Composition, Diversity and Functional Analysis of the Modern Microbiome of the Middle Triassic Cava Superiore Beds (Monte San Giorgio, Switzerland)

Sania Arif,Joachim Reitner,Michael Hoppert

doi:10.1038/s41598-019-55955-5

Sania Arif, Joachim Reitner + Show 1 more

Open Access

https://doi.org/10.1038/s41598-019-55955-5

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Journal: Scientific Reports	Publication Date: Dec 1, 2019
Citations: 1	License type: open-access

Affiliation: University of Göttingen

Abstract

Organic-rich laminated shales and limestones from the Monte San Giorgio (Lugano Prealps, Switzerland) are known as famous fossil lagerstätten for excellently preserved fossils from the Middle Triassic Period. The various bituminous shales from Monte San Giorgio are thermally immature and rich in diverse organic compounds, which provide unique substrates for active soil microbial communities. We selected the Cava superior beds of the Acqua del Ghiffo site for this study. To investigate its microbial structure and diversity, contig assembly, Operational Taxonomic Units (OTUs) clustering, and rarefaction analysis were performed for bacterial 16S rDNA preparations from bituminous and non-bituminous limestone strata with the MetaAmp pipeline. Principal coordinates analysis shows that the microbial communities from the bituminous strata differ significantly from limestone samples (P < 0.05 Unifrac weighted). Moreover, metagenomic tools could also be used effectively to analyze the microbial communities shift during enrichment in specific growth media. In the nutrient-rich media, one or few taxa, mainly Proteobacteria and Firmicutes, were enriched which led to the drastic diversity loss while oligotrophic media could enrich many taxa simultaneously and sustain the richness and diversity of the inoculum. Piphillin, METAGENassist and MicrobiomeAnalyst pipeline also predicted that the Monte San Giorgio bituminous shales and oligotrophic enriched microbiomes degrade complex polycyclic aromatic hydrocarbons.

Highlights

Compounds, among them hopanes, hopenes, and methylhopanoids[12] and their metagenomic biodiversity analysis of the non-culturable microbiome is interesting from a microbiological, geochemical as well as a biotechnological point of view
We examined the microbial communities of Monte San Giorgio organic-rich shale and limestone rocks samples via Illumina MiSeq sequencing, followed by microbial growth in enrichment media to elucidate the correlation of the microbial communities and enrichment effect of media
The analysis of variance (ANOVA) validated that the outside rock surface sample of the shale was prevalent in Armatimonadetes, Saccharibacteria, SM2F11, Chlorobi, Bacteroidetes, and TM6 (p < 0.05)

Summary

Introduction

Compounds, among them hopanes, hopenes, and methylhopanoids[12] and their metagenomic biodiversity analysis of the non-culturable microbiome is interesting from a microbiological, geochemical as well as a biotechnological point of view. The other objective was to investigate how the microbial growth and diversity can be influenced by different enrichment media and which hydrocarbon-degrading metabolic groups may be enriched from the environment. For this purpose, we examined the microbial communities of Monte San Giorgio organic-rich shale and limestone rocks samples via Illumina MiSeq sequencing, followed by microbial growth in enrichment media to elucidate the correlation of the microbial communities and enrichment effect of media. The geochemical and bioremediation metabolic potential of the microbiomes were predicted with the online available tools METAGENassist[13] and Piphillin[14]

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