Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
Abstract
While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae,Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to usemore »
- Authors:
-
[2];
more »
- Univ. of Colorado, Boulder, CO (United States)
- Univ. of California, Riverside, CA (United States)
- Univ. of Kansas, Lawrence, KS (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Univ. of California, Merced, CA (United States)
- Univ. of Arizona, Tucson, AZ (United States)
- Pennsylvania State Univ., University Park, PA (United States)
- Louisiana State Univ., Baton Rouge, LA (United States)
- Idaho State Univ., Pocatello, ID (United States)
- Univ. of Washington, Seattle, WA (United States)
- Univ. of Illinois at Urbana-Champaign, IL (United States)
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Northwestern Univ., Evanston, IL (United States)
- Univ. of Pennsylvania, Philadelphia, PA (United States)
- Duke Univ., Durham, NC (United States)
- Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); National Science Foundation (NSF)
- OSTI Identifier:
- 1599173
- Alternate Identifier(s):
- OSTI ID: 1646563
- Report Number(s):
- LLNL-JRNL-791438
Journal ID: ISSN 2150-7511; 156495
- Grant/Contract Number:
- AC02-06CH11357; ICER-1541047; EF-1550920; AC52-07NA27344; SCW1478
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 10; Journal Issue: 5; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; critical zone; metagenomics; microbial ecology; microbial traits; soil microbiology
Citation Formats
Brewer, Tess E., Aronson, Emma L., Arogyaswamy, Keshav, Billings, Sharon A., Botthoff, Jon K., Campbell, Ashley N., Dove, Nicholas C., Fairbanks, Dawson, Gallery, Rachel E., Hart, Stephen C., Kaye, Jason, King, Gary, Logan, Geoffrey, Lohse, Kathleen A., Maltz, Mia R., Mayorga, Emilio, O’Neill, Caitlin, Owens, Sarah M., Packman, Aaron, Pett-Ridge, Jennifer, Plante, Alain F., Richter, Daniel D., Silver, Whendee L., Yang, Wendy H., and Fierer, Noah. Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons. United States: N. p., 2019.
Web. doi:10.1128/mBio.01318-19.
Brewer, Tess E., Aronson, Emma L., Arogyaswamy, Keshav, Billings, Sharon A., Botthoff, Jon K., Campbell, Ashley N., Dove, Nicholas C., Fairbanks, Dawson, Gallery, Rachel E., Hart, Stephen C., Kaye, Jason, King, Gary, Logan, Geoffrey, Lohse, Kathleen A., Maltz, Mia R., Mayorga, Emilio, O’Neill, Caitlin, Owens, Sarah M., Packman, Aaron, Pett-Ridge, Jennifer, Plante, Alain F., Richter, Daniel D., Silver, Whendee L., Yang, Wendy H., & Fierer, Noah. Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons. United States. https://doi.org/10.1128/mBio.01318-19
Brewer, Tess E., Aronson, Emma L., Arogyaswamy, Keshav, Billings, Sharon A., Botthoff, Jon K., Campbell, Ashley N., Dove, Nicholas C., Fairbanks, Dawson, Gallery, Rachel E., Hart, Stephen C., Kaye, Jason, King, Gary, Logan, Geoffrey, Lohse, Kathleen A., Maltz, Mia R., Mayorga, Emilio, O’Neill, Caitlin, Owens, Sarah M., Packman, Aaron, Pett-Ridge, Jennifer, Plante, Alain F., Richter, Daniel D., Silver, Whendee L., Yang, Wendy H., and Fierer, Noah. Tue .
"Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons". United States. https://doi.org/10.1128/mBio.01318-19. https://www.osti.gov/servlets/purl/1599173.
