U.S. Department of EnergyOffice of Scientific and Technical Information
Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing
Abstract
Biological soil crusts (biocrusts) are microbial communities that are a feature of arid surface soils worldwide. In drylands where precipitation is pulsed and ephemeral, the ability of biocrust microbiota to rapidly initiate metabolic activity is critical to their survival. Community gene expression was compared after a short duration (1 h) wetting pulse in both intact and soils disturbed by chronic foot trampling. Across the metatranscriptomes the majority of transcripts were cyanobacterial in origin, suggesting that cyanobacteria accounted for the bulk of the transcriptionally active cells. Chronic trampling substantially altered the functional profile of the metatranscriptomes, specifically resulting in a significant decrease in transcripts for nitrogen fixation. Soil depth (biocrust and below crust) was a relatively small factor in differentiating the metatranscriptomes, suggesting that the metabolically active bacteria were similar between shallow soil horizons. The dry samples were consistently enriched for hydrogenase genes, indicating that molecular hydrogen may serve as an energy source for the desiccated soil communities. The water pulse was associated with a restructuring of the metatranscriptome, particularly for the biocrusts. Biocrusts increased transcripts for photosynthesis and carbon fixation, suggesting a rapid resuscitation upon wetting. In contrast, the trampled surface soils showed a much smaller response to wetting, indicatingmore »
- Authors:
-
[3]
- Connecticut Agricultural Experiment Station, New Haven, CT (United States). Dept. of Environmental Sciences
- Southwest Biological Science Center, Moab, UT (United States). United States Geological Survey, Moab
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1479950
- Report Number(s):
- LA-UR-17-31418
Journal ID: ISSN 1664-302X
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 9; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological Science
Citation Formats
Steven, Blaire, Belnap, Jayne, and Kuske, Cheryl R. Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing. United States: N. p., 2018.
Web. doi:10.3389/fmicb.2018.02382.
Steven, Blaire, Belnap, Jayne, & Kuske, Cheryl R. Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing. United States. https://doi.org/10.3389/fmicb.2018.02382
Steven, Blaire, Belnap, Jayne, and Kuske, Cheryl R. 2018.
"Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing". United States. https://doi.org/10.3389/fmicb.2018.02382. https://www.osti.gov/servlets/purl/1479950.
@article{osti_1479950,
title = {Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing},
author = {Steven, Blaire and Belnap, Jayne and Kuske, Cheryl R.},
abstractNote = {Biological soil crusts (biocrusts) are microbial communities that are a feature of arid surface soils worldwide. In drylands where precipitation is pulsed and ephemeral, the ability of biocrust microbiota to rapidly initiate metabolic activity is critical to their survival. Community gene expression was compared after a short duration (1 h) wetting pulse in both intact and soils disturbed by chronic foot trampling. Across the metatranscriptomes the majority of transcripts were cyanobacterial in origin, suggesting that cyanobacteria accounted for the bulk of the transcriptionally active cells. Chronic trampling substantially altered the functional profile of the metatranscriptomes, specifically resulting in a significant decrease in transcripts for nitrogen fixation. Soil depth (biocrust and below crust) was a relatively small factor in differentiating the metatranscriptomes, suggesting that the metabolically active bacteria were similar between shallow soil horizons. The dry samples were consistently enriched for hydrogenase genes, indicating that molecular hydrogen may serve as an energy source for the desiccated soil communities. The water pulse was associated with a restructuring of the metatranscriptome, particularly for the biocrusts. Biocrusts increased transcripts for photosynthesis and carbon fixation, suggesting a rapid resuscitation upon wetting. In contrast, the trampled surface soils showed a much smaller response