Kachalkin
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1-12, 119991, Moscow, Russia.,All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms (IBPM RAS), Russian Academy of Sciences, Prospect Nauki 5, 142290, Puschino, Russia
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Vassili Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701, Athens, Greece
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) CONICET - Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Rio Negro, Argentina
| | - Xinzhan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China
| | - Thomas Maier
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, 2006, Australia.,Westmead Institute for Medical Research, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia.,Westmead Hospital (Research and Education Network), Darcy Rd, Westmead, NSW, 2145, Australia
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, Budapest, H-1118, Hungary
| | - Marcin Piątek
- Department of Mycology, W. Szafer Institute of Botany of the Polish Academy of Sciences, Lubicz ul. 46, 31-512, Kraków, Poland
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Carlos A Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Jose Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal.,Departamento de Ciências da Vida, PYCC - Portuguese Yeast Culture Collection, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4010, Hungary
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2 Chome-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Junta Sugiyama
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.,TechnoSuruga Laboratory Co., Ltd., 388-1, Nagasaki, Shimuzu, Shizuoka, 424-0065, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China.,College of Life Sciences, Hebei University, 180 Wusi Dong Road, Lian Chi District, Baoding City, Hebei Province, 071002, People's Republic of China
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, The Netherlands
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17
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Canini F, Geml J, Buzzini P, Turchetti B, Onofri S, D’Acqui LP, Ripa C, Zucconi L. Growth Forms and Functional Guilds Distribution of Soil Fungi in Coastal Versus Inland Sites of Victoria Land, Antarctica. Biology (Basel) 2021; 10:biology10040320. [PMID: 33920495 PMCID: PMC8070035 DOI: 10.3390/biology10040320] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/02/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022]
Abstract
In Victoria Land, Antarctica, ice-free areas are restricted to coastal regions and dominate the landscape of the McMurdo Dry Valleys. These two environments are subjected to different pressures that determine the establishment of highly adapted fungal communities. Within the kingdom of fungi, filamentous, yeasts and meristematic/microcolonial growth forms on one side and different lifestyles on the other side may be considered adaptive strategies of particular interest in the frame of Antarctic constraints. In this optic, soil fungal communities from both coastal and Dry Valleys sites, already characterized thorough ITS1 metabarcoding sequencing, have been compared to determine the different distribution of phyla, growth forms, and lifestyles. Though we did not find significant differences in the richness between the two environments, the communities were highly differentiated and Dry Valleys sites had a higher evenness compared to coastal ones. Additionally, the distribution of different growth forms and lifestyles were well differentiated, and their diversity and composition were likely influenced by soil abiotic parameters, among which soil granulometry, pH, P, and C contents were the potential main determinants.
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Affiliation(s)
- Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
- Correspondence: ; Tel.: +39-0761357138
| | - József Geml
- Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands;
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, H-3300 Eger, Hungary
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (P.B.); (B.T.)
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (P.B.); (B.T.)
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
| | - Luigi Paolo D’Acqui
- Research Institute of Terrestrial Ecosystems, National Research Council of Italy (IRET-CNR), 50019 Sesto Fiorentino, Italy;
| | - Caterina Ripa
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
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18
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Franzetti A, Pittino F, Gandolfi I, Azzoni RS, Diolaiuti G, Smiraglia C, Pelfini M, Compostella C, Turchetti B, Buzzini P, Ambrosini R. Early ecological succession patterns of bacterial, fungal and plant communities along a chronosequence in a recently deglaciated area of the Italian Alps. FEMS Microbiol Ecol 2021; 96:5894918. [PMID: 32815995 DOI: 10.1093/femsec/fiaa165] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/12/2020] [Indexed: 12/31/2022] Open
Abstract
In this study, the early ecological succession patterns of Forni Glacier (Ortles-Cevedale group, Italian Alps) forefield along an 18-year long chronosequence (with a temporal resolution of 1 year) has been reported. Bacterial and fungal community structures were inferred by high-throughput sequencing of 16S rRNA gene and ITS, respectively. In addition, the occurrence of both herbaceous and arboreous plants was also recorded at each plot. A significant decrease of alpha-diversity in more recently deglaciated areas was observed for both bacteria and plants. Time since deglaciation and pH affected the structure of both fungal and bacterial communities. Pioneer plants could be a major source of colonization for both bacterial and fungal communities. Consistently, some of the most abundant bacterial taxa and some of those significantly varying with pH along the chronosequence (Polaromonas, Granulicella, Thiobacillus, Acidiferrobacter) are known to be actively involved in rock-weathering processes due to their chemolithotrophic metabolism, thus suggesting that the early phase of the chronosequence could be mainly shaped by the biologically controlled bioavailability of metals and inorganic compounds. Fungal communities were dominated by ascomycetous filamentous fungi and basidiomycetous yeasts. Their role as cold-adapted organic matter decomposers, due to their heterotrophic metabolism, was suggested.
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Affiliation(s)
- A Franzetti
- Department of Earth and Environmental Sciences (DISAT) - University of Milano-Bicocca, Milano, Italy
| | - F Pittino
- Department of Earth and Environmental Sciences (DISAT) - University of Milano-Bicocca, Milano, Italy
| | - I Gandolfi
- Department of Earth and Environmental Sciences (DISAT) - University of Milano-Bicocca, Milano, Italy
| | - R S Azzoni
- Department of Environmental Science and Policy, University of Milano, Milano, Italy
| | - G Diolaiuti
- Department of Environmental Science and Policy, University of Milano, Milano, Italy
| | - C Smiraglia
- Department of Earth Science "Ardito Desio", University of Milano, Milano, Italy
| | - M Pelfini
- Department of Earth Science "Ardito Desio", University of Milano, Milano, Italy
| | - C Compostella
- Department of Earth Science "Ardito Desio", University of Milano, Milano, Italy
| | - B Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - P Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - R Ambrosini
- Department of Environmental Science and Policy, University of Milano, Milano, Italy
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19
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Verkley G, Perrone G, Piña M, Scholz AH, Overmann J, Zuzuarregui A, Perugini I, Turchetti B, Hendrickx M, Stacey G, Law S, Russell J, Smith D, Lima N. New ECCO model documents for Material Deposit and Transfer Agreements in compliance with the Nagoya Protocol. FEMS Microbiol Lett 2020; 367:5800986. [PMID: 32149346 PMCID: PMC7164777 DOI: 10.1093/femsle/fnaa044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/05/2020] [Indexed: 12/04/2022] Open
Abstract
The European Culture Collections’ Organisation presents two new model documents for Material Deposit Agreement (MDA) and Material Transfer Agreement (MTA) designed to enable microbial culture collection leaders to draft appropriate agreement documents for, respectively, deposit and supply of materials from a public collection. These tools provide guidance to collections seeking to draft an MDA and MTA, and are available in open access to be used, modified, and shared. The MDA model consists of a set of core fields typically included in a ‘deposit form’ to collect relevant information to facilitate assessment of the status of the material under access and benefit sharing (ABS) legislation. It also includes a set of exemplary clauses to be included in ‘terms and conditions of use’ for culture collection management and third parties. The MTA model addresses key issues including intellectual property rights, quality, safety, security and traceability. Reference is made to other important tools such as best practices and code of conduct related to ABS issues. Besides public collections, the MDA and MTA model documents can also be useful for individual researchers and microbial laboratories that collect or receive microbial cultures, keep a working collection, and wish to share their material with others.
