Isolation of a significant fraction of non-phototroph diversity from a desert biological soil crust

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

Research output: Contribution to journalArticle

23 Citations (Scopus)

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.

Original languageEnglish (US)
Article number277
JournalFrontiers in Microbiology
Volume6
Issue numberMAR
DOIs
StatePublished - 2015

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Soil
Metagenome
Axenic Culture
Food
Sequence Homology
rRNA Genes
Population
Minerals
Ecosystem
Oxidative Stress
Light

Keywords

  • Biological soil crusts
  • Culturability
  • Dryland microbiology
  • Isolation
  • Microbial diversity

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Isolation of a significant fraction of non-phototroph diversity from a desert biological soil crust. / da Rocha, Ulisses Nunes; Cadillo-Quiroz, Hinsby; Karaoz, Ulas; Rajeev, Lara; Klitgord, Niels; Dunn, Sean; Truong, Viet; Buenrostro, Mayra; Bowen, Benjamin Paul; Garcia-Pichel, Ferran; Mukhopadhyay, Aindrila; Northen, Trent Russell; Brodie, Eoin L.

In: Frontiers in Microbiology, Vol. 6, No. MAR, 277, 2015.

Research output: Contribution to journalArticle

da Rocha, UN, Cadillo-Quiroz, H, Karaoz, U, Rajeev, L, Klitgord, N, Dunn, S, Truong, V, Buenrostro, M, Bowen, BP, Garcia-Pichel, F, Mukhopadhyay, A, Northen, TR & Brodie, EL 2015, 'Isolation of a significant fraction of non-phototroph diversity from a desert biological soil crust', Frontiers in Microbiology, vol. 6, no. MAR, 277. https://doi.org/10.3389/fmicb.2015.00277
da Rocha, Ulisses Nunes ; Cadillo-Quiroz, Hinsby ; Karaoz, Ulas ; Rajeev, Lara ; Klitgord, Niels ; Dunn, Sean ; Truong, Viet ; Buenrostro, Mayra ; Bowen, Benjamin Paul ; Garcia-Pichel, Ferran ; Mukhopadhyay, Aindrila ; Northen, Trent Russell ; Brodie, Eoin L. / Isolation of a significant fraction of non-phototroph diversity from a desert biological soil crust. In: Frontiers in Microbiology. 2015 ; Vol. 6, No. MAR.
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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.",
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AU - da Rocha, Ulisses Nunes

AU - Cadillo-Quiroz, Hinsby

AU - Karaoz, Ulas

AU - Rajeev, Lara

AU - Klitgord, Niels

AU - Dunn, Sean

AU - Truong, Viet

AU - Buenrostro, Mayra

AU - Bowen, Benjamin Paul

AU - Garcia-Pichel, Ferran

AU - Mukhopadhyay, Aindrila

AU - Northen, Trent Russell

AU - Brodie, Eoin L.

PY - 2015

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