to wetting, indicating that trampling altered the metabolic response of the community. Finally, several biogeochemical cycling genes in carbon and nitrogen cycling were assessed for their change in abundance due to wetting in the biocrusts. Different transcripts encoding the same gene product did not show a consensus response, with some more abundant in dry or wet biocrusts, highlighting the challenges in relating transcript abundance to biogeochemical cycling rates. These observations demonstrate that metatranscriptome sequencing was able to distinguish alterations in the function of arid soil microbial communities at two varying temporal scales, a long-term ecosystems disturbance through foot trampling, and a short term wetting pulse. Thus, community metatranscriptomes have the potential to inform studies on the response and resilience of biocrusts to various environmental perturbations.},
doi = {10.3389/fmicb.2018.02382},
url = {https://www.osti.gov/biblio/1479950},
journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 9,
place = {United States},
year = {Mon Oct 08 00:00:00 EDT 2018},
month = {Mon Oct 08 00:00:00 EDT 2018}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 18 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
FIGURE 1: (A) Photograph of field plots. The control plots show well-developed biocrusts directly adjacent to a trampled plot (separated by a nylon rope). A pen is included for scale. (B) NMDS plot showing the relationship of metatranscriptome datasets. Intergroup distances were calculated with the Bray–Curtis metric. The colored ellipsesmore »
All figures and tables
(12 total)
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:
Rapid Recovery of Cyanobacterial Pigments in Desiccated Biological Soil Crusts following Addition of Water
journal, November 2014
- Abed, Raeid M. M.; Polerecky, Lubos; Al-Habsi, Amal
- PLoS ONE, Vol. 9, Issue 11
Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil
journal, May 2018
- Albright, Michaeline B. N.; Johansen, Renee; Lopez, Deanna
- Applied and Environmental Microbiology, Vol. 84, Issue 15
Resistance, resilience, and redundancy in microbial communities
journal, August 2008
- Allison, S. D.; Martiny, J. B. H.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1
Impacts of Biological Soil Crust Disturbance and Composition on C and N Loss from Water Erosion
journal, February 2006
- Barger, Nichole N.; Herrick, Jeffrey E.; Van Zee, Justin
- Biogeochemistry, Vol. 77, Issue 2
The World at Your Feet: Desert Biological Soil Crusts
journal, May 2003
- Belnap, Jayne
- Frontiers in Ecology and the Environment, Vol. 1, Issue 4
The potential roles of biological soil crusts in dryland hydrologic cycles
journal, January 2006
- Belnap, Jayne
- Hydrological Processes, Vol. 20, Issue 15
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
journal, July 2002
- Bernstein, J. A.; Khodursky, A. B.; Lin, P. -H.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 15
Near-optimal probabilistic RNA-seq quantification
journal, April 2016
- Bray, Nicolas L.; Pimentel, Harold; Melsted, Páll
- Nature Biotechnology, Vol. 34, Issue 5
Fast and sensitive protein alignment using DIAMOND
journal, November 2014
- Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
- Nature Methods, Vol. 12, Issue 1
Biosynthesis of the arabinogalactan-peptidoglycan complex of Mycobacterium tuberculosis
journal, September 2001
- Crick, D. C.; Mahapatra, S.; Brennan, P. J.
- Glycobiology, Vol. 11, Issue 9
Determination of the Glycogen Content in Cyanobacteria
journal, January 2017
- De Porcellinis, Alice; Frigaard, Niels-Ulrik; Sakuragi, Yumiko
- Journal of Visualized Experiments, Issue 125
VEGAN, a package of R functions for community ecology
journal, April 2003
- Dixon, Philip
- Journal of Vegetation Science, Vol. 14, Issue 6
Growth rate-stoichiometry couplings in diverse biota
journal, October 2003
- Elser, J. J.; Acharya, K.; Kyle, M.
- Ecology Letters, Vol. 6, Issue 10
Desiccation: An environmental and food industry stress that bacteria commonly face
journal, February 2018
- Esbelin, Julia; Santos, Tiago; Hébraud, Michel
- Food Microbiology, Vol. 69
Long-Term Consequences of Disturbance on Nitrogen Dynamics in an arid Ecosystem
journal, January 1999
- Evans, R. D.; Belnap, J.
