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Monaco P, Baldoni A, Naclerio G, Scippa GS, Bucci A. Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review. Microorganisms 2024; 12:1276. [PMID: 39065045 PMCID: PMC11279295 DOI: 10.3390/microorganisms12071276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.
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Affiliation(s)
- Pamela Monaco
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
| | | | | | | | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
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Čejka T, Trnka M, Büntgen U. Sustainable cultivation of the white truffle (Tuber magnatum) requires ecological understanding. MYCORRHIZA 2023; 33:291-302. [PMID: 37462722 PMCID: PMC10752849 DOI: 10.1007/s00572-023-01120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/29/2023] [Indexed: 12/29/2023]
Abstract
The white truffle (Tuber magnatum Picco.; WT) is the most expensive and arguably also the most delicious species within the genus Tuber. Due to its hidden belowground life cycle, complex host symbiosis, and yet unknown distribution, cultivation of the enigmatic species has only recently been achieved at some plantations in France. A sustainable production of WTs under future climate change, however, requires a better ecological understanding of the species' natural occurrence. Here, we combine information from truffle hunters with a literature review to assess the climatic, edaphic, geographic, and symbiotic characteristics of 231 reported WT sites in southeast Europe. Our meta-study shows that 75% of the WT sites are located outside the species' most famous harvest region, the Piedmont in northern Italy. Spanning a wide geographic range from ~ 37° N in Sicily to ~ 47° N in Hungary, and elevations between sea level in the north and 1000 m asl in the south, all WT sites are characterised by mean winter temperatures > 0.4 °C and summer precipitation totals of ~ 50 mm. Often formed during past flood or landslide events, current soil conditions of the WT sites exhibit pH levels between 6.4 and 8.7, high macroporosity, and a cation exchange capacity of ~ 17 meq/100 g. At least 26 potential host species from 12 genera were reported at the WT sites, with Populus alba and Quercus cerris accounting for 23.5% of all plant species. We expect our findings to contribute to a sustainable WT industry under changing environmental and economic conditions.
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Affiliation(s)
- Tomáš Čejka
- Department of Climate Change Impacts On Agroecosystems, Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4, 603 00, Brno, Czech Republic.
- Department of Ecology and Environmental Sciences, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71, Olomouc, Czech Republic.
| | - Miroslav Trnka
- Department of Climate Change Impacts On Agroecosystems, Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4, 603 00, Brno, Czech Republic
- Department of Agrosystems and Bioclimatology, Faculty of Agronomy, Mendel University, Zemědělská 1, 613 00, Brno, Czech Republic
| | - Ulf Büntgen
- Department of Climate Change Impacts On Agroecosystems, Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4, 603 00, Brno, Czech Republic
- Department of Geography, Faculty of Science, Masaryk University, Kotlářská 2, 602 00, Brno, Czech Republic
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
- Department of Geography, University of Cambridge, Downing Place, Cambridge, CB2 3EN, UK
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Bucci A, Monaco P, Naclerio G. Tuber magnatum Picco: the challenge to identify ascoma-associated bacteria as markers for geographic traceability. Front Microbiol 2023; 14:1142214. [PMID: 37260692 PMCID: PMC10227511 DOI: 10.3389/fmicb.2023.1142214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023] Open
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Monaco P, Naclerio G, Mello A, Bucci A. Role and potentialities of bacteria associated with Tuber magnatum: A mini-review. Front Microbiol 2022; 13:1017089. [PMID: 36274685 PMCID: PMC9584545 DOI: 10.3389/fmicb.2022.1017089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Among the hypogeous ectomycorrhizal fungi, the white truffle Tuber magnatum Picco is the species of greatest interest, both from an ecological and economic point of view. The increasing market demand of the precious white truffle along with the fall in its natural production led to a growing interest in cultivation techniques and encouraged truffle growers and researchers to deeper investigate factors that could affect and improve T. magnatum productivity. In this context, microbial communities play a central role. Indeed, in the last few years, the hypothesis of a potential link between microbial community composition and truffle orchard productivity is arousing a greater attention. Moreover, since the value of the prized T. magnatum can vary in relation to its provenience, the need to define a reliable tracking system is also emerging and bacteria appear to be a promising tool. Accordingly, the present mini-review summarises the knowledge currently available on T. magnatum microbial communities, focusing on the role of truffle-associated bacteria and highlighting similarities and differences between samples of different origin, to address the following issues: (i) Is there a correlation between microbial taxa and truffle ground productivity? (ii) Can bacteria actually be used as markers of T. magnatum geographic origin? The identification of microorganisms able to promote T. magnatum formation may represent an important advance in the field of truffle farming. Similarly, the detection of bacterial taxa that can be used as markers of T. magnatum origin could have a considerable impact on truffle industry and trade, even at local scale.
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Affiliation(s)
- Pamela Monaco
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Antonietta Mello
- Institute for Sustainable Plant Protection (IPSP), Turin Unit, National Research Council, Turin, Italy
| | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
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Gohar D, Põldmaa K, Tedersoo L, Aslani F, Furneaux B, Henkel TW, Saar I, Smith ME, Bahram M. Global diversity and distribution of mushroom-inhabiting bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:254-264. [PMID: 35102713 DOI: 10.1111/1758-2229.13045] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.
