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8. The hidden layers of microbial community structure: Extracting the concealed diversity dimensions from our sequencing data

Author

Fasolo, A., Treu, L., Stevanato, P., Concheri, G., Campanaro, S., and Squartini, A.

Subjects
DNA, Bacterial, Relation (database), OTU Success Index, Microbiology, 16S sequencing, 03 medical and health sciences, 0302 clinical medicine, RNA, Ribosomal, 16S, OTU-centered Rank Power, Genetics, OSI, Cluster analysis, Molecular Biology, Bacterial metabarcoding, Ecosystem, Soil Microbiology, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, Bacteria, OTUs abundance, Phylum, Microbiota, Bacterial diversity, 16S sequencing, OTU-centered Rank Power, Abundance-centered Rank Power, OTU Success Index, OSI, Biodiversity, Sequence Analysis, DNA, Geography, Taxon, Habitat, Microbial population biology, Bacterial diversity, Evolutionary biology, Abundance-centered Rank Power, 030217 neurology & neurosurgery, Diversity (business)
Abstract

Microbial metabarcoding is the standard approach to assess communities’ diversity. However reports are often limited to simple OTU abundances for each phylum, giving rather one-dimensional views of microbial assemblages, overlooking other accessible aspects. The first is masked by databases incompleteness; OTU picking involves clustering at 97% (near-species) sequence identity, but different OTUs regularly end up under a same taxon name. When expressing diversity as number of obtained taxonomical names, a large portion of the real diversity lying within the data remains underestimated. Using the 16S sequencing results of an environmental transect across a gradient of 17 coastal habitats we first extracted the number of OTUs hidden under the same name. Further, we observed which was the deepest rank yielded by annotation, revealing for which microbial groups are we missing most knowledge. Data were then used to infer an evolutionary aspect: what is, in each phylum the success of the present time individuals (abundances for each OTU) in relation to their prior evolutionary success in differentiation (number of OTUs). This information reveals whether the past speciation/diversification force is matched by the present competitiveness in reproduction/persistence. The final layer explored is functional diversity, i.e. abundances of groups involved in specific environmental processes.

Published
2020

34. Compost Application in the Vineyard and Its Influence on Soil Characteristics, Vegetative and Productive Behaviour of Grapevine

Author

Ponchia G., Bozzolo A., Tateo F., and Concheri G.

Abstract

Research was carried out in two vineyards planted with the variety 'Merlot' in order to evaluate the effect of soil compost addition on soil organic matter and grapevine production and quality. The vineyards were established in Valnogaredo and Zovon, on the Euganean Hills, Italy. Two treatments were compared: application of 5 t/ha of compost versus no compost application. Soil and microbial analyses were performed. SPAD values and leaf chlorophyll content were measured during the growing season. Quantitative and qualitative parameters of vine production were evaluated. The soil of the two vineyards was calcareous and gravelly, with clay texture and alkaline pH. Organic matter content increased after the compost treatment, whereas the other investigated parameters did not change significantly. The organic C content increased in Valnogaredo but not in Zovon. The humification index and microbial biomass increased in both vineyards. In 2007 and 2008 SPAD values in the leaves were higher for the compost treated vines compared with those untreated and strong correlations were found with leaf chlorophyll contents. At harvest, in Valnogaredo in 2007 and 2008, in Zovon in 2008 and 2009, an increase in the yield/vine of bunch and berry weight and volume and qualitative parameters were observed in plants treated with compost. In conclusion, compost application, depending on soil characteristics, can increase soil organic matter and microbial biomass but can also affect vine productivity.

Published
2012

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