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

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.

Microbial Nursery Production of High-Quality Biological Soil Crust Biomass for Restoration of Degraded Dryland Soils

“…Cyanobacteria were important overall in all treatments and inoculum communities, along with Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes; this overall distribution is also quite typical for biocrusts (9,41). Bray-Curtis distances in community composition, calculated between each treatment and its respective inoculum, varied Fig.…”

“…Biocrusts are complex, topsoil microbial assemblages that develop on the primary production of soil cyanobacteria, microalgae (sometimes in algal symbioses), or mosses and that support a large diversity of heterotrophic bacteria (9), archaea (10), and fungi (11). Considered to be a "mantle of fertility" in arid lands (12), biocrusts provide essential goods and services; they stabilize soils and thus reduce rates of wind erosion and dust particle production (13), can influence soil temperature (14,15), contribute significantly to soil C and N inputs into the ecosystem (16), increase the lixiviation of micronutrients (17), control soil hydrological dynamics (18), and are thought to provide good conditions for plant germination and establishment (19).…”

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

“…The importance of EPSs for microbial life in natural environments has been discussed in many review articles Flemming and Wingender, 2010;More et al, 2014). Especially in arid or semi-arid environments, the role of EPSs secreted by Cyanobacteria is crucial for microbial communities surviving within (and below) biocrusts (De Philippis and Vincenzini, 1998;Pereira et al, 2009;Mager and Thomas, 2011;Rossi et al, 2012;Colica et al, 2014;Rossi and De Philippis, 2015).…”

“…These data generally delineate the interplay between multilevel trophic interactions Nunes da Rocha et al, 2015;Pepe-Ranney et al, 2016) and surrounding environmental conditions (Caruso et al, 2011). Biocrusts host a complex community of diverse autotrophs and heterotrophs (hundreds of species including about 20 generic or subgeneric taxa of Cyanobacteria) (Bowker et al, 2010a, b;Garcia-Pichel et al, 2013).…”

“…The key ingredient in biocrust functioning is the highly dynamic and spatially self-organising microbial community. For simplicity, we considered four microbial groups: photoautotrophs (primarily Cyanobacteria), aerobic heterotrophs, anaerobic heterotrophs (denitrifiers), and chemoautotrophs (Garcia-Pichel and Belnap, 2002;Johnson et al, 2005Johnson et al, , 2007Abed et al, 2010Abed et al, , 2013Nunes da Rocha et al, 2015) and consider their role in carbon and nitrogen cycling. Figure 1 summaries the model in terms of processes, variables, parameters, and simulated results in this work.…”