- Ecology, Vol. 80, Issue 1
Relating the metatranscriptome and metagenome of the human gut
journal, May 2014
- Franzosa, E. A.; Morgan, X. C.; Segata, N.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 22
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis
journal, January 2014
- Gao, Bei; Zhang, Daoyuan; Li, Xiaoshuang
- BMC Research Notes, Vol. 7, Issue 1
Microenvironments and Microscale Productivity of Cyanobacterial Desert Crusts1
journal, October 1996
- Garcia-Pichel, Ferran; Belnap, Jayne
- Journal of Phycology, Vol. 32, Issue 5
Small-Scale Vertical Distribution of Bacterial Biomass and Diversity in Biological Soil Crusts from Arid Lands in the Colorado Plateau
journal, November 2003
- Garcia-Pichel, F.; Johnson, S. L.; Youngkin, D.
- Microbial Ecology, Vol. 46, Issue 3
Cyanobacteria track water in desert soils
journal, September 2001
- Garcia-Pichel, Ferran; Pringault, Olivier
- Nature, Vol. 413, Issue 6854
Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging
journal, August 2015
- Greening, Chris; Carere, Carlo R.; Rushton-Green, Rowena
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 33
Historic variation of warm-season rainfall, Southern Colorado Plateau, Southwestern U.S.A.
journal, November 1992
- Hereford, Richard; Webb, Robert H.
- Climatic Change, Vol. 22, Issue 3
Accumulation of Trehalose and Sucrose in Cyanobacteria Exposed to Matric Water Stress †
journal, January 1991
- Hershkovitz, Nitzan; Oren, Aharon; Cohen, Yehuda
- Applied and Environmental Microbiology, Vol. 57, Issue 3
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
journal, June 2016
- Huson, Daniel H.; Beier, Sina; Flade, Isabell
- PLOS Computational Biology, Vol. 12, Issue 6
Precipitation pulses and carbon fluxes in semiarid and arid ecosystems
journal, August 2004
- Huxman, Travis E.; Snyder, Keirith A.; Tissue, David
- Oecologia, Vol. 141, Issue 2
Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity
journal, March 2018
- Karaoz, Ulas; Couradeau, Estelle; da Rocha, Ulisses Nunes
- mBio, Vol. 9, Issue 2
Assembly, function and evolution of cyanobacterial carboxysomes
journal, June 2016
- Kerfeld, Cheryl A.; Melnicki, Matthew R.
- Current Opinion in Plant Biology, Vol. 31
Soil organic matter in arid and semiarid ecosystems: Sources, accumulation, and distribution
journal, January 1989
- Klemmedson, James O.
- Arid Soil Research and Rehabilitation, Vol. 3, Issue 2
Diversity in hydrogen evolution from bidirectional hydrogenases in cyanobacteria from terrestrial, freshwater and marine intertidal environments
journal, November 2012
- Kothari, Ankita; Potrafka, Ruth; Garcia-Pichel, Ferran
- Journal of Biotechnology, Vol. 162, Issue 1
Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands
journal, November 2011
- Kuske, Cheryl R.; Yeager, Chris M.; Johnson, Shannon
- The ISME Journal, Vol. 6, Issue 4
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
journal, June 2016
- Li, Dinghua; Luo, Ruibang; Liu, Chi-Man
- Methods, Vol. 102
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
The role of cyanobacterial exopolysaccharides in structuring desert microbial crusts
journal, October 1996
- Mazor, Gideon; Kidron, Giora J.; Vonshak, Ahuva
- FEMS Microbiology Ecology, Vol. 21, Issue 2
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
journal, April 2013
- McMurdie, Paul J.; Holmes, Susan
- PLoS ONE, Vol. 8, Issue 4
Differential Expression of Photosynthesis and Nitrogen Fixation Genes in the Cyanobacterium Plectonema boryanum
journal, March 2000
- Misra, Hari S.; Tuli, Rakesh
- Plant Physiology, Vol. 122, Issue 3
Sizing up metatranscriptomics
journal, August 2012
- Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M.
- The ISME Journal, Vol. 7, Issue 2
Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland
journal, September 2015
- Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.
- Frontiers in Microbiology, Vol. 6
Heterocyst-forming Filamentous Cyanobacteria Encode Proteins that Resemble Eukaryotic RNA-binding Proteins of the RNP Family
journal, January 1994
- Mulligan, Martin E.; Jackman, Donna M.; Murphy, Stephen T.
- Journal of Molecular Biology, Vol. 235, Issue 3
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
journal, December 2016
- Narayanasamy, Shaman; Jarosz, Yohan; Muller, Emilie E. L.
