Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.
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.
Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA ; Quantitative Microbial Ecology Group, Department of Molecular and Cell Physiology, Faculty of Earth and Life Sciences, VU Amsterdam Amsterdam, Netherlands.
Ulisses
U
Nunes da Rocha
Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA.
Hinsby
H
Cadillo-Quiroz
Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA.
Ulas
U
Karaoz
Lawrence Berkeley National Laboratory, Physical Biosciences Division Berkeley, CA, USA.
Lara
L
Rajeev
Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA.
Niels
N
Klitgord
Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA.
Sean
S
Dunn
Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA.
Viet
V
Truong
Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA.
Mayra
M
Buenrostro
Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA.
Benjamin P
BP
Bowen
Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA ; Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA.
Ferran
F
Garcia-Pichel
Lawrence Berkeley National Laboratory, Physical Biosciences Division Berkeley, CA, USA.
Aindrila
A
Mukhopadhyay
Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA.
Trent R
TR
Northen
Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA ; Department of Environmental Science, Policy and Management, University of California, Berkeley Berkeley, CA, USA.
Eoin L
EL
Brodie
biological soil crusts; culturability; dryland microbiology; isolation; microbial diversity