@article{osti_1599173,
title = {Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons},
author = {Brewer, Tess E. and Aronson, Emma L. and Arogyaswamy, Keshav and Billings, Sharon A. and Botthoff, Jon K. and Campbell, Ashley N. and Dove, Nicholas C. and Fairbanks, Dawson and Gallery, Rachel E. and Hart, Stephen C. and Kaye, Jason and King, Gary and Logan, Geoffrey and Lohse, Kathleen A. and Maltz, Mia R. and Mayorga, Emilio and O’Neill, Caitlin and Owens, Sarah M. and Packman, Aaron and Pett-Ridge, Jennifer and Plante, Alain F. and Richter, Daniel D. and Silver, Whendee L. and Yang, Wendy H. and Fierer, Noah},
abstractNote = {While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae,Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.},
doi = {10.1128/mBio.01318-19},
journal = {mBio (Online)},
number = 5,
volume = 10,
place = {United States},
year = {Tue Oct 01 00:00:00 EDT 2019},
month = {Tue Oct 01 00:00:00 EDT 2019}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 91 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Soil organic matter in soil depth profiles: Distinct carbon preferences of microbial groups during carbon transformation
journal, February 2008
- Kramer, Christiane; Gleixner, Gerd
- Soil Biology and Biochemistry, Vol. 40, Issue 2
Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest
journal, April 2014
- Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W.
- The ISME Journal, Vol. 8, Issue 9
Temporal variation in surface and subsoil abundance and function of the soil microbial community in an arable soil
journal, June 2013
- Kramer, Susanne; Marhan, Sven; Haslwimmer, Heike
- Soil Biology and Biochemistry, Vol. 61
Ethanol and Isopropyl Alcohol Exposure Increases Biofilm Formation in Staphylococcus aureus and Staphylococcus epidermidis
journal, May 2015
- Luther, Megan K.; Bilida, Sarah; Mermel, Leonard A.
- Infectious Diseases and Therapy, Vol. 4, Issue 2
Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development
journal, May 2017
- Turner, Stephanie; Mikutta, Robert; Meyer-Stüve, Sandra
- Frontiers in Microbiology, Vol. 8
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils
journal, July 2003
- Zhou, Jizhong; Xia, Beicheng; Huang, Heshu
- Soil Biology and Biochemistry, Vol. 35, Issue 7
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
journal, May 2016
- Browne, Hilary P.; Forster, Samuel C.; Anonye, Blessing O.
- Nature, Vol. 533, Issue 7604
Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil
journal, June 2015
- Banning, Natasha C.; Maccarone, Linda D.; Fisk, Louise M.
- Scientific Reports, Vol. 5, Issue 1
VEGAN, a package of R functions for community ecology
journal, January 2003
- Dixon, Philip
- Journal of Vegetation Science, Vol. 14, Issue 6
Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria
journal, May 2010
- Yabe, S.; Aiba, Y.; Sakai, Y.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 4
Atmosphere–soil carbon transfer as a function of soil depth
journal, July 2018
- Balesdent, Jérôme; Basile-Doelsch, Isabelle; Chadoeuf, Joël
- Nature, Vol. 559, Issue 7715
Functional microbial community response to nutrient pulses by artificial groundwater recharge practice in surface soils and subsoils: Soil microbial community response to groundwater recharge
journal, February 2010
- Schütz, Kirsten; Kandeler, Ellen; Nagel, Peter
- FEMS Microbiology Ecology, Vol. 72, Issue 3
Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site: Hanford Site subsurface microbial communities
journal, November 2011
- Lin, Xueju; Kennedy, David; Fredrickson, Jim
- Environmental Microbiology, Vol. 14, Issue 2
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- Bioinformatics, Vol. 31, Issue 10
Distribution, diversity and ecology of aerobic CO-oxidizing bacteria
journal, February 2007
- King, Gary M.; Weber, Carolyn F.
- Nature Reviews Microbiology, Vol. 5, Issue 2
The relationships of soil total nitrogen concentrations, pools and C:N ratios with climate, vegetation types and nitrate deposition in temperate and boreal forests of eastern Canada
journal, May 2017
- Marty, C.; Houle, D.; Gagnon, C.