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Affiliation(s)
- Daniyal Gohar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- Natural History Museum and Botanical Garden, University of Tartu, Vanemuise 46, Tartu, 51003, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Farzad Aslani
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
- School of Environmental and Rural Sciences, University of New England, Armidale, NSW, Australia
| | - Brendan Furneaux
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi St. 2, Tartu, 50409, Estonia
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, Uppsala, 756 51, Sweden
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Monaco P, Bucci A, Naclerio G, Mello A. Heterogeneity of the white truffle Tuber magnatum in a limited geographic area of Central-Southern Italy. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:591-599. [PMID: 33943006 DOI: 10.1111/1758-2229.12956] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/19/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Molise region (Central-Southern Italy) is one of the Italian richest areas of truffles and contributes significantly to the national production of the precious Tuber magnatum. Nevertheless, Molise truffle has received little scientific attention. Accordingly, in the present study, two T. magnatum populations collected in two different sites of Molise region were characterised from a morphological, genetic and microbiological point of view. A considerable variability between and within the two analysed groups emerged, suggesting an interesting heterogeneity of Molise white truffle populations. Ascocarps of the two groups significantly differed in size and maturation degree, although no linear correlation between weight and maturity was found. Genetic investigations focused on the Sequence-Characterised Amplified Region SCAR A21-inf. Three haplotypes, randomly distributed within the two truffle groups regardless of their collection sites, were detected. The 16S rRNA gene amplicon high-throughput sequencing provided an overview of the composition of the ascocarp-associated bacterial communities. A predominance of α-Proteobacteria was observed, with Bradyrhizobium among the main genera. However, some truffles showed unusual microbial profiles, with Pedobacter, Polaromonas and other bacterial genera as dominant taxa.
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Affiliation(s)
- Pamela Monaco
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, Pesche (IS), 86090, Italy
| | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, Pesche (IS), 86090, Italy
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, Pesche (IS), 86090, Italy
| | - Antonietta Mello
- Institute for Sustainable Plant Protection (IPSP), Turin Unit, National Research Council, Viale P.A. Mattioli 25, Turin, 10125, Italy
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Soil Metabarcoding Offers a New Tool for the Investigation and Hunting of Truffles in Northern Thailand. J Fungi (Basel) 2021; 7:jof7040293. [PMID: 33924673 PMCID: PMC8069821 DOI: 10.3390/jof7040293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/06/2023] Open
Abstract
Truffles (Tuber spp.) are well-known as edible ectomycorrhizal mushrooms, and some species are one of the most expensive foods in the world. During the fruiting process, truffles produce hypogeous ascocarps; a trained pig or dog is needed to locate the ascocarps under the ground. Truffles in northern Thailand have been recorded in association with Betulaalnoides and Carpinus poilanei. In this study, we investigated the soil mycobiota diversity of soil samples from both of these truffle host plants in native forests using environmental DNA metabarcoding to target the internal transcribed spacer 1 (ITS1) region of the rDNA gene for the purposes of investigation of truffle diversity and locating truffles during the non-fruiting phase. In this study, a total of 38 soil samples were collected from different locations. Of these, truffles had been found at three of these locations. Subsequently, a total of 1341 putative taxonomic units (OTUs) were obtained. The overall fungal community was dominated by phylum-level sequences assigned to Ascomycota (57.63%), Basidiomycota (37.26%), Blastocladiomycota (0.007%), Chytridiomycota (0.21%), Glomeromycota (0.01%), Kickxellomycota (0.01%), Mortierellomycota (2.08%), Mucoromycota (0.24%), Rozellomycota (0.01%), Zoopagomycota (0.003%), and unidentified (2.54%). The results revealed that six OTUs were determined to be representative and belonged to the genus Tuber. OTU162, OTU187, OTU447, and OTU530 belonged to T. thailandicum, T. lannaense, T. bomiense, and T. magnatum, whereas OTU105 and OTU720 were acknowledged as unrecognized Tuber species. From 38 locations, OTUs of truffles were found in 33 locations (including three previously known truffle locations). Thus, 30 collection sites were considered new locations for T. thailandicum, T. bomiense, and other unrecognized Tuber species. Interestingly, at 16 new locations, mature ascocarps of truffles that were undergoing the fruiting phase were located underground. All 16 truffle samples were identified as T. thailandicum based on morphological characteristics and molecular phylogenetic analysis. However, ascocarps of other truffle species were not found at the new OTUs representative locations. The knowledge gained from this study can be used to lead researchers to a better understanding of the occurrence of truffles using soil mycobiota diversity investigation. The outcomes of this study will be particularly beneficial with respect to the search and hunt for truffles without the need for trained animals. In addition, the findings of this study will be useful for the management and conservation of truffle habitats in northern Thailand.
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Monaco P, Divino F, Naclerio G, Bucci A. Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01604-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Purpose
Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).
Methods
Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.
Result
The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.
Conclusion
The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.
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