- Genome Biology, Vol. 17, Issue 1
Germination—Still a mystery
journal, December 2010
- Nonogaki, Hiroyuki; Bassel, George W.; Bewley, J. Derek
- Plant Science, Vol. 179, Issue 6
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013
- Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
- Nucleic Acids Research, Vol. 42, Issue D1
Involvement of the compatible solutes trehalose and sucrose in the response to salt stress of a cyanobacterial Scytonema species isolated from desert soils
journal, November 1999
- Page-Sharp, Madhu; Behm, Carolyn A.; Smith, Geoffrey D.
- Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1472, Issue 3
STAMP: statistical analysis of taxonomic and functional profiles
journal, July 2014
- Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip
- Bioinformatics, Vol. 30, Issue 21
Escherichia coli ribosomes translate in vivo with variable rate.
journal, December 1984
- Pedersen, S.
- The EMBO Journal, Vol. 3, Issue 12
Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation
journal, June 2015
- Pepe-Ranney, Charles; Koechli, Chantal; Potrafka, Ruth
- The ISME Journal, Vol. 10, Issue 2
Differential analysis of RNA-seq incorporating quantification uncertainty
journal, June 2017
- Pimentel, Harold; Bray, Nicolas L.; Puente, Suzette
- Nature Methods, Vol. 14, Issue 7
Microbial colonization and controls in dryland systems
journal, July 2012
- Pointing, Stephen B.; Belnap, Jayne
- Nature Reviews Microbiology, Vol. 10, Issue 8
A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: comparative genomic and experimental evidence for a cryptic role in thiamin metabolism
journal, May 2011
- Pribat, Anne; Blaby, Ian K.; Lara-Núñez, Aurora
- Functional & Integrative Genomics, Vol. 11, Issue 3
Hydrotaxis of Cyanobacteria in Desert Crusts
journal, November 2003
- Pringault, O.; Garcia-Pichel, F.
- Microbial Ecology, Vol. 47, Issue 4
Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology
journal, June 2015
- Prosser, James I.
- Nature Reviews Microbiology, Vol. 13, Issue 7
Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
journal, June 2013
- Rajeev, Lara; da Rocha, Ulisses Nunes; Klitgord, Niels
- The ISME Journal, Vol. 7, Issue 11
In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings
journal, October 2016
- Reichel, Marlene; Liao, Yalin; Rettel, Mandy
- The Plant Cell, Vol. 28, Issue 10
The role of the exopolysaccharides in enhancing hydraulic conductivity of biological soil crusts
journal, March 2012
- Rossi, Federico; Potrafka, Ruth M.; Pichel, Ferran Garcia
- Soil Biology and Biochemistry, Vol. 46
Interdependence of Cell Growth and Gene Expression: Origins and Consequences
journal, November 2010
- Scott, M.; Gunderson, C. W.; Mateescu, E. M.
- Science, Vol. 330, Issue 6007
Precipitation pulses and soil CO 2 flux in a Sonoran Desert ecosystem
journal, February 2007
- Sponseller, Ryan A.
- Global Change Biology, Vol. 13, Issue 2
Genome of the Cyanobacterium Microcoleus vaginatusFGP-2, a Photosynthetic Ecosystem Engineer of Arid Land Soil Biocrusts Worldwide
journal, June 2011
- Starkenburg, S. R.; Reitenga, K. G.; Freitas, T.
- Journal of Bacteriology, Vol. 193, Issue 17
Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material
journal, May 2013
- Steven, Blaire; Gallegos-Graves, La Verne; Belnap, Jayne
- FEMS Microbiology Ecology, Vol. 86, Issue 1
Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study: Sequencing to describe dryland soil communities
journal, February 2012
- Steven, Blaire; Gallegos-Graves, La Verne; Starkenburg, Shawn R.