- CATENA, Vol. 152
The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics
journal, January 2010
- Vieira-Silva, Sara; Rocha, Eduardo P. C.
- PLoS Genetics, Vol. 6, Issue 1
Embracing the unknown: disentangling the complexities of the soil microbiome
journal, August 2017
- Fierer, Noah
- Nature Reviews Microbiology, Vol. 15, Issue 10
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015
- Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.
- Bioinformatics, Vol. 32, Issue 4
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
journal, August 2018
- Parks, Donovan H.; Chuvochina, Maria; Waite, David W.
- Nature Biotechnology, Vol. 36, Issue 10
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Ribosomal Database Project: data and tools for high throughput rRNA analysis
journal, November 2013
- Cole, James R.; Wang, Qiong; Fish, Jordan A.
- Nucleic Acids Research, Vol. 42, Issue D1
Carbon Monoxide Dehydrogenase Activity in Bradyrhizobium japonicum
journal, May 2000
- Lorite, M. J.; Tachil, J.; Sanjuan, J.
- Applied and Environmental Microbiology, Vol. 66, Issue 5
Genome-centric view of carbon processing in thawing permafrost
journal, July 2018
- Woodcroft, Ben J.; Singleton, Caitlin M.; Boyd, Joel A.
- Nature, Vol. 560, Issue 7716
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
journal, August 2015
- Leff, Jonathan W.; Jones, Stuart E.; Prober, Suzanne M.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 35
Evidence that entry into sporulation in Bacillus subtilis is governed by a gradual increase in the level and activity of the master regulator Spo0A
journal, September 2005
- Fujita, M.
- Genes & Development, Vol. 19, Issue 18
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016
- Letunic, Ivica; Bork, Peer
- Nucleic Acids Research, Vol. 44, Issue W1
Exploiting rRNA operon copy number to investigate bacterial reproductive strategies
journal, September 2016
- Roller, Benjamin R. K.; Stoddard, Steven F.; Schmidt, Thomas M.
- Nature Microbiology, Vol. 1, Issue 11
Rhizogenic Fe–C redox cycling: a hypothetical biogeochemical mechanism that drives crustal weathering in upland soils
journal, February 2008
- Fimmen, Ryan L.; Richter, Daniel deB.; Vasudevan, Dharni
- Biogeochemistry, Vol. 87, Issue 2
Loss of deep roots limits biogenic agents of soil development that are
only partially restored by decades of forest regeneration
journal, January 2018
- Billings, Sharon A.; Hirmas, Daniel; Sullivan, Pamela L.
- Elem Sci Anth, Vol. 6, Issue 1
Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes
journal, September 2018
- Lloyd, Karen G.; Steen, Andrew D.; Ladau, Joshua
- mSystems, Vol. 3, Issue 5
Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils
journal, October 2017
- Schwarz, Alexandra; Adetutu, Eric M.; Juhasz, Albert L.
- Microbial Ecology, Vol. 75, Issue 4
Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias
journal, August 2002
- Novembre, John A.
- Molecular Biology and Evolution, Vol. 19, Issue 8
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients
journal, December 2011
- Fierer, Noah; Lauber, Christian L.; Ramirez, Kelly S.
- The ISME Journal, Vol. 6, Issue 5
Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database
journal, May 2016
- Bissett, Andrew; Fitzgerald, Anna; Meintjes, Thys
- GigaScience, Vol. 5, Issue 1
The rapid generation of mutation data matrices from protein sequences
journal, January 1992
- Jones, David T.; Taylor, William R.; Thornton, Janet M.
- Bioinformatics, Vol. 8, Issue 3
Towards a Genome-Based Taxonomy for Prokaryotes
journal, September 2005
- Konstantinidis, K. T.; Tiedje, J. M.