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Affiliation(s)
- Gerard Verkley
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Mery Piña
- CRBIP-Biological Resource Centre, Department of Microbiology, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Amber Hartman Scholz
- German Collection of Microorganisms and Cell Cultures (DSMZ), Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- German Collection of Microorganisms and Cell Cultures (DSMZ), Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Aurora Zuzuarregui
- Spanish Type Culture Collection (CECT), Edificio 3 CUE, Parc Científic Universitat de València, Catedrático Agustín Escardino 9, 46980 Paterna (Valencia), Spain
| | - Iolanda Perugini
- Mycotheca Universitatis Taurinensis (MUT), Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
| | - Benedetta Turchetti
- Industrial Yeasts Collection (DBVPG), Department of Agriculture, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - Marijke Hendrickx
- BCCM/IHEM Fungal Collection, Mycology & Aerobiology, Sciensano, Juliette Wytsmanstraat 14, B-1050 Brussels, Belgium
| | - Glyn Stacey
- International Stem Cell Banking initiative, Barley, Hertfordshire, SG88HZ, UK
| | - Samantha Law
- National Collection of Industrial, Food and Marine Bacteria (NCIMB), Ferguson Building, Craibstone Estate, Bucksburn AR21 9YA, Aberdeen, UK
| | - Julie Russell
- Public Health England (PHE) Culture Collections, Porton Down, SP4 0JG Salisbury, UK
| | | | - Nelson Lima
- Micoteca da Universidade do Minho (MUM), CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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20
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Turchetti B, Sannino C, Mezzasoma A, Zucconi L, Onofri S, Buzzini P. Mrakia stelviica sp. nov. and Mrakia montana sp. nov., two novel basidiomycetous yeast species isolated from cold environments. Int J Syst Evol Microbiol 2020; 70:4704-4713. [PMID: 32697190 DOI: 10.1099/ijsem.0.004336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Five yeast strains were isolated from soil and sediments collected from Alps and Apennines glaciers during sampling campaigns carried out in summer 2007 and 2017, respectively. Based on morphological and physiological tests and on phylogenetic analyses reconstructed with ITS and D1/D2 sequences, the five strains were considered to belong to two related but hitherto unknown species within the genus Mrakia, in an intermediate position between Mrakia cryoconiti and Mrakia arctica. The names Mrakia stelviica (holotype DBVPG 10734T) and Mrakia montana (holotype DBVPG 10736T) are proposed for the two novel species and a detailed description of their morphological, physiological and phylogenetic features are presented. Both species fermented glucose, sucrose and trehalose, which is an uncommon feature in basidiomycetous yeasts, and showed septate hyphae with teliospore formation.
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Affiliation(s)
- Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences & Industrial yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - Ambra Mezzasoma
- Department of Agricultural, Food and Environmental Sciences & Industrial yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences & Industrial yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
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21
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Sannino C, Borruso L, Mezzasoma A, Battistel D, Zucconi L, Selbmann L, Azzaro M, Onofri S, Turchetti B, Buzzini P, Guglielmin M. Intra- and inter-cores fungal diversity suggests interconnection of different habitats in an Antarctic frozen lake (Boulder Clay, Northern Victoria Land). Environ Microbiol 2020; 22:3463-3477. [PMID: 32510727 DOI: 10.1111/1462-2920.15117] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 01/28/2023]
Abstract
A perennially frozen lake at Boulder Clay site (Victoria Land, Antarctica), characterized by the presence of frost mounds, have been selected as an in situ model for ecological studies. Different samples of permafrost, glacier ice and brines have been studied as a unique habitat system. An additional sample of brines (collected in another frozen lake close to the previous one) was also considered. Alpha- and beta-diversity of fungal communities showed both intra- and inter-cores significant (p < 0.05) differences, which suggest the presence of interconnection among the habitats. Therefore, the layers of frost mound and the deep glacier could be interconnected while the brines could probably be considered as an open habitat system not interconnected with each other. Moreover, the absence of similarity between the lake ice and the underlying permafrost suggested that the lake is perennially frozen based. The predominance of positive significant (p < 0.05) co-occurrences among some fungal taxa allowed to postulate the existence of an ecological equilibrium in the habitats systems. The positive significant (p < 0.05) correlation between salt concentration, total organic carbon and pH, and some fungal taxa suggests that a few abiotic parameters could drive fungal diversity inside these ecological niches.
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Affiliation(s)
- Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX giugno 74, Perugia, 06121, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
| | - Ambra Mezzasoma
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX giugno 74, Perugia, 06121, Italy
| | - Dario Battistel
- Department of Environmental Science, Informatics and Statistics, University Ca' Foscari, Venice, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council, Messina, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX giugno 74, Perugia, 06121, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX giugno 74, Perugia, 06121, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, Insubria University, Varese, Italy
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22
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Coleine C, Pombubpa N, Zucconi L, Onofri S, Turchetti B, Buzzini P, Stajich JE, Selbmann L. Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling three Representative Locations of the Victoria Land. Microorganisms 2020; 8:E942. [PMID: 32585947 PMCID: PMC7356261 DOI: 10.3390/microorganisms8060942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/03/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 11/16/2022] Open
Abstract
The endolithic niche represents an ultimate refuge to microorganisms in the Mars-like environment of the Antarctic desert. In an era of rapid global change and desertification, the interest in these border ecosystems is increasing due to speculation on how they maintain balance and functionality at the dry limits of life. To assure a reliable estimation of microbial diversity, proper sampling must be planned in order to avoid the necessity of re-sampling as reaching these remote locations is risky and requires tremendous logistical and economical efforts. In this study, we seek to determine the minimum number of samples for uncovering comprehensive bacterial and fungal diversity, comparing communities in strict vicinity to each other. We selected three different locations of the Victoria Land (Continental Antarctica) at different altitudes and showing sandstone outcrops of a diverse nature and origin-Battleship promontory (834 m above sea level (a.s.l.), Southern VL), Trio Nunatak (1,470 m a.s.l., Northern VL) and Mt New Zealand (3,100 m a.s.l., Northern VL). Overall, we found that a wider sampling would be required to capture the whole amplitude of microbial diversity, particularly in Northern VL. We concluded that the inhomogeneity of the rock matrix and the stronger environmental pressure at higher altitudes may force the communities to a higher local diversification.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; (N.P.); (J.E.S.)
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (B.T.); (P.B.)
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (B.T.); (P.B.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; (N.P.); (J.E.S.)
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
- Italian National Antarctic Museum (MNA), Mycological Section, 16166 Genoa, Italy
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23
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Sannino C, Borruso L, Smiraglia C, Bani A, Mezzasoma A, Brusetti L, Turchetti B, Buzzini P. Dynamics of in situ growth and taxonomic structure of fungal communities in Alpine supraglacial debris. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2019.100891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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24
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Li AH, Yuan FX, Groenewald M, Bensch K, Yurkov AM, Li K, Han PJ, Guo LD, Aime MC, Sampaio JP, Jindamorakot S, Turchetti B, Inacio J, Fungsin B, Wang QM, Bai FY. Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species. Stud Mycol 2020; 96:17-140. [PMID: 32206137 PMCID: PMC7082220 DOI: 10.1016/j.simyco.2020.01.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [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] [Indexed: 11/29/2022] Open
Abstract
Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.
