Kadnikov, V. | Search bioRxiv

bioRxiv2019

A global perspective on microbial diversity in the terrestrial deep subsurface

While recent efforts to catalogue Earths microbial diversity have focused upon surface and marine habitats, 12% to 20% of Earths bacterial and archaeal biomass is suggested to inhabit the terrestrial deep subsurface, compared to [~]1.8% in the deep subseafloor 1-3. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities 4-6. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Here, we show the diversity of bacterial communities in deep subsurface groundwater is controlled by aquifer lithology globally, by using 16S rRNA gene datasets collected across five countries on two continents and from fifteen rock types over the past decade. Furthermore, our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, likely as a function of the diverse metabolic strategies of these taxa. Despite this similarity, evidence was found not only for aquifer-specific microbial communities, but also for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacterial OTUs across the localities. This finding implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, that may play an important role in colonising and sustaining microbial habitats in the deep terrestrial subsurface. An in-silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

microbiology↗

bioRxiv2017

Sugar metabolism of the first thermophilic Planctomycetes Thermogutta terrifontis: comparative genomic and transcriptomic approache

Xanthan gum, a complex polysaccharide comprising glucose, mannose and glucuronic acid residues, is involved in numerous biotechnological applications in cosmetics, agriculture, pharmaceuticals, food and petroleum industries. Additionally, its oligosaccharides were shown to possess antimicrobial, antioxidant and few other properties. Yet, despite its extensive usage, little is known about xanthan gum degradation pathways and mechanisms.\n\nThermogutta terrifontis R1 was described as the first thermophilic representative of the Planctomycetes phylum. As other cultivated planctomycetes, it grows well on various carbohydrates including oligo- and polysaccharides, however, its capability of anaerobic growth with or without electron acceptors was a novel finding among the representatives of this phylum.\n\nThe aim of this work is to examine T. terrifontis catabolic pathways with a special focus on the xanthan gum degradation pathway using genomic and transriptomic sequencing. Genomic analysis revealed more than a hundred glycosidases, polysaccharide lyases and other CAZymes, involved in oligo- and polysaccharide degradation by T. terrifontis, proteins of central carbohydrate metabolism and aerobic and anaerobic respiration. Furthermore, the combination of genomic and transcriptomic approaches revealed a putative novel xanthan gum degradation pathway involving unusual catalytic steps and enzymes: novel glycosidase(s) of DUF1080 family, hydrolyzing xanthan gum beta-glucosidic backbone linkages and beta-mannosidases instead of xanthan lyases for degradation of terminal beta-mannosidic linkages. Surprisingly, the genes coding DUF1080 proteins were found in high number in T. terrifontis and in many other Planctomycetes genomes, which, together with our observation that xanthan gum being a selective substrate for many planctomycetes, supports the important role of DUF1080 in xanthan gum degradation. Our findings shed light on the metabolism of the first thermophilic planctomycete, capable to degrade a number of polysaccharides, either aerobically or anaerobically, including the biotechnologically important bacterial polysaccharide xanthan gum. The results serve as good foundation for future exploration of T. terrifontis and its enzymes in biotechnological applications.

microbiology↗