- Journal of Bacteriology, Vol. 187, Issue 18
Molybdenum-containing hydroxylases
journal, January 2005
- Hille, Russ
- Archives of Biochemistry and Biophysics, Vol. 433, Issue 1
Microbial carbon use efficiency and biomass turnover times depending on soil depth – Implications for carbon cycling
journal, May 2016
- Spohn, Marie; Klaus, Karoline; Wanek, Wolfgang
- Soil Biology and Biochemistry, Vol. 96
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
posted_content, October 2016
- Edgar, Robert C.
- BioRxiv
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
journal, February 2016
- Eloe-Fadrosh, Emiley A.; Ivanova, Natalia N.; Woyke, Tanja
- Nature Microbiology, Vol. 1, Issue 4
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
journal, December 2016
- Carini, Paul; Marsden, Patrick J.; Leff, Jonathan W.
- Nature Microbiology, Vol. 2, Issue 3
Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska
journal, August 2014
- Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne
- FEMS Microbiology Ecology, Vol. 89, Issue 2
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016
- Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
- Molecular Biology and Evolution, Vol. 33, Issue 7
Isolation and Characterization of Endophytic Colonizing Bacteria from Agronomic Crops and Prairie Plants
journal, May 2002
- Zinniel, D. K.; Lambrecht, P.; Harris, N. B.
- Applied and Environmental Microbiology, Vol. 68, Issue 5
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
journal, March 2015
- Bengtsson-Palme, Johan; Hartmann, Martin; Eriksson, Karl Martin
- Molecular Ecology Resources, Vol. 15, Issue 6
Intercellular Signaling During Fruiting-Body Development of Myxococcus xanthus
journal, October 1999
- Shimkets, Lawrence J.
- Annual Review of Microbiology, Vol. 53, Issue 1
Regulation of glycogen metabolism in yeast and bacteria
journal, November 2010
- Wilson, Wayne A.; Roach, Peter J.; Montero, Manuel
- FEMS Microbiology Reviews, Vol. 34, Issue 6
VEGAN, a package of R functions for community ecology
journal, April 2003
- Dixon, Philip
- Journal of Vegetation Science, Vol. 14, Issue 6
Strategies for culture of ‘unculturable’ bacteria: Culturing the unculturable
journal, April 2010
- Vartoukian, Sonia R.; Palmer, Richard M.; Wade, William G.
- FEMS Microbiology Letters
Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil
journal, July 2012
- Eilers, Kathryn G.; Debenport, Spencer; Anderson, Suzanne
- Soil Biology and Biochemistry, Vol. 50
The Vertical Distribution of Soil Organic Carbon and Its Relation to Climate and Vegetation
journal, April 2000
- Jobbagy, Esteban G.; Jackson, Robert B.
- Ecological Applications, Vol. 10, Issue 2
Variations in microbial community composition through two soil depth profiles
journal, January 2003
- Fierer, Noah; Schimel, Joshua P.; Holden, Patricia A.
- Soil Biology and Biochemistry, Vol. 35, Issue 1
Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes
journal, August 2010
- Will, C.; Thurmer, A.; Wollherr, A.
- Applied and Environmental Microbiology, Vol. 76, Issue 20
New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil
journal, June 2006
- Cavaletti, L.; Monciardini, P.; Bamonte, R.
- Applied and Environmental Microbiology, Vol. 72, Issue 6
Effects of carbon additions on iron reduction and phosphorus availability in a humid tropical forest soil
journal, August 2009
- Liptzin, Daniel; Silver, Whendee L.
- Soil Biology and Biochemistry, Vol. 41, Issue 8
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
journal, September 2008
- Meyer, F.; Paarmann, D.; D'Souza, M.
- BMC Bioinformatics, Vol. 9, Issue 1
Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization
journal, November 2004
- Rocha, E. P. C.
- Genome Research, Vol. 14, Issue 11
Elemental translocation and loss from three highly weathered soil–bedrock profiles in the southeastern United States
journal, May 2005
- Oh, Neung-Hwan; Richter, Daniel D.
