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

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.

Influence of ancient anthropogenic activities on the mangrove soil microbiome.

Mangroves are highly productive ecosystems located at the transition between the terrestrial and marine environments. Mangroves play an important role in carbon storage, nutrient cycling and support for the marine food web. Mangrove soils are formed by fine particles rich in organic carbon and are subject to constant fluctuations in oxygen, salinity and nutrient availability due to fresh water flux and tidal variations. Microbes play an important role in nutrient cycling in mangrove soils; however, studies on the mangrove soil microbiome are scarce. Here we compare the microbiome of pristine mangrove soil located in an environmentally protected area in Guaratuba, Southern Brazil, with the microbiome of mangrove soil affected by the presence of carbonaceaous debris eroding from an archeological site known as Sambaqui. We show that although the Sambaqui site has a major effect on soil chemistry, increasing the soil pH by 2.6 units, only minor changes in the soil microbiome were detected indicating resilience of the microbial community to pH variations. The high alpha diversity indexes and predicted metabolic potential suggest that the mangrove soil microbiome not only provides important ecological services but also may host a broad range of microbes and genes of biotechnological interest.