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Key Words
- Apiotrichum xylopini S.O. Suh, C.F. Lee, Gujjari & J.J. Zhou ex Kachalkin, Yurkov & Boekhout
- Bannozyma arctica Vishniac & M. Takash. ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Basidiomycetous yeasts
- Begerowomyces Q.M. Wang & F.Y. Bai
- Begerowomyces foliicola Q.M. Wang, F.Y. Bai & A.H. Li
- Bensingtonia pseudorectispora Q.M. Wang, F.Y. Bai & A.H. Li
- Bensingtonia wuzhishanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Boekhoutia Q.M. Wang & F.Y. Bai
- Boekhoutia sterigmata Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium cremeum Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium elongatum Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium panici Fungsin, M. Takash. & Nakase ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleribasidium phyllophilum Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium phyllostachydis Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium pseudopanici Q.M. Wang, F.Y. Bai & A.H. Li
- Bulleribasidium siamense Fungsin, M. Takash. & Nakase ex Q.M. Wang, F.Y. Bai, Boekhout & Nakase
- Carcinomyces arundinariae Fungsin, M. Takash. & Nakase ex Yurkov
- Carlosrosaea foliicola Q.M. Wang, F.Y. Bai & A.H. Li
- Carlosrosaea simaoensis Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma cylindrica Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma flava Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma fusiformis Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma iridis Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma pseudogriseoflava Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma sambuci Q.M. Wang, F.Y. Bai & A.H. Li
- Chrysozyma sorbariae Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea aletridis Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea hydrangeae Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Colacogloea subericola (Belloch, Villa-Carv., Á;lv.-Rodríg. & Coque) Q.M. Wang, & F.Y. Bai
- Cystobasidium alpinum Turchetti, Selbmann, Onofri & Buzzini
- Cystobasidium portillonense Laich, Vaca & R. Chávez ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidium raffinophilum Q.M. Wang, F.Y. Bai & A.H. Li
- Cystobasidium terricola Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces bifurcus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces cylindricus F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang
- Derxomyces elongatus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces hubeiensis F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang
- Derxomyces longicylindricus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces longiovatus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces melastomatis Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces nakasei F.Y. Bai, Q.M. Wang & M. Takash. ex F.Y. Bai & Q.M. Wang
- Derxomyces napiformis Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces ovatus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces polymorphus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces pseudoboekhoutii Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces pseudoyunnanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces taiwanicus Q.M. Wang, F.Y. Bai & A.H. Li
- Derxomyces xingshanicus Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia heilongjiangensis Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia kandeliae Q.M. Wang, F.Y. Bai, L.D. Guo & A.H. Li
- Dioszegia maotaiensis Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia milinica Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia ovata Q.M. Wang, F.Y. Bai & A.H. Li
- Dioszegia zsoltii F.Y. Bai, M. Takash. & Nakase
- F.Y. Bai, M. Groenew. & Boekhout
- Filobasidium dingjieense Q.M. Wang, F.Y. Bai & A.H. Li
- Filobasidium globosum Q.M. Wang, F.Y. Bai & A.H. Li
- Filobasidium mali Q.M. Wang, F.Y. Bai & A.H. Li
- Filobasidium mucilaginum Q.M. Wang, F.Y. Bai & A.H. Li
- Genolevuria bromeliarum Landell & P. Valente ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Genolevuria pseudoamylolytica Q.M. Wang, F.Y. Bai & A.H. Li
- Glaciozyma Turchetti, Connell, Thomas-Hall & Boekhout ex M. Groenew. & Q.M. Wang
- Glaciozyma antarctica (Fell, Statzell, I.L. Hunter & Phaff) M. Groenew. & Q.M. Wang
- Glaciozyma martinii Turchetti, Connell, Thomas-Hall & Boekhout
- Glaciozyma watsonii Turchetti, Connell, Thomas-Hall & Boekhout
- Heitmania cylindrica Q.M. Wang, F.Y. Bai & A.H. Li
- Heitmania tridentata Q.M. Wang, F.Y. Bai & A.H. Li
- Heitmaniaceae Q.M. Wang & F.Y. Bai
- Heitmaniales Q.M. Wang & F.Y. Bai
- Holtermannia saccardoi Q.M. Wang, F.Y. Bai & A.H. Li
- Jianyuniaceae Q.M. Wang & F.Y. Bai
- Kockovaella haikouensis Q.M. Wang, F.Y. Bai & A.H. Li
- Kockovaella ischaemi Q.M. Wang, F.Y. Bai & A.H. Li
- Kockovaella mexicana Lopandić, O. Molnár & Prillinger ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kockovaella nitrophila Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa arboricola Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa chamaenerii Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa cylindrica Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa daliangziensis Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa foliicola Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa lulangica Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa myxariophila Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa ribitophobia Q.M. Wang, F.Y. Bai & A.H. Li
- Kondoa thailandica Fungsin, Hamam. & Nakase ex Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- Kwoniella newhampshirensis K. Sylvester, Q.M. Wang & C.T. Hittinger
- Kwoniella ovata Q.M. Wang, F.Y. Bai & A.H. Li
- Kwoniella shandongensis R. Chen, Y.M. Jiang & S.C. Wei ex M. Groenew. & Q.M. Wang
- Leucosporidium creatinivorum (Golubev) M. Groenew. & Q.M. Wang
- Leucosporidium fragarium (J.A. Barnett & Buhagiar) M. Groenew. & Q.M. Wang
- Leucosporidium intermedium (Nakase & M. Suzuki) M. Groenew. & Q.M. Wang
- Leucosporidium muscorum (Di Menna) M. Groenew. & Q.M. Wang
- Leucosporidium yakuticum (Golubev) M. Groenew. & Q.M. Wang
- Meniscomyces Q.M. Wang & F.Y. Bai
- Meniscomyces layueensis Q.M. Wang, F.Y. Bai & A.H. Li
- Microbotryozyma swertiae Q.M. Wang, F.Y. Bai & A.H. Li
- Microsporomyces ellipsoideus Q.M. Wang, F.Y. Bai & A.H. Li
- Microsporomyces pseudomagnisporus Q.M. Wang, F.Y. Bai & A.H. Li
- Microsporomyces rubellus Q.M. Wang, F.Y. Bai & A.H. Li
- Molecular phylogeny
- Naganishia onofrii Turchetti, Selbmann & Zucconi ex Yurkov
- Naganishia vaughanmartiniae Turchetti, Blanchette & Arenz ex Yurkov
- Nielozyma Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozyma formosana Nakase, Tsuzuki, F.L. Lee & M. Takash. ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozyma melastomatis Nakase, Tsuzuki, F.L. Lee & M. Takash. ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozyma dicranopteridis Q.M. Wang, F.Y. Bai & A.H. Li
- Oberwinklerozyma nepetae Q.M. Wang, F.Y. Bai & A.H. Li
- Oberwinklerozyma silvestris Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozyma straminea Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema aspenensis (Ferreira-Paim, et al.) Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema baii Yurkov, M.A. Guerreiro & Á;. Fonseca ex Yurkov
- Papiliotrema frias V. de García, Zalar, Brizzio, Gunde-Cim. & Van Broock ex Yurkov
- Papiliotrema hoabinhensis D.T. Luong, M. Takash., Ty, Dung & Nakase ex Yurkov
- Papiliotrema japonica J.P. Samp., Fonseca & Fell ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema terrestris Crestani, Landell, Faganello, Vainstein, Vishniac & P. Valente ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotrema wisconsinensis K. Sylvester, Q.M. Wang & Hittinger ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Phaeotremella lactea Q.M. Wang, F.Y. Bai & A.H. Li
- Phaeotremella ovata Q.M. Wang, F.Y. Bai & A.H. Li
- Phaffia aurantiaca Q.M. Wang, F.Y. Bai & A.H. Li
- Phyllozyma aceris Q.M. Wang, F.Y. Bai & A.H. Li
- Phyllozyma jiayinensis Q.M. Wang, F.Y. Bai & A.H. Li
- Piskurozyma fildesensis T.T. Zhang & Li Y. Yu ex Yurkov
- Piskurozyma taiwanensis Nakase, Tsuzuki & M. Takash. ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pseudobensingtonia fusiformis Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudohyphozyma hydrangeae Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudohyphozyma lulangensis Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudoleucosporidium V. de García, et al. ex M. Groenew. & Q.M. Wang
- Pseudoleucosporidium fasciculatum (Babeva & Lisichk.) M. Groenew. & Q.M. Wang
- Pseudosterigmatospora Q.M. Wang & F.Y. Bai
- Pseudosterigmatospora motuoensis Q.M. Wang, F.Y. Bai & A.H. Li
- Pseudotremella lacticolour Satoh & Makimura ex Yurkov
- Rhodosporidiobolus fuzhouensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rhodosporidiobolus jianfalingensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rhodosporidiobolus platycladi Q.M. Wang, F.Y. Bai & A.H. Li
- Rhynchogastrema complexa (Landell, et al.) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema fermentans (C.F. Lee) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema glucofermentans (S.O. Suh & M. Blackw.) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema nanyangensis F.L. Hui & Q.H. Niu ex Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema tunnelae (Boekhout, Fell, Scorzetti & Theelen) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout & Yurkov
- Rhynchogastrema visegradensis (G. Péter & Dlauchy) Xin Zhan Liu, F.Y. Bai, M. Groenew., Boekhout &Yurkov
- Robertozyma Q.M. Wang & F.Y. Bai
- Robertozyma ningxiaensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozyma Q.M. Wang & F.Y. Bai
- Rosettozyma cystopteridis Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozyma motuoensis Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozyma petaloides Q.M. Wang, F.Y. Bai & A.H. Li
- Rosettozymaceae Q.M. Wang & F.Y. Bai
- Rosettozymales Q.M. Wang & F.Y. Bai
