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%more »
- Authors:
-
- 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)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1200858
- Alternate Identifier(s):
- OSTI ID: 1407291
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; biological soil crusts; culturability; isolation; dryland microbiology; microbial diversity
Citation Formats
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., and Brodie, Eoin L. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. United States: N. p., 2015.
Web. doi:10.3389/fmicb.2015.00277.
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. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. United States. https://doi.org/10.3389/fmicb.2015.00277
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., and Brodie, Eoin L. Tue .
"Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust". United States. https://doi.org/10.3389/fmicb.2015.00277. https://www.osti.gov/servlets/purl/1200858.
@article{osti_1200858,
title = {Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust},
author = {Nunes da Rocha, Ulisses and Cadillo-Quiroz, Hinsby and Karaoz, Ulas and Rajeev, Lara and Klitgord, Niels and Dunn, Sean and Truong, Viet and Buenrostro, Mayra and Bowen, Benjamin P. and Garcia-Pichel, Ferran and Mukhopadhyay, Aindrila and Northen, Trent R. and Brodie, Eoin L.},
abstractNote = {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.},
doi = {10.3389/fmicb.2015.00277},
journal = {Frontiers in Microbiology},
number = ,
volume = 6,
place = {United States},
year = {Tue Apr 14 00:00:00 EDT 2015},
month = {Tue Apr 14 00:00:00 EDT 2015}
}
Web of Science
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Inferring biological soil crust successional stage using combined PLFA, DGGE, physical and biophysiological analyses
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Diversity of free-living and lichenized fungal communities in biological soil crusts of the Sultanate of Oman and their role in improving soil properties
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Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands
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Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
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Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
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