- Environmental Microbiology Reports, Vol. 4, Issue 2
Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils
journal, February 2014
- Steven, Blaire; Gallegos-Graves, La Verne; Yeager, Chris
- Soil Biology and Biochemistry, Vol. 69
Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant
journal, March 2017
- Steven, Blaire; Hesse, Cedar; Soghigian, John
- Applied and Environmental Microbiology, Vol. 83, Issue 11
Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities
journal, August 2015
- Steven, Blaire; Kuske, Cheryl R.; Gallegos-Graves, La Verne
- Applied and Environmental Microbiology, Vol. 81, Issue 21
Targeted deletion of genes for eukaryotic RNA-binding proteins, Rbp1 and Rbp2, in the cyanobacterium Synechococcus sp. strain PCC7942: Rbp1 is indispensable for cell growth at low temperatures
journal, July 1999
- Sugita, Chieko; Mutsuda, Michinori; Sugiura, Masahiro
- FEMS Microbiology Letters, Vol. 176, Issue 1
Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria
journal, January 2013
- Taylor, Ronald C.; Webb Robertson, Bobbie-Jo M.; Markillie, Lye Meng
- Integrative Biology, Vol. 5, Issue 11
The concurrent use of novel soil surface microclimate measurements to evaluate CO2 pulses in biocrusted interspaces in a cool desert ecosystem
journal, September 2017
- Tucker, Colin L.; McHugh, Theresa A.; Howell, Armin
- Biogeochemistry, Vol. 135, Issue 3
Average Gene Length Is Highly Conserved in Prokaryotes and Eukaryotes and Diverges Only Between the Two Kingdoms
journal, April 2006
- Xu, Lin; Chen, Hong; Hu, Xiaohua
- Molecular Biology and Evolution, Vol. 23, Issue 6
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
journal, August 2015
- Ye, Yuzhen; Tang, Haixu
- Bioinformatics, Vol. 32, Issue 7
Differential Responses of Dinitrogen Fixation, Diazotrophic Cyanobacteria and Ammonia Oxidation Reveal a Potential Warming-Induced Imbalance of the N-Cycle in Biological Soil Crusts
journal, October 2016
- Zhou, Xiaobing; Smith, Hilda; Giraldo Silva, Ana
- PLOS ONE, Vol. 11, Issue 10
The potential roles of biological soil crusts in dryland hydrologic cycles
journal, January 2006
- Belnap, Jayne
- Hydrological Processes, Vol. 20, Issue 15
Heterocyst-forming Filamentous Cyanobacteria Encode Proteins that Resemble Eukaryotic RNA-binding Proteins of the RNP Family
journal, January 1994
- Mulligan, Martin E.; Jackman, Donna M.; Murphy, Stephen T.
- Journal of Molecular Biology, Vol. 235, Issue 3
Biological Soil Crusts as an Organizing Principle in Drylands
book, January 2016
- Belnap, Jayne; Weber, Bettina; Büdel, Burkhard
- Biological Soil Crusts: An Organizing Principle in Drylands
Heterotrophic growth of the filamentous blue-green alga Plectonema boryanum
journal, January 1975
- White, Alan W.; Shilo, Moshe
- Archives of Microbiology, Vol. 102, Issue 1
Hydrotaxis of Cyanobacteria in Desert Crusts
journal, November 2003
- Pringault, O.; Garcia-Pichel, F.
- Microbial Ecology, Vol. 47, Issue 4
Small-Scale Vertical Distribution of Bacterial Biomass and Diversity in Biological Soil Crusts from Arid Lands in the Colorado Plateau
journal, November 2003
- Garcia-Pichel, F.; Johnson, S. L.; Youngkin, D.
- Microbial Ecology, Vol. 46, Issue 3
Precipitation pulses and carbon fluxes in semiarid and arid ecosystems
journal, August 2004
- Huxman, Travis E.; Snyder, Keirith A.; Tissue, David
- Oecologia, Vol. 141, Issue 2
The concurrent use of novel soil surface microclimate measurements to evaluate CO2 pulses in biocrusted interspaces in a cool desert ecosystem
journal, September 2017
- Tucker, Colin L.; McHugh, Theresa A.; Howell, Armin
- Biogeochemistry, Vol. 135, Issue 3
Desiccation: An environmental and food industry stress that bacteria commonly face
journal, February 2018
- Esbelin, Julia; Santos, Tiago; Hébraud, Michel
- Food Microbiology, Vol. 69
Diversity in hydrogen evolution from bidirectional hydrogenases in cyanobacteria from terrestrial, freshwater and marine intertidal environments
journal, November 2012
- Kothari, Ankita; Potrafka, Ruth; Garcia-Pichel, Ferran
- Journal of Biotechnology, Vol. 162, Issue 1
Assembly, function and evolution of cyanobacterial carboxysomes
journal, June 2016
- Kerfeld, Cheryl A.; Melnicki, Matthew R.