- Ruinenia bangxiensis Q.M. Wang, F.Y. Bai & A.H. Li
- Ruinenia diospyri Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash. ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruinenia fanjingshanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Ruinenia lunata Q.M. Wang, F.Y. Bai & A.H. Li
- Ruinenia pyrrosiae Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash. ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Saitozyma ninhbinhensis (D.T. Luong, M. Takash., Dung & Nakase)Yurkov
- Saitozyma paraflava Golubev & J.P. Samp. ex Xin Zhan Liu
- Saitozyma pseudoflava Q.M. Wang, F.Y. Bai & A.H. Li
- Sakaguchia melibiophila M. Groenew., Q.M. Wang & F.Y. Bai
- Slooffia globosa Q.M. Wang, F.Y. Bai & A.H. Li
- Solicoccozyma gelidoterrea Q.M. Wang, F.Y. Bai & A.H. Li
- Species diversity
- Sporobolomyces cellobiolyticus Q.M. Wang, F.Y. Bai & A.H. Li
- Sporobolomyces ellipsoideus Q.M. Wang, F.Y. Bai & A.H. Li
- Sporobolomyces primogenomicus Q.M. Wang & F.Y. Bai
- Sporobolomyces reniformis Q.M. Wang, F.Y. Bai & A.H. Li
- Sterigmatospora Q.M. Wang & F.Y. Bai
- Sterigmatospora layueensis Q.M. Wang, F.Y. Bai & A.H. Li
- Symmetrospora oryzicola (Nakase & M. Suzuki) Q.M. Wang & F.Y. Bai
- Symmetrospora rhododendri Q.M. Wang, F.Y. Bai & A.H. Li
- Taxonomy
- Teunia Q.M. Wang & F.Y. Bai
- Teunia betulae K. Sylvester, Q.M. Wang & Hittinger ex Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia cuniculi (K.S. Shin & Y.H. Park) Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia globosa Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia helanensis Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia korlaensis Q.M. Wang, F.Y. Bai & A.H. Li
- Teunia tronadorensis V. de Garcia, Zalar, Brizzio, Gunde-Cim. & van Brook ex Q.M. Wang, F.Y. Bai & A.H. Li
- Tremella basidiomaticola Xin Zhan Liu & F.Y. Bai
- Tremella shuangheensis Q.M. Wang, F.Y. Bai & A.H. Li
- Trimorphomyces sakaeraticus Fungsin, M. Takash. & Nakase ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vanrija meifongana C.F. Lee ex Kachalkin Yurkov & Boekhout
- Vanrija nantouana C.F. Lee ex Kachalkin Yurkov & Boekhout
- Vanrija thermophila Vogelmann, S. Chaves & C. Hertel ex Kachalkin Yurkov & Boekhout
- Vishniacozyma europaea Q.M. Wang, F.Y. Bai & A.H. Li
- Vishniacozyma foliicola Q.M. Wang & F.Y. Bai ex Yurkov
- Vishniacozyma heimaeyensis Vishniac ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vishniacozyma melezitolytica Q.M. Wang, F.Y. Bai & A.H. Li
- Vishniacozyma pseudopenaeus Q.M. Wang, F.Y. Bai & A.H. Li
- Vishniacozyma psychrotolerans V. de García, Zalar, Brizzio, Gunde-Cim. & Van Broock ex Yurkov
- Vishniacozyma taibaiensis Q.M. Wang & F.Y. Bai ex Yurkov
- Vishniacozyma tephrensis Vishniac ex Xin Zhan Liu, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces rosulatus Golubev & Scorzetti ex Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces terricola Q.M. Wang, F.Y. Bai & A.H. Li
- Yurkovia longicylindrica Q.M. Wang, F.Y. Bai & A.H. Li
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Affiliation(s)
- A-H Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - F-X Yuan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,North Minzu University, Yinchuan, Ningxia, 750030, China
| | - M Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - K Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - K Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - P-J Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - L-D Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - M C Aime
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN, 47901, USA
| | - J P Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,PYCC - Portuguese Yeast Culture Collection, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - S Jindamorakot
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - B Turchetti
- Department of Agriculture, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, 74 - I-06121, Italy
| | - J Inacio
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK
| | - B Fungsin
- TISTR Culture Collection, Thailand Institute of Scientific and Technological Research (TISTR), 35 M 3, Technopolis, Khlong Ha, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Q-M Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, Hebei University, Baoding, Hebei Province, 071002, China
| | - F-Y Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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25
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De Vero L, Boniotti MB, Budroni M, Buzzini P, Cassanelli S, Comunian R, Gullo M, Logrieco AF, Mannazzu I, Musumeci R, Perugini I, Perrone G, Pulvirenti A, Romano P, Turchetti B, Varese GC. Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections. Microorganisms 2019; 7:microorganisms7120685. [PMID: 31842279 PMCID: PMC6956255 DOI: 10.3390/microorganisms7120685] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 10/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023] Open
Abstract
Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs.
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Affiliation(s)
- Luciana De Vero
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
- Correspondence: ; Tel.: +39-0522-522-057
| | - Maria Beatrice Boniotti
- Biobank of Veterinary Resources, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, via Bianchi 9, 25124 Brescia, Italy;
| | - Marilena Budroni
- Department of Agricultural Science, University of Sassari, viale Italia 39, 07100 Sassari, Italy; (M.B.); (I.M.)
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Science, University of Perugia, borgo XX Giugno, 74, I-06121 Perugia, Italy; (P.B.); (B.T.)
| | - Stefano Cassanelli
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Roberta Comunian
- Agris Sardegna, Agenzia regionale per la ricerca in agricoltura, Loc. Bonassai, km 18.600 SS291, 07100 Sassari, Italy;
| | - Maria Gullo
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy; (A.F.L.); (G.P.)
| | - Ilaria Mannazzu
- Department of Agricultural Science, University of Sassari, viale Italia 39, 07100 Sassari, Italy; (M.B.); (I.M.)
| | - Rosario Musumeci
- MicroMiB Culture Collection, Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy;
| | - Iolanda Perugini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Torino, Italy; (I.P.); (G.C.V.)
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy; (A.F.L.); (G.P.)
| | - Andrea Pulvirenti
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Paolo Romano
- Mass Spectrometry and Proteomics, Scientific Direction, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy;
| | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Science, University of Perugia, borgo XX Giugno, 74, I-06121 Perugia, Italy; (P.B.); (B.T.)
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Torino, Italy; (I.P.); (G.C.V.)
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26
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Troilo A, De Francesco G, Marconi O, Sileoni V, Turchetti B, Perretti G. Low Carbohydrate Beers Produced by a Selected Yeast Strain from an Alternative Source. Journal of the American Society of Brewing Chemists 2019. [DOI: 10.1080/03610470.2019.1682887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Antonio Troilo
- Department of Agricultural, Food and Environmental Sciences – DSAAA, University of Perugia, Perugia, Italy
| | | | - Ombretta Marconi
- Italian Brewing Research Centre – CERB, University of Perugia, Perugia, Italy
| | - Valeria Sileoni
- Department of Agricultural, Food and Environmental Sciences – DSAAA, University of Perugia, Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences – DSAAA, University of Perugia, Perugia, Italy
- Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Giuseppe Perretti
- Department of Agricultural, Food and Environmental Sciences – DSAAA, University of Perugia, Perugia, Italy
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27
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Yurkov AM, Sannino C, Turchetti B. Mrakia fibulata sp. nov., a psychrotolerant yeast from temperate and cold habitats. Antonie Van Leeuwenhoek 2019; 113:499-510. [PMID: 31754948 DOI: 10.1007/s10482-019-01359-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/08/2019] [Indexed: 01/21/2023]
Abstract
Tree fluxes are sugar-rich, sometimes ephemeral, substrates occurring on sites where tree sap (xylem or phloem) is leaking through damages of tree bark. Tree sap infested with microorganisms has been the source of isolation of many species, including the biotechnologically relevant carotenoid yeast Phaffia rhodozyma. Tree fluxes recently sampled in Germany yielded 19 species, including several psychrophilic yeasts of the genus Mrakia. Four strains from tree fluxes represented a potential novel Mrakia species previously known from two isolates from superficial glacial melting water of Calderone Glacier (Italy). The Italian isolates, originally identified as Mrakia aquatica, and two strains from Germany did not show any sexual structures. But another culture collected in Germany produced clamped hyphae with teliospores. A detailed examination of the five isolates (three from Germany and two from Italy) proved them to be a novel yeast species, which is described in this manuscript as Mrakia fibulata sp. nov. (MB 830398), holotype DSM 103931 and isotype DBVPG 8059. In contrast to other sexually reproducing Mrakia species, M. fibulata produces true hyphae with clamp connections. Also, this is the first psychrotolerant Mrakia species which grows above 20 °C. Spring tree fluxes are widespread and can be recognized and sampled by amateurs in a Citizen Science project. This substrate is a prominent source of yeasts, and may harbor unknown species, as demonstrated in the present work. The description of Mrakia fibulata is dedicated to our volunteer helpers and amateurs, like Anna Yurkova (9-years-old daughter of Andrey Yurkov), who collected the sample which yielded the type strain of this species.
