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

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

doi:10.3389/fmicb.2015.00277

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

Journal Article · Tue Apr 14 00:00:00 EDT 2015 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2015.00277· OSTI ID:1200858

Nunes da Rocha, Ulisses ^[1]; Cadillo-Quiroz, Hinsby ^[2]; Karaoz, Ulas ^[3]; Rajeev, Lara ^[3]; Klitgord, Niels ^[3]; Dunn, Sean ^[2]; Truong, Viet ^[2]; Buenrostro, Mayra ^[2]; Bowen, Benjamin P. ^[3]; Garcia-Pichel, Ferran ^[4]; Mukhopadhyay, Aindrila ^[3]; Northen, Trent R. ^[3]; Brodie, Eoin L. ^[5]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Quantitative Microbial Ecology Group, Amsterdam (Netherlands)
Arizona State Univ., Tucson, AZ (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Arizona State Univ., Tucson, AZ (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1200858

Alternate ID(s):: OSTI ID: 1407291

Journal Information:: Frontiers in Microbiology, Vol. 6; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 42 works

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A “Cultural” Renaissance: Genomics Breathes New Life into an Old Craft Carini, Paul mSystems, Vol. 4, Issue 3 https://doi.org/10.1128/msystems.00092-19	journal	May 2019
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