Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.

Ulisses Nunes Da Rocha,Aindrila Mukhopadhyay,Niels Klitgord,Benjamin P Bowen,Trent R Northen,Hinsby Cadillo-Quiroz,Sean Dunn,Ferran Garcia-Pichel,Mayra Buenrostro,Viet Truong,Lara Rajeev,Eoin L Brodie,Ulas Karaoz

doi:10.3389/fmicb.2015.00277

Abstract

Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.

Highlights

Dryland regions, including hyperarid, semiarid, arid, alpine and polar regions, cover approximately one third of the Earth’s land surface (Belnap, 2006)
Isolate recovery trajectories from Biological Soil Crusts (BSCs) pre-incubated under dark conditions showed divergent patterns from those under light conditions with 1/100 R2G showing a slower rate of accumulation
After 50 days of incubation, there was a general trend of more Colony Forming Unit (CFU) per gram of dry soil being obtained in samples preincubated in the dark relative to those pre-incubated in the light (Figure 1)

Summary

Introduction

Dryland regions, including hyperarid, semiarid, arid, alpine and polar regions, cover approximately one third of the Earth’s land surface (Belnap, 2006) Large expanses of these drylands are covered by Biological Soil Crusts (BSCs) (Bowker et al, 2002). In early successional stages of BSCs, Microcoleus vaginatus, a filamentous cyanobacterium, forms a polysaccharide mesh derived from fixed atmospheric C (Mazor et al, 1996). This bed helps further colonization of BSCs by diazotrophic cyanobacteria, other bacteria, fungi, lichens and mosses in a temporal succession (Mazor et al, 1996; Kuske et al, 2012). M. vaginatus is the most dominant organism in early successional stages of BSCs (Büdel et al, 2008; Zaady et al, 2010), but a pioneer in the development of this ecosystem

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Discussion

Conclusion