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Affiliation(s)
- A M Yurkov
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Brunswick, Germany.
| | - C Sannino
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - B Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
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Tasselli G, Filippucci S, D'Antonio S, Cavalaglio G, Turchetti B, Cotana F, Buzzini P. Optimization of enzymatic hydrolysis of cellulosic fraction obtained from stranded driftwood feedstocks for lipid production by Solicoccozyma terricola. ACTA ACUST UNITED AC 2019; 24:e00367. [PMID: 31453116 PMCID: PMC6704348 DOI: 10.1016/j.btre.2019.e00367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/15/2019] [Revised: 07/04/2019] [Accepted: 08/06/2019] [Indexed: 12/01/2022]
Abstract
Stranded driftwood feedstocks (SD) were steam exploded and hydrolyzed. The enzymatic hydrolysis was optimized using a multivariate approach (RSM). The conversion of carbohydrates into lipids by S. terricola was high (YL = 25.26%). The fatty acid profile achieved was similar to that reported for palm oil. SD feedstocks resulted a cheap C-source for biofuels and biochemicals production.
Stranded driftwood feedstocks may represent, after pretreatment with steam explosion and enzymatic hydrolysis, a cheap C-source for producing biochemicals and biofuels using oleaginous yeasts. The hydrolysis was optimized using a response surface methodology (RSM). The solid loading (SL) and the dosage of enzyme cocktail (ED) were variated following a central composite design (CCD) aimed at optimizing the conversion of carbohydrates into lipids (YL) by the yeast Solicoccozyma terricola DBVPG 5870. A second-order polynomial equation was computed for describing the effect of ED and SL on YL. The best combination (ED = 3.10%; SL = 22.07%) for releasing the optimal concentration of carbohydrates which gave the highest predicted YL (27.32%) was then validated by a new hydrolysis. The resulting value of YL (25.26%) was close to the theoretical maximum value. Interestingly, fatty acid profile achieved under the optimized conditions was similar to that reported for palm oil.
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Key Words
- A600, absorbance at 600 nm
- ANOVA, analysis of variance
- C/N, carbon/nitrogen
- C10:0, capric acid (decanoic acid)
- C12:0, lauric acid (dodecanoic acid)
- C14:0, myristic acid (tetradecanoic acid)
- C16:0, palmitic acid (hexadecanoic acid)
- C18:0, stearic acid (octadecanoic acid)
- C20:0, arachic acid (eicosanoic acid)
- C22:0, behenic acid (docosanoic acid)
- C24:0, lignoceric acid (tetracosanoic acid)
- C5, carbohydrates with five carbon atoms
- C6, carbohydrates with six carbon atoms
- C8:0, caprylic acid (octanoic acid)
- CBU, cellobiase unit
- CCD, Central Composite Design
- DW, dry weight
- ED, enzyme dosage
- Enzymatic hydrolysis
- Eq, equation
- F.A.M.E., fatty acid methyl ester
- FA, fatty acid
- FPU, filterpaper unit
- GC, Gas Chromatography
- GC-FID, Gas Chromatography – Flame Ionization Detector
- HLF, hydrolyzed liquid fraction
- HPLC, high performance liquid chromatography
- LF, liquid fraction
- NREL, National Renewable Energy Laboratory
- PL, total lipid production
- PL/DW, % of total intracellular lipid on cellbiomass
- PL/d, lipid production per day
- RI, refractive index
- RSM, response surface methodology
- Response surface methodology
- Rpm, revolutions per minute
- SD, stranded driftwood
- SE, steam explosion
- SFA, saturated fatty acid
- SL, solid loading
- Solicoccozyma terricola
- Stranded driftwood feedstocks
- TAGs, Tryacylglicerols
- UFA, unsaturated fatty acid
- UI, unsaturation index
- WIS, water insoluble substrate
- XG, Xilose and Galactose
- YL, lipid yied
- YPD, Yeast Extract Peptone Dextrose
- Yeast biochemicals and biofuels
- Yoleic, oleic acid yield
- g, gravity force
- h, hours
- min, minutes
- p, p-value
- v/v, concentration in volume/volume percent
- Δ13C22:1, erucic acid [(13Z)-docos-13-enoic acid]
- Δ9,12,15C18:3, linolenic acid [(9Z,12Z,15Z)-9,12,15-octadecatrienoic acid]
- Δ9,12C18:2, linoleic acid [(9Z,12Z)-9,12-octadecadienoic acid]
- Δ9C16:1, palmitoleic acid [(9Z)-hexadec-9-enoic acid]
- Δ9C18:1, oleic acid [(9E9Z)-octadec-9-enoic acid]
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Affiliation(s)
- Giorgia Tasselli
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Italy.,CIRIAF - Biomass Research Centre, University of Perugia, Italy
| | - Sara Filippucci
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | | | - Gianluca Cavalaglio
- CIRIAF - Biomass Research Centre, University of Perugia, Italy.,Department of Engineering, University of Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Italy
| | - Franco Cotana
- CIRIAF - Biomass Research Centre, University of Perugia, Italy.,Department of Engineering, University of Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Italy.,CIRIAF - Biomass Research Centre, University of Perugia, Italy
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Kachalkin AV, Turchetti B, Inácio J, Carvalho C, Mašínová T, Pontes A, Röhl O, Glushakova AM, Akulov A, Baldrian P, Begerow D, Buzzini P, Sampaio JP, Yurkov AM. Rare and undersampled dimorphic basidiomycetes. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01491-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Khroustalyova G, Giovannitti G, Severini D, Scherbaka R, Turchetti B, Buzzini P, Rapoport A. Anhydrobiosis in yeasts: Psychrotolerant yeasts are highly resistant to dehydration. Yeast 2019; 36:375-379. [DOI: 10.1002/yea.3382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/07/2019] [Accepted: 01/30/2019] [Indexed: 02/06/2023] Open
Affiliation(s)
- Galina Khroustalyova
- Laboratory of Cell Biology, Institute of Microbiology and BiotechnologyUniversity of Latvia Riga Latvia
| | - Gaia Giovannitti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPGUniversity of Perugia Perugia Italy
| | - Daria Severini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPGUniversity of Perugia Perugia Italy
| | - Rita Scherbaka
- Laboratory of Cell Biology, Institute of Microbiology and BiotechnologyUniversity of Latvia Riga Latvia
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPGUniversity of Perugia Perugia Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPGUniversity of Perugia Perugia Italy
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and BiotechnologyUniversity of Latvia Riga Latvia
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De Francesco G, Sannino C, Sileoni V, Marconi O, Filippucci S, Tasselli G, Turchetti B. Mrakia gelida in brewing process: An innovative production of low alcohol beer using a psychrophilic yeast strain. Food Microbiol 2018; 76:354-362. [DOI: 10.1016/j.fm.2018.06.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 02/06/2023]
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Rossi S, Turchetti B, Sileoni V, Marconi O, Perretti G. Evaluation of Saccharomyces cerevisiae
strains isolated from non-brewing environments in beer production. J Inst Brew 2018. [DOI: 10.1002/jib.503] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Serena Rossi
- University of Perugia; Department of Agricultural, Food and Environmental Sciences; Perugia Italy
| | - Benedetta Turchetti
- University of Perugia; Department of Agricultural, Food and Environmental Sciences; Perugia Italy
| | - Valeria Sileoni
- University of Perugia; Department of Agricultural, Food and Environmental Sciences; Perugia Italy
- University of Perugia; Italian Brewing Research Center; Perugia Italy
| | - Ombretta Marconi
- University of Perugia; Department of Agricultural, Food and Environmental Sciences; Perugia Italy
- University of Perugia; Italian Brewing Research Center; Perugia Italy
| | - Giuseppe Perretti
- University of Perugia; Department of Agricultural, Food and Environmental Sciences; Perugia Italy
- University of Perugia; Italian Brewing Research Center; Perugia Italy
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Tasselli G, Filippucci S, Borsella E, D’Antonio S, Gelosia M, Cavalaglio G, Turchetti B, Sannino C, Onofri A, Mastrolitti S, De Bari I, Cotana F, Buzzini P. Yeast lipids from cardoon stalks, stranded driftwood and olive tree pruning residues as possible extra sources of oils for producing biofuels and biochemicals. Biotechnol Biofuels 2018; 11:147. [PMID: 29796088 PMCID: PMC5964688 DOI: 10.1186/s13068-018-1142-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/03/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Some lignocellulosic biomass feedstocks occur in Mediterranean Countries. They are still largely unexploited and cause considerable problems due to the lack of cost-effective harvesting, storage and disposal technologies. Recent studies found that some basidiomycetous yeasts are able to accumulate high amount of intracellular lipids for biorefinery processes (i.e., biofuels and biochemicals). Accordingly, the above biomass feedstocks could be used as carbon sources (after their pre-treatment and hydrolysis) for lipid accumulation by oleaginous yeasts. RESULTS Cardoon stalks, stranded driftwood and olive tree pruning residues were pre-treated with steam-explosion and enzymatic hydrolysis for releasing free mono- and oligosaccharides. Lipid accumulation tests were performed at two temperatures (20 and 25 °C) using Leucosporidium creatinivorum DBVPG 4794, Naganishia adeliensis DBVPG 5195 and Solicoccozyma terricola DBVPG 5870. S. terricola grown on cardoon stalks at 20 °C exhibited the highest lipid production (13.20 g/l), a lipid yield (28.95%) close to the maximum theoretical value and a lipid composition similar to that found in palm oil. On the contrary, N. adeliensis grown on stranded driftwood and olive tree pruning residues exhibited a lipid composition similar to those of olive and almonds oils. A predictive evaluation of the physical properties of the potential biodiesel obtainable by lipids produced by tested yeast strains has been reported and discussed. CONCLUSIONS Lipids produced by some basidiomycetous yeasts grown on Mediterranean lignocellulosic biomass feedstocks could be used as supplementary sources of oils for producing biofuels and biochemicals.