- Geoderma, Vol. 126, Issue 1-2
Surface and subsurface microbial biomass, community structure and metabolic activity as a function of soil depth and season
journal, June 2002
- Blume, E.; Bischoff, M.; Reichert, J. M.
- Applied Soil Ecology, Vol. 20, Issue 3
Changes in extracellular enzyme activity and microbial community structure with soil depth at the Luquillo Critical Zone Observatory
journal, August 2014
- Stone, M. M.; DeForest, J. L.; Plante, A. F.
- Soil Biology and Biochemistry, Vol. 75
Drivers and patterns of iron redox cycling from surface to bedrock in a deep tropical forest soil: a new conceptual model
journal, September 2016
- Hall, Steven J.; Liptzin, Daniel; Buss, Heather L.
- Biogeochemistry, Vol. 130, Issue 1-2
Trehalose synthesis is induced upon exposure of Escherichia coli to cold and is essential for viability at low temperatures
journal, July 2002
- Kandror, O.; DeLeon, A.; Goldberg, A. L.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 15
Atmospheric trace gases support primary production in Antarctic desert surface soil
journal, December 2017
- Ji, Mukan; Greening, Chris; Vanwonterghem, Inka
- Nature, Vol. 552, Issue 7685
Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method
journal, March 2021
- Das, Sayak; Roy, Goshaidas; Najar, Ishfaq Nabi
- Folia Microbiologica, Vol. 66, Issue 3
Evolutionary stasis of a deep subsurface microbial lineage
journal, April 2021
- Becraft, Eric D.; Lau Vetter, Maggie C. Y.; Bezuidt, Oliver K. I.
- The ISME Journal
An SHR–SCR module specifies legume cortical cell fate to enable nodulation
journal, December 2020
- Dong, Wentao; Zhu, Yayun; Chang, Huizhong
- Nature, Vol. 589, Issue 7843
Microbial Dysbiosis During Simian Immunodeficiency Virus Infection is Partially Reverted with Combination Anti-retroviral Therapy
journal, April 2020
- Blum, Faith C.; Hardy, Britney L.; Bishop-Lilly, Kimberly A.
- Scientific Reports, Vol. 10, Issue 1
Brucella melitensis: A nasty bug with hidden credentials for virulence
journal, January 2002
- Moreno, E.; Moriyon, I.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 1
Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite
journal, June 2016
- Hébert, François Olivier; Grambauer, Stephan; Barber, Iain
- GigaScience, Vol. 5, Issue 1
Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach
journal, June 2017
- Lindemann, Stephen R.; Mobberley, Jennifer M.; Cole, Jessica K.
- Frontiers in Microbiology, Vol. 8
Transformation of leukocytes by Theileria parva and T. annulata.
text, January 1999
- Dobbelaere, D.; Heussler, Volker
- Annual Reviews
Transformation of Leukocytes by Theileria parva and T. annulata
journal, October 1999
- Dobbelaere, Dirk; Heussler, Volker
- Annual Review of Microbiology, Vol. 53, Issue 1
Microbial community dynamics in soil depth profiles over 120,000 years of ecosystem development
other, January 2017
- Turner, Stephanie; Mikutta, Robert; Meyer-Stüve, Sandra
- Lausanne : Frontiers Research Foundation
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
preprint, January 2014
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- arXiv
Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity
dataset, January 2020
- Dove, Nicholas
- Dryad
Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity
dataset, January 2020
- Dove, Nicholas
- Dryad
Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils
journal, October 2017
- Schwarz, Alexandra; Adetutu, Eric M.; Juhasz, Albert L.