- Current Opinion in Plant Biology, Vol. 31
The role of the exopolysaccharides in enhancing hydraulic conductivity of biological soil crusts
journal, March 2012
- Rossi, Federico; Potrafka, Ruth M.; Pichel, Ferran Garcia
- Soil Biology and Biochemistry, Vol. 46
Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils
journal, February 2014
- Steven, Blaire; Gallegos-Graves, La Verne; Yeager, Chris
- Soil Biology and Biochemistry, Vol. 69
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
journal, June 2016
- Li, Dinghua; Luo, Ruibang; Liu, Chi-Man
- Methods, Vol. 102
Nitrogen status modulates the expression of RNA-binding proteins in cyanobacteria
journal, October 2003
- Mori, Shahram; Castoreno, Adam; Mulligan, Martin E.
- FEMS Microbiology Letters, Vol. 227, Issue 2
Cyanobacteria track water in desert soils
journal, September 2001
- Garcia-Pichel, Ferran; Pringault, Olivier
- Nature, Vol. 413, Issue 6854
Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands
journal, November 2011
- Kuske, Cheryl R.; Yeager, Chris M.; Johnson, Shannon
- The ISME Journal, Vol. 6, Issue 4
Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
journal, June 2013
- Rajeev, Lara; da Rocha, Ulisses Nunes; Klitgord, Niels
- The ISME Journal, Vol. 7, Issue 11
Near-optimal probabilistic RNA-seq quantification
journal, April 2016
- Bray, Nicolas L.; Pimentel, Harold; Melsted, Páll
- Nature Biotechnology, Vol. 34, Issue 5
Microbial colonization and controls in dryland systems
journal, July 2012
- Pointing, Stephen B.; Belnap, Jayne
- Nature Reviews Microbiology, Vol. 10, Issue 8
Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology
journal, June 2015
- Prosser, James I.
- Nature Reviews Microbiology, Vol. 13, Issue 7
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
journal, January 2021
- Karst, Søren M.; Ziels, Ryan M.; Kirkegaard, Rasmus H.
- Nature Methods, Vol. 18, Issue 2
Transcriptomics differentiate two novel bioactive strains of Paenibacillus sp. isolated from the perennial ryegrass seed microbiome
journal, July 2021
- Li, Tongda; Mann, Ross; Kaur, Jatinder
- Scientific Reports, Vol. 11, Issue 1
Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria
journal, January 2013
- Taylor, Ronald C.; Webb Robertson, Bobbie-Jo M.; Markillie, Lye Meng
- Integrative Biology, Vol. 5, Issue 11
Uptake hydrogenase in cyanobacteria: novel input from non-heterocystous strains
journal, February 2005
- Tamagnini, P.; Leitão, E.; Oxelfelt, F.
- Biochemical Society Transactions, Vol. 33, Issue 1
Growth rate-stoichiometry couplings in diverse biota
journal, October 2003
- Elser, J. J.; Acharya, K.; Kyle, M.