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Affiliation(s)
- Giorgia Tasselli
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
- CIRIAF-Biomass Research Centre, University of Perugia, Perugia, Italy
| | - Sara Filippucci
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Elisabetta Borsella
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Matera, Italy
| | - Silvia D’Antonio
- CIRIAF-Biomass Research Centre, University of Perugia, Perugia, Italy
| | - Mattia Gelosia
- CIRIAF-Biomass Research Centre, University of Perugia, Perugia, Italy
| | - Gianluca Cavalaglio
- CIRIAF-Biomass Research Centre, University of Perugia, Perugia, Italy
- Department of Engineering, University of Perugia, Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Andrea Onofri
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Silvio Mastrolitti
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Matera, Italy
| | - Isabella De Bari
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Matera, Italy
| | - Franco Cotana
- CIRIAF-Biomass Research Centre, University of Perugia, Perugia, Italy
- Department of Engineering, University of Perugia, Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
- CIRIAF-Biomass Research Centre, University of Perugia, Perugia, Italy
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Buzzini P, Turchetti B, Yurkov A. Extremophilic yeasts: the toughest yeasts around? Yeast 2018; 35:487-497. [PMID: 29577430 DOI: 10.1002/yea.3314] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/31/2018] [Accepted: 03/06/2018] [Indexed: 11/09/2022] Open
Abstract
Microorganisms are widely distributed in a multitude of environments including ecosystems that show challenging features to most life forms. The combination of extreme physical and chemical factors contributes to the definition of extreme habitats although the definition of extreme environments changes depending on one's point of view: anthropocentric, microbial-centric or zymo-centric. Microorganisms that live under conditions that cause hard survival are called extremophiles. In particular organisms that require extreme conditions are called true extremophiles while organisms that tolerate them to some extent are termed extremotolerant. Deviation of temperature, pH, osmotic stress, pressure and radiation from the common range delineates extreme environments. Yeasts are versatile eukaryotic organisms that are not frequently considered the toughest microorganisms in comparison with prokaryotes. Nevertheless extremophilic or extremotolerant species are present also within this group. Here a brief description is provided of the main extreme habitats and the metabolic and physiological modifications adopted by yeasts depending on their adverse conditions. Additionally the main extremophilic and extremotolerant yeast species associated with a few extreme habitats are listed.
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Affiliation(s)
- Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Italy
| | - Andrey Yurkov
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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35
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Turchetti B, Selbmann L, Gunde-Cimerman N, Buzzini P, Sampaio JP, Zalar P. Cystobasidium alpinum sp. nov. and Rhodosporidiobolus oreadorum sp. nov. from European Cold Environments and Arctic Region. Life (Basel) 2018; 8:life8020009. [PMID: 29734727 PMCID: PMC6027198 DOI: 10.3390/life8020009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 04/06/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 11/16/2022] Open
Abstract
Over 80% of the Earth’s environments are permanently or periodically exposed to temperatures below 5 °C. Cold habitats harbour a wide diversity of psychrophilic and psychrotolerant yeasts. During ecological studies of yeast communities carried out in cold ecosystem in the Italian Alps, Svalbard (Norway, Arctic region), and Portugal, 23 yeast strains that could not be assigned to any known fungal taxa were isolated. In particular, two of them were first identified as Rhodotorula sp., showing the highest degree of D1/D2 sequence identity with Cystobasidum laryngis accounted to only 97% with the type strain (C. laryngis CBS 2221). The other 21 strains, exhibiting identical D1/D2 sequences, had low identity (97%) with Rhodosporidiobolus lusitaniae and Rhodosporidiobolus colostri. Similarly, ITS sequences of the type strains of the most closely related species (93⁻94%). In a 2-genes multilocus D1/D2 and ITS ML phylogenetic tree, the studied strains pooled in two well separated and supported groups. In order to classify the new 23 isolates based on phylogenetic evidences, we propose the description of two novel species Cystobasidium alpinum sp. nov. and Rhodosporidiobolus oreadorum sp. nov.
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Affiliation(s)
- Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, 06121 Perugia, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia.
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, 06121 Perugia, Italy.
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia.
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Trochine A, Turchetti B, Vaz ABM, Brandao L, Rosa LH, Buzzini P, Rosa C, Libkind D. Description of Dioszegia patagonica sp. nov., a novel carotenogenic yeast isolated from cold environments. Int J Syst Evol Microbiol 2017; 67:4332-4339. [DOI: 10.1099/ijsem.0.002211] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrea Trochine
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de levaduras, Instituto Andino-Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), CONICET – UNComahue. Quintral 1250, (8400), Bariloche, Río Negro, Argentina
| | - Benedetta Turchetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia and Industrial Yeasts Collection DBVPG, Borgo XX Giugno, 74, Perugia, Italy
| | - Aline B. M. Vaz
- Departamento de Microbiologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luciana Brandao
- Departamento de Microbiologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luiz H. Rosa
- Departamento de Microbiologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pietro Buzzini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia and Industrial Yeasts Collection DBVPG, Borgo XX Giugno, 74, Perugia, Italy
| | - Carlos Rosa
- Departamento de Microbiologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de levaduras, Instituto Andino-Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), CONICET – UNComahue. Quintral 1250, (8400), Bariloche, Río Negro, Argentina
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Jagielski T, Bakuła Z, Di Mauro S, Casciari C, Cambiotti V, Krukowski H, Turchetti B, Ricchi M, Manuali E, Buzzini P. A comparative study of the in vitro activity of iodopropynyl butylcarbamate and amphotericin B against Prototheca spp. isolates from European dairy herds. J Dairy Sci 2017; 100:7435-7445. [DOI: 10.3168/jds.2017-12597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 05/24/2017] [Indexed: 11/19/2022]
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38
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Filippucci S, Tasselli G, Scardua A, Di Mauro S, Cramarossa MR, Perini D, Turchetti B, Onofri A, Forti L, Buzzini P. Study of Holtermanniella wattica, Leucosporidium creatinivorum, Naganishia adeliensis, Solicoccozyma aeria, and Solicoccozyma terricola for their lipogenic aptitude from different carbon sources. Biotechnol Biofuels 2016; 9:259. [PMID: 27933101 PMCID: PMC5126845 DOI: 10.1186/s13068-016-0672-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/17/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND The ability of some microorganisms to accumulate lipids is well known; however, only recently the number of studies on microbial lipid biosynthesis for obtaining oleochemical products, namely biofuels and some building blocks for chemistry, is rapidly and spectacularly increased. Since 1990s, some oleaginous yeasts were studied for their ability to accumulate lipids up to 60-70% of their dry weight. Due to the vast array of engineering techniques currently available, the recombinant DNA technology was the main approach followed so far for obtaining lipid-overproducing yeasts, mainly belonging to the Yarrowia lipolytica. However, an alternative approach can be offered by worldwide diversity as source of novel oleaginous yeasts. Lipogenic aptitude of a number of yeast strains has been reviewed, but many of these studies utilized a limited number of species and/or different culture conditions that make impossible the comparison of different results. Accordingly, the lipogenic aptitude inside the yeast world is still far from being fully explored, and finding new oleaginous yeast species can acquire a strategic importance. RESULTS Holtermanniella wattica, Leucosporidium creatinivorum, Naganishia adeliensis, Solicoccozyma aeria, and Solicoccozyma terricola strains were selected as a result of a large-scale screening on 706 yeasts (both Ascomycota and Basidiomycota). Lipid yields and fatty acid profiles of selected strains were evaluated at 20 and 25 °C on glucose, and on glycerol, xylose, galactose, sucrose, maltose, and cellobiose. A variable fatty acid profile was observed in dependence of both temperature and different carbon sources. On the whole, L. creatinivorum exhibited the highest performances: total lipid yield (YL) >7 g/l on glucose and glycerol, % of intracellular lipids on cell biomass (YL/DW) >70% at 20 °C on glucose, lipid coefficient (YL/Glu) around 20% on glucose, and daily productivity (YL/d) on glucose and sucrose >1.6 g/(l*d). CONCLUSIONS This study provides some meaningful information about the lipogenic ability of some yeast species. Variable lipid yields and fatty acid profiles were observed in dependence of both temperature and different carbon sources. L. creatinivorum exhibited the highest lipogenic performances.