- Microbial Ecology, Vol. 75, Issue 4
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment
journal, June 2021
- Kim, Minji; Lee, Ki-Eun; Cha, In-Tae
- Current Microbiology, Vol. 78, Issue 8
Rhizogenic Fe–C redox cycling: a hypothetical biogeochemical mechanism that drives crustal weathering in upland soils
journal, February 2008
- Fimmen, Ryan L.; Richter, Daniel deB.; Vasudevan, Dharni
- Biogeochemistry, Vol. 87, Issue 2
Drivers and patterns of iron redox cycling from surface to bedrock in a deep tropical forest soil: a new conceptual model
journal, September 2016
- Hall, Steven J.; Liptzin, Daniel; Buss, Heather L.
- Biogeochemistry, Vol. 130, Issue 1-2
Metagenomic analyses, isolation and characterization of endophytic bacteria associated with Eucalyptus urophylla BRS07-01 in vitro plants
journal, August 2021
- de França Bettencourt, Gisela Manuela; Degenhardt, Juliana; dos Santos, Germana Davila
- World Journal of Microbiology and Biotechnology, Vol. 37, Issue 10
Ethanol and Isopropyl Alcohol Exposure Increases Biofilm Formation in Staphylococcus aureus and Staphylococcus epidermidis
journal, May 2015
- Luther, Megan K.; Bilida, Sarah; Mermel, Leonard A.
- Infectious Diseases and Therapy, Vol. 4, Issue 2
Soil organic matter in soil depth profiles: Distinct carbon preferences of microbial groups during carbon transformation
journal, February 2008
- Kramer, Christiane; Gleixner, Gerd
- Soil Biology and Biochemistry, Vol. 40, Issue 2
Effects of carbon additions on iron reduction and phosphorus availability in a humid tropical forest soil
journal, August 2009
- Liptzin, Daniel; Silver, Whendee L.
- Soil Biology and Biochemistry, Vol. 41, Issue 8
Temporal variation in surface and subsoil abundance and function of the soil microbial community in an arable soil
journal, June 2013
- Kramer, Susanne; Marhan, Sven; Haslwimmer, Heike
- Soil Biology and Biochemistry, Vol. 61
Changes in extracellular enzyme activity and microbial community structure with soil depth at the Luquillo Critical Zone Observatory
journal, August 2014
- Stone, M. M.; DeForest, J. L.; Plante, A. F.
- Soil Biology and Biochemistry, Vol. 75
Microbial carbon use efficiency and biomass turnover times depending on soil depth – Implications for carbon cycling
journal, May 2016
- Spohn, Marie; Klaus, Karoline; Wanek, Wolfgang
- Soil Biology and Biochemistry, Vol. 96
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
journal, May 2016
- Browne, Hilary P.; Forster, Samuel C.; Anonye, Blessing O.
- Nature, Vol. 533, Issue 7604
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, July 2018
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 36, Issue 7
Embracing the unknown: disentangling the complexities of the soil microbiome
journal, August 2017
- Fierer, Noah
- Nature Reviews Microbiology, Vol. 15, Issue 10
Distribution, diversity and ecology of aerobic CO-oxidizing bacteria
journal, February 2007
- King, Gary M.; Weber, Carolyn F.
- Nature Reviews Microbiology, Vol. 5, Issue 2
Rhizosphere bacteriome structure and functions
journal, February 2022
- Ling, Ning; Wang, Tingting; Kuzyakov, Yakov
- Nature Communications, Vol. 13, Issue 1
The majority is uncultured
journal, October 2018
- Hofer, Ursula
- Nature Reviews Microbiology, Vol. 16, Issue 12
Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi
journal, September 2020
- Hughes, Riley L.; Arnold, Charles D.; Young, Rebecca R.
- Scientific Reports, Vol. 10, Issue 1
Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans
journal, February 2022
- Androsiuk, Piotr; Okorski, Adam; Paukszto, Łukasz
- Scientific Reports, Vol. 12, Issue 1
Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil
journal, June 2015
- Banning, Natasha C.; Maccarone, Linda D.; Fisk, Louise M.