- Ecology Letters, Vol. 6, Issue 10
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
journal, July 2002
- Bernstein, J. A.; Khodursky, A. B.; Lin, P. -H.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 15
Relating the metatranscriptome and metagenome of the human gut
journal, May 2014
- Franzosa, E. A.; Morgan, X. C.; Segata, N.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 22
Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging
journal, August 2015
- Greening, Chris; Carere, Carlo R.; Rushton-Green, Rowena
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 33
STAMP: statistical analysis of taxonomic and functional profiles
journal, July 2014
- Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip
- Bioinformatics, Vol. 30, Issue 21
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013
- Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
- Nucleic Acids Research, Vol. 42, Issue D1
Differential Expression of Photosynthesis and Nitrogen Fixation Genes in the Cyanobacterium Plectonema boryanum
journal, March 2000
- Misra, Hari S.; Tuli, Rakesh
- Plant Physiology, Vol. 122, Issue 3
In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings
journal, October 2016
- Reichel, Marlene; Liao, Yalin; Rettel, Mandy
- The Plant Cell, Vol. 28, Issue 10
Microenvironments and Microscale Productivity of Cyanobacterial Desert Crusts1
journal, October 1996
- Garcia-Pichel, Ferran; Belnap, Jayne
- Journal of Phycology, Vol. 32, Issue 5
Precipitation pulses and soil CO 2 flux in a Sonoran Desert ecosystem
journal, February 2007
- Sponseller, Ryan A.
- Global Change Biology, Vol. 13, Issue 2
The role of cyanobacterial exopolysaccharides in structuring desert microbial crusts
journal, October 1996
- Mazor, Gideon; Kidron, Giora J.; Vonshak, Ahuva
- FEMS Microbiology Ecology, Vol. 21, Issue 2
Targeted deletion of genes for eukaryotic RNA-binding proteins, Rbp1 and Rbp2, in the cyanobacterium Synechococcus sp. strain PCC7942: Rbp1 is indispensable for cell growth at low temperatures
journal, July 1999
- Sugita, Chieko; Mutsuda, Michinori; Sugiura, Masahiro
- FEMS Microbiology Letters, Vol. 176, Issue 1
VEGAN, a package of R functions for community ecology
journal, April 2003
- Dixon, Philip
- Journal of Vegetation Science, Vol. 14, Issue 6
Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study: Sequencing to describe dryland soil communities
journal, February 2012
- Steven, Blaire; Gallegos-Graves, La Verne; Starkenburg, Shawn R.
- Environmental Microbiology Reports, Vol. 4, Issue 2
Interdependence of Cell Growth and Gene Expression: Origins and Consequences
journal, November 2010
- Scott, M.; Gunderson, C. W.; Mateescu, E. M.
- Science, Vol. 330, Issue 6007
Comparison of Nucleic Acid Hybridization and Fluorometry for Measurement of the Relationship between RNA/DNA Ratio and Growth Rate in a Marine Bacterium
journal, January 1993
- Kerkhof, L.; Ward, B. B.
- Applied and Environmental Microbiology, Vol. 59, Issue 5
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis
journal, January 2014
- Gao, Bei; Zhang, Daoyuan; Li, Xiaoshuang
- BMC Research Notes, Vol. 7, Issue 1
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
journal, December 2016
- Narayanasamy, Shaman; Jarosz, Yohan; Muller, Emilie E. L.
- Genome Biology, Vol. 17, Issue 1
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
journal, April 2013
- McMurdie, Paul J.; Holmes, Susan
- PLoS ONE, Vol. 8, Issue 4
Rapid Recovery of Cyanobacterial Pigments in Desiccated Biological Soil Crusts following Addition of Water
journal, November 2014
- Abed, Raeid M. M.; Polerecky, Lubos; Al-Habsi, Amal
- PLoS ONE, Vol. 9, Issue 11
Differential Responses of Dinitrogen Fixation, Diazotrophic Cyanobacteria and Ammonia Oxidation Reveal a Potential Warming-Induced Imbalance of the N-Cycle in Biological Soil Crusts
journal, October 2016
- Zhou, Xiaobing; Smith, Hilda; Giraldo Silva, Ana
- PLOS ONE, Vol. 11, Issue 10
Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland
journal, September 2015
- Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.
- Frontiers in Microbiology, Vol. 6
Determination of the Glycogen Content in Cyanobacteria
journal, July 2017
- De Porcellinis, Alice; Frigaard, Niels-Ulrik; Sakuragi, Yumiko
- Journal of Visualized Experiments, Issue 125
Works referencing / citing this record:
The Ecology of Subaerial Biofilms in Dry and Inhospitable Terrestrial Environments
journal, September 2019
- Villa, Federica; Cappitelli, Francesca
- Microorganisms, Vol. 7, Issue 10
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.