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Affiliation(s)
- Sara Filippucci
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Giorgia Tasselli
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Alessandro Scardua
- Laboratories of Biotechnology, Novamont S.p.A, via Fauser 8, Novara, 28100 Italy
| | - Simone Di Mauro
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Maria Rita Cramarossa
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125 Italy
| | - Davide Perini
- Laboratories of Biotechnology, Novamont S.p.A, via Fauser 8, Novara, 28100 Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Andrea Onofri
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Luca Forti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125 Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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França L, Sannino C, Turchetti B, Buzzini P, Margesin R. Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils. Extremophiles 2016; 20:855-873. [PMID: 27620454 PMCID: PMC5085987 DOI: 10.1007/s00792-016-0874-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 05/31/2016] [Accepted: 08/25/2016] [Indexed: 11/04/2022]
Abstract
The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545–2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts.
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Affiliation(s)
- Luís França
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
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Boundy-Mills KL, Glantschnig E, Roberts IN, Yurkov A, Casaregola S, Daniel HM, Groenewald M, Turchetti B. Yeast culture collections in the twenty-first century: new opportunities and challenges. Yeast 2016; 33:243-60. [PMID: 27144478 DOI: 10.1002/yea.3171] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 11/06/2022] Open
Abstract
The twenty-first century has brought new opportunities and challenges to yeast culture collections, whether they are long-standing or recently established. Basic functions such as archiving, characterizing and distributing yeasts continue, but with expanded responsibilities and emerging opportunities. In addition to a number of well-known, large public repositories, there are dozens of smaller public collections that differ in the range of species and strains preserved, field of emphasis and services offered. Several collections have converted their catalogues to comprehensive databases and synchronize them continuously through public services, making it easier for users worldwide to locate a suitable source for specific yeast strains and the data associated with these yeasts. In-house research such as yeast taxonomy continues to be important at culture collections. Because yeast culture collections preserve a broad diversity of species and strains within a species, they are able to make discoveries in many other areas as well, such as biotechnology, functional, comparative and evolution genomics, bioprocesses and novel products. Due to the implementation of the Convention of Biological Diversity (CBD) and the Nagoya Protocol (NP), there are new requirements for both depositors and users to ensure that yeasts were collected following proper procedures and to guarantee that the country of origin will be considered if benefits arise from a yeast's utilization. Intellectual property rights (IPRs) are extremely relevant to the current access and benefit-sharing (ABS) mechanisms; most research and development involving genetic resources and associated traditional knowledge will be subject to this topic. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Kyria L Boundy-Mills
- Phaff Yeast Culture Collection. Food Science and Technology, University of California, Davis, Davis, CA, USA
| | | | - Ian N Roberts
- National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Andrey Yurkov
- Leibniz Institute DSMZ - German Collection of Micro-organisms and Cell Cultures, Braunschweig, Germany
| | - Serge Casaregola
- Micalis Institute INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, Thiverval-Grignon, France
| | - Heide-Marie Daniel
- Mycothéque de l'Université Catholique de Louvain (BCCM/MUCL), Earth and Life Institute, Applied Microbiology, Laboratory of Mycology, Louvain-la-Neuve, Belgium
| | | | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
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Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras JL, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Gonçalves P, Sampaio JP. A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol Ecol 2015; 24:5412-27. [PMID: 26248006 DOI: 10.1111/mec.13341] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022]
Abstract
The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.
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Affiliation(s)
- Pedro Almeida
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Raquel Barbosa
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Yumi Imanishi
- Department of Applied Material and Life Science, College of Engineering, Kanto Gakuin University, Mutsuura-higashi 1-50-1, Kanazawa-ku, Yokohama, 236-8501, Japan
| | - Kiminori Shimizu
- Medical Mycology Research Center, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8673, Japan
| | - Benedetta Turchetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali & Industrial Yeasts Collection DBVPG, Università degli Studi di Perugia, Borgo XX Giugno, 74 - 06121, Perugia, Italy
| | - Jean-Luc Legras
- Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France
| | - Marta Serra
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Sylvie Dequin
- Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France
| | - Arnaud Couloux
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France
| | - Julie Guy
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France
| | - Douda Bensasson
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Paula Gonçalves
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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Garofalo C, Osimani A, Milanović V, Aquilanti L, De Filippis F, Stellato G, Di Mauro S, Turchetti B, Buzzini P, Ercolini D, Clementi F. Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol 2015; 49:123-33. [DOI: 10.1016/j.fm.2015.01.017] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/07/2015] [Accepted: 01/31/2015] [Indexed: 01/23/2023]
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Forti L, Di Mauro S, Cramarossa MR, Filippucci S, Turchetti B, Buzzini P. Non-Conventional Yeasts Whole Cells as Efficient Biocatalysts for the Production of Flavors and Fragrances. Molecules 2015; 20:10377-98. [PMID: 26053491 PMCID: PMC6272320 DOI: 10.3390/molecules200610377] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 05/31/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022] Open
Abstract
The rising consumer requests for natural flavors and fragrances have generated great interest in the aroma industry to seek new methods to obtain fragrance and flavor compounds naturally. An alternative and attractive route for these compounds is based on bio-transformations. In this review, the application of biocatalysis by Non Conventional Yeasts (NCYs) whole cells for the production of flavor and fragrances is illustrated by a discussion of the production of different class of compounds, namely Aldehydes, Ketones and related compounds, Alcohols, Lactones, Terpenes and Terpenoids, Alkenes, and Phenols.