- Scientific Reports, Vol. 5, Issue 1
Trehalose synthesis is induced upon exposure of Escherichia coli to cold and is essential for viability at low temperatures
journal, July 2002
- Kandror, O.; DeLeon, A.; Goldberg, A. L.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 15
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
journal, August 2015
- Leff, Jonathan W.; Jones, Stuart E.; Prober, Suzanne M.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 35
The rapid generation of mutation data matrices from protein sequences
journal, January 1992
- Jones, David T.; Taylor, William R.; Thornton, Janet M.
- Bioinformatics, Vol. 8, Issue 3
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- Bioinformatics, Vol. 31, Issue 10
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
journal, October 2015
- Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.
- Bioinformatics, Vol. 32, Issue 4
Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias
journal, August 2002
- Novembre, John A.
- Molecular Biology and Evolution, Vol. 19, Issue 8
Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria
journal, May 2010
- Yabe, S.; Aiba, Y.; Sakai, Y.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 61, Issue 4
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
posted_content, October 2016
- Edgar, Robert C.
- BioRxiv
Evidence that entry into sporulation in Bacillus subtilis is governed by a gradual increase in the level and activity of the master regulator Spo0A
journal, September 2005
- Fujita, M.
- Genes & Development, Vol. 19, Issue 18
Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization
journal, November 2004
- Rocha, E. P. C.
- Genome Research, Vol. 14, Issue 11
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
journal, March 2015
- Bengtsson-Palme, Johan; Hartmann, Martin; Eriksson, Karl Martin
- Molecular Ecology Resources, Vol. 15, Issue 6
Functional microbial community response to nutrient pulses by artificial groundwater recharge practice in surface soils and subsoils: Soil microbial community response to groundwater recharge
journal, February 2010
- Schütz, Kirsten; Kandeler, Ellen; Nagel, Peter
- FEMS Microbiology Ecology, Vol. 72, Issue 3
Strategies for culture of ‘unculturable’ bacteria: Culturing the unculturable
journal, April 2010
- Vartoukian, Sonia R.; Palmer, Richard M.; Wade, William G.
- FEMS Microbiology Letters
Regulation of glycogen metabolism in yeast and bacteria
journal, November 2010
- Wilson, Wayne A.; Roach, Peter J.; Montero, Manuel
- FEMS Microbiology Reviews, Vol. 34, Issue 6
VEGAN, a package of R functions for community ecology
journal, April 2003
- Dixon, Philip
- Journal of Vegetation Science, Vol. 14, Issue 6
Updating Prokaryotic Taxonomy
journal, September 2005
- Rosselló-Mora, Ramon
- Journal of Bacteriology, Vol. 187, Issue 18
Intercellular Signaling During Fruiting-Body Development of Myxococcus xanthus
journal, October 1999
- Shimkets, Lawrence J.
- Annual Review of Microbiology, Vol. 53, Issue 1
Loss of deep roots limits biogenic agents of soil development that are
only partially restored by decades of forest regeneration
journal, January 2018
- Billings, Sharon A.; Hirmas, Daniel; Sullivan, Pamela L.
- Elem Sci Anth, Vol. 6, Issue 1
Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database
text, January 2023
- Bissett, A.; Fitzgerald, A.; Meintjes, T.
- La Trobe
Works referencing / citing this record:
Identifying Mechanisms for Successful Ecological Restoration with Salvaged Topsoil in Coastal Sage Scrub Communities
journal, April 2020
- Schmidt, Katharina T.; Maltz, Mia; Ta, Priscilla
- Diversity, Vol. 12, Issue 4
Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation
journal, January 2020
- Bartelme, Ryan P.; Custer, Joy M.; Dupont, Christopher L.
- mSphere, Vol. 5, Issue 1
Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity
dataset, January 2020
- Dove, Nicholas
- Dryad
Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity
dataset, January 2020
- Dove, Nicholas
- Dryad
Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation
journal, January 2020
- Bartelme, Ryan P.; Custer, Joy M.; Dupont, Christopher L.
- mSphere, Vol. 5, Issue 1