High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

Abstract

One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.

Hydrocarbon-Contaminated Sites: Is There Something More Than Exophiala xenobiotica? New Insights into Black Fungal Diversity Using the Long Cold Incubation Method

“…The behavior of individual species can, in fact, be frequently explained in a community context by its interaction with other organisms, which are often unculturable under laboratory conditions [44]. Only a small fraction of the world's microbial diversity can be cultured under standard microbiological tools and media [45]. If, for bacteria, the "1% culturability paradigm" (recently revised by Martiny [46,47]) is generally accepted (according to which around 99% of them are unculturable), for fungi, it is somehow different.…”

Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites

“…The relationship between soil location and taxonomy in chemical discovery remains murky, and therefore it might be just as productive to seek novelty in the drained lake basins in the arctic 69 or the drylands of the Tabernas Desert in Spain. 70 Biosynthetic surveys that focus on historically neglected microbial taxa suggest that there is value in exploring taxonomic diversity as well. 71 For those who focus efforts on the rain forests, a fruitful source are the symbionts of the staggering diversity of plants and animals that are likely a prolic source of novel bacterial species, and consequently, chemical diversity.…”

Belnapia mucosa sp. nov. and Belnapia arida sp. nov., isolated from desert biocrust

“…Cell morphology was observed under an optical microscope with crystal violet glass stain. Growth at different temperatures (4,10,15,20,23,30,37,40, 42 and 45 °C) and NaCl concentrations (0.0-4.0% at intervals of 0.5%) was checked on R2A. Growth at different pH values (4.0-10.0 at intervals of 1.0 pH unit) was examined by growing the strains in liquid R2A using the buffers MES (pH 4-6), HEPES (pH 7-8) and CHES (pH 9-10) at a final concentration of 10 mM.…”

“…Strains T6 T and T18 T were isolated in the vicinity of the Tabernas Desert (Almería, Spain) during a study on the culturable microbial diversity in European drylands [ 4 ]. The Tabernas Desert is considered the only arid desert in Europe.…”

“…Genomic DNA extraction was carried out using the DNeasy Power Soil kit (Qiagen), according to the manufacturer’s instructions, but incubating at 65 °C after the addition of C1. Whole 16S rRNA gene PCR was carried out with universal primers 8F (5′-AGAGTTTGATCCTGGCTCAG-3′) [ 7 ] and 1492R (5′-GGTTACCTTGTTACGACTT-3′) [ 8 ] following procedures described previously [ 4 ]. Phylogenetic trees based on the 16S rRNA gene sequences were reconstructed using the maximum-likelihood (ML) [ 9 ] and neighbour-joining (NJ) [ 10 ] methods with the software mega X v.10.1.7.…”