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Affiliation(s)
- Luca Forti
- Department of Life Sciences, University of Modena & Reggio Emilia, via G. Campi 103, Modena 41125, Italy.
| | - Simone Di Mauro
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
| | - Maria Rita Cramarossa
- Department of Life Sciences, University of Modena & Reggio Emilia, via G. Campi 103, Modena 41125, Italy.
| | - Sara Filippucci
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
| | - Benedetta Turchetti
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
| | - Pietro Buzzini
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
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Labbani FZK, Turchetti B, Bennamoun L, Dakhmouche S, Roberti R, Corazzi L, Meraihi Z, Buzzini P. A novel killer protein from Pichia kluyveri isolated from an Algerian soil: purification and characterization of its in vitro activity against food and beverage spoilage yeasts. Antonie Van Leeuwenhoek 2015; 107:961-70. [PMID: 25618417 DOI: 10.1007/s10482-015-0388-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/16/2015] [Indexed: 10/24/2022]
Abstract
A novel killer protein (Pkkp) secreted by a Pichia kluyveri strain isolated from an Algerian soil was active against food and beverage spoilage yeasts of the genera Dekkera, Kluyveromyces, Pichia, Saccharomyces, Torulaspora, Wickerhamomyces and Zygosaccharomyces. After purification by gel filtration chromatography Pkkp revealed an apparent molecular mass of 54 kDa with SDS-PAGE. Minimum inhibitory concentrations (MICs) of purified Pkkp exhibited a high in vitro activity against Dekkera bruxellensis (MICs from 64,000- to 256,000-fold lower than that exhibited by potassium metabisulphite) and Saccharomyces cerevisiae (MICs from 32,000- to 64,000- fold lower than potassium sorbate). No in vitro synergistic interactions (calculated by FIC index - Σ FIC) were observed when Pkkp was used in combination with potassium metabisulphite, potassium sorbate, or ethanol. Pkkp exhibited a dose-response effect against D. bruxellensis and S. cerevisiae in a low-alcoholic drink and fruit juice, respectively. The results of the present study suggest that Pkkp could be proposed as a novel food-grade compound useful for the control of food and beverage spoilage yeasts.
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Affiliation(s)
- Fatima-Zohra Kenza Labbani
- Department of Molecular and Cellular Biology, Natural and Life Sciences Faculty, Abbes Laghrour University of Khenchela, Route Batna, 40004, Khenchela, Algeria,
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De Francesco G, Turchetti B, Sileoni V, Marconi O, Perretti G. Screening of new strains ofSaccharomycodes ludwigiiandZygosaccharomyces rouxiito produce low-alcohol beer. J Inst Brew 2015. [DOI: 10.1002/jib.185] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Giovanni De Francesco
- Department of Agricultural, Food and Environmental Science; University of Perugia; Via San Costanzo 06126 Perugia Italy
| | - Benedetta Turchetti
- Department of Agriculture, Environmental and Food Science, and Industrial Yeasts Collection DBVPG; University of Perugia; Borgo XX Giugno, 74 06121 Perugia Italy
| | - Valeria Sileoni
- Italian Brewing Research Centre; University of Perugia; Via San Costanzo 06126 Perugia Italy
| | - Ombretta Marconi
- Italian Brewing Research Centre; University of Perugia; Via San Costanzo 06126 Perugia Italy
| | - Giuseppe Perretti
- Department of Agricultural, Food and Environmental Science; University of Perugia; Via San Costanzo 06126 Perugia Italy
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46
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Goretti M, Ponzoni C, Caselli E, Marchegiani E, Cramarossa MR, Turchetti B, Buzzini P, Forti L. Corrigendum to “Biotransformation of electron-poor alkenes by yeasts: Asymmetric reduction of (4S)-(+)-carvone by yeast enoate reductases” [Enzyme Microb. Technol. 45 (2009) 463–468]. Enzyme Microb Technol 2014. [DOI: 10.1016/j.enzmictec.2014.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Turchetti B, Selbmann L, Blanchette RA, Di Mauro S, Marchegiani E, Zucconi L, Arenz BE, Buzzini P. Cryptococcus vaughanmartiniae sp. nov. and Cryptococcus onofrii sp. nov.: two new species isolated from worldwide cold environments. Extremophiles 2014; 19:149-59. [DOI: 10.1007/s00792-014-0692-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 08/31/2014] [Indexed: 11/25/2022]
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Selbmann L, Zucconi L, Onofri S, Cecchini C, Isola D, Turchetti B, Buzzini P. Taxonomic and phenotypic characterization of yeasts isolated from worldwide cold rock-associated habitats. Fungal Biol 2014; 118:61-71. [DOI: 10.1016/j.funbio.2013.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 10/28/2013] [Accepted: 11/04/2013] [Indexed: 11/28/2022]
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Turchetti B, Goretti M, Branda E, Diolaiuti G, D'Agata C, Smiraglia C, Onofri A, Buzzini P. Influence of abiotic variables on culturable yeast diversity in two distinct Alpine glaciers. FEMS Microbiol Ecol 2013; 86:327-40. [PMID: 23772605 DOI: 10.1111/1574-6941.12164] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 11/26/2022] Open
Abstract
The influence of some abiotic variables (pH, dry weight, organic carbon, nitrogen and phosphorous) on culturable yeast diversity in two distinct, but adjacent Alpine glaciers (Glacier du Géant, France, and Miage Glacier, Italy) was investigated. In all, 682 yeast strains were isolated and identified by D1/D2 and ITS sequencing as belonging to species of the genera Aureobasidium, Candida, Bulleromyces, Cryptococcus, Cystofilobasidium, Dioszegia, Guehomyces, Holtermanniella, Leucosporidiella, Mrakia, Mrakiella, Rhodotorula, Sporidiobolus, Sporobolomyces and Udenyomyces. Overall, the most represented genera were Cryptococcus (55% of isolates), Rhodotorula (17%) and Mrakia (10%). About 10% of strains, presumably belonging to new species (yet to be described), were preliminarily identified at the genus level. Principal component analysis (PCA) revealed that organic carbon, nitrogen and phosphorous are apparently mostly related to culturable yeast abundance and diversity. In this context, the hypothesis that the frequency of isolation of certain species may be correlated with some organic nutrients (with special emphasis for phosphorous) is discussed.
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Affiliation(s)
- Benedetta Turchetti
- Department of Agricultural, Environmental and Food Science & Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
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50
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Goretti M, Turchetti B, Cramarossa MR, Forti L, Buzzini P. Production of flavours and fragrances via bioreduction of (4R)-(-)-carvone and (1R)-(-)-myrtenal by non-conventional yeast whole-cells. Molecules 2013; 18:5736-48. [PMID: 23681058 PMCID: PMC6270020 DOI: 10.3390/molecules18055736] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 04/29/2013] [Accepted: 05/10/2013] [Indexed: 11/16/2022] Open
Abstract
As part of a program aiming at the selection of yeast strains which might be of interest as sources of natural flavours and fragrances, the bioreduction of (4R)-(-)-carvone and (1R)-(-)-myrtenal by whole-cells of non-conventional yeasts (NCYs) belonging to the genera Candida, Cryptococcus, Debaryomyces, Hanseniaspora, Kazachstania, Kluyveromyces, Lindnera, Nakaseomyces, Vanderwaltozyma and Wickerhamomyces was studied. Volatiles produced were sampled by means of headspace solid-phase microextraction (SPME) and the compounds were analysed and identified by gas chromatography-mass spectroscopy (GC-MS). Yields (expressed as % of biotransformation) varied in dependence of the strain. The reduction of both (4R)-(-)-carvone and (1R)-(-)-myrtenal were catalyzed by some ene-reductases (ERs) and/or carbonyl reductases (CRs), which determined the formation of (1R,4R)-dihydrocarvone and (1R)-myrtenol respectively, as main flavouring products. The potential of NCYs as novel whole-cell biocatalysts for selective biotransformation of electron-poor alkenes for producing flavours and fragrances of industrial interest is discussed.
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Affiliation(s)
- Marta Goretti
- Department of Agricultural, Environmental and Food Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy; E-Mails: (M.G.); (B.T.)
| | - Benedetta Turchetti
- Department of Agricultural, Environmental and Food Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy; E-Mails: (M.G.); (B.T.)
| | - Maria Rita Cramarossa
- Department of Life Sciences, University of Modena & Reggio Emilia, via G. Campi 183, Modena 41125, Italy; E-Mail:
| | - Luca Forti
- Department of Life Sciences, University of Modena & Reggio Emilia, via G. Campi 183, Modena 41125, Italy; E-Mail:
- Authors to whom correspondence should be addressed: E-Mails: (L.F.); (P.B.); Tel.: +39-059-2055110 (L.F.); Fax: +39-059-373543 (L.F.); Tel.: +39-075-5856455 (P.B.); Fax: +39-075-5856470 (P.B.)
| | - Pietro Buzzini
- Department of Agricultural, Environmental and Food Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy; E-Mails: (M.G.); (B.T.)
- Authors to whom correspondence should be addressed: E-Mails: (L.F.); (P.B.); Tel.: +39-059-2055110 (L.F.); Fax: +39-059-373543 (L.F.); Tel.: +39-075-5856455 (P.B.); Fax: +39-075-5856470 (P.B.)
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