The microbiome of a shell mound: ancient anthropogenic waste as a source of Streptomyces degrading recalcitrant polysaccharides.

Thalita R Tuleski,Edileusa C M Gerhardt,Fábio O Pedrosa,Emanuel M Souza,Rodrigo A Reis,Marcelo Conzentino,Luciano F Huergo,Valter A Baura,Leonardo M Cruz,Govind Chandra,Dieval Guizelini,Araceli Pires,Maria V Gonçalves,Marcos V Gernet,Eduardo Balsanelli

doi:10.1007/s11274-021-03174-4

Thalita R Tuleski, Edileusa C M Gerhardt + Show 13 more

Open Access

https://doi.org/10.1007/s11274-021-03174-4

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Abstract

Metagenome amplicon DNA sequencing and traditional cell culture techniques are helping to uncover the diversity and the biotechnological potential of prokaryotes in different habitats around the world. It has also had a profound impact on microbial taxonomy in the last decades. Here we used metagenome 16S rDNA amplicon sequencing to reveal the microbiome composition of different layers of an anthropogenic soil collected at a shell mound Sambaqui archeological site. The Samabaqui soil microbiome is mainly composed by phyla Acidobacteria, Rokubacteria, Proteobacteria and Thaumarchaeota. Using culture-dependent analysis we obtained few Streptomyces isolates from the Sambaqui soil. One of the isolates, named Streptomyces sp. S3, was able to grow in minimal medium containing recalcitrant polysaccharides including chitin, xylan, carboxymethylcellulose or microcrystalline cellulose as sole carbon sources. The activities of enzymes degrading these compounds were confirmed in cell free supernatants. The genome sequence revealed not only an arsenal of genes related to polysaccharides degradation but also biosynthetic gene clusters which may be involved in the production of biotechnologically interesting secondary metabolites.

Highlights

Microbiomes constitute an important source for the prospection of industrially relevant enzymes and bioactive metabolites such as antibiotics or chemotherapeutic drugs
The amplicon sequence variants (ASV) were taxonomically classified; 13.8% and 9.3% of the ASV were classified as Archaea in S and B samples, respectively
In this study we provide the first microbiome analysis of the anthropogenic soil layers of an archeological Sambaqui site located in the South of Brazil

Summary

Introduction

Microbiomes constitute an important source for the prospection of industrially relevant enzymes and bioactive metabolites such as antibiotics or chemotherapeutic drugs. Most of the antibiotics used in the clinics nowadays are still the fruits of valuable prospection of Streptomyces strains from the environment, mostly from soil (Liu et al, 2013). The recent advances in metagenomic 16S rDNA amplicon sequencing and whole metagenome DNA sequencing is helping to uncover the microbial diversity and their biotechnological potential at an unprecedent scale (Nayfach et al, 2020; Thompson et al, 2017) Global efforts such as the earths microbiome is providing valuable data on how microbial diversity is distributed around the globe and how microbial taxa correlate in similar environments in distant locations (Stevens et al, 2017). In addition to these high-tech platforms, microbial diversity can be accessed using traditional culture isolation techniques. Traditional methods are still very effective in the discovery of novel bacterial strains with biotechnological potential (Wilson et al, 2014)

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