Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil
Abstract
The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several 13C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily 13C-labeled bacterialmore »
- Authors:
-
[4];
[3];
[6];
[7];
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Lincoln Science Centre, AgResearch Ltd., Christchurch, New Zealand
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA, Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Biofilm Center, University of Duisburg—Essen, Essen, Germany
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA, Department of Earth and Planetary Science, University of California, Berkeley, California, USA, Innovative Genomics Institute, Berkeley, California, USA, Chan Zuckerberg Biohub, San Francisco, California, USA
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); German Science Foundation; National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1818172
- Alternate Identifier(s):
- OSTI ID: 1855191; OSTI ID: 1867551
- Report Number(s):
- LLNL-JRNL-814137
Journal ID: ISSN 2379-5042; e00085-21
- Grant/Contract Number:
- SC0010570; SC0016247; SC10010566; SC0020172; SCW1589; SCW1632; AC02-05CH11231; DFG1603-1/1; AC52-07NA27344; CZO EAR-1331940; SC0010566; EAR-1331940
- Resource Type:
- Published Article
- Journal Name:
- mSphere
- Additional Journal Information:
- Journal Name: mSphere Journal Volume: 6 Journal Issue: 5; Journal ID: ISSN 2379-5042
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; plant growth; labeling; density separation; sequencing; enrichment; growth; 58 GEOSCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 54 ENVIRONMENTAL SCIENCES
Citation Formats
Starr, Evan P., Shi, Shengjing, Blazewicz, Steven J., Koch, Benjamin J., Probst, Alexander J., Hungate, Bruce A., Pett-Ridge, Jennifer, Firestone, Mary K., Banfield, Jillian F., and Young, ed., Vincent B. Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil. United States: N. p., 2021.
Web. doi:10.1128/mSphere.00085-21.
Starr, Evan P., Shi, Shengjing, Blazewicz, Steven J., Koch, Benjamin J., Probst, Alexander J., Hungate, Bruce A., Pett-Ridge, Jennifer, Firestone, Mary K., Banfield, Jillian F., & Young, ed., Vincent B. Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil. United States. https://doi.org/10.1128/mSphere.00085-21
Starr, Evan P., Shi, Shengjing, Blazewicz, Steven J., Koch, Benjamin J., Probst, Alexander J., Hungate, Bruce A., Pett-Ridge, Jennifer, Firestone, Mary K., Banfield, Jillian F., and Young, ed., Vincent B. Wed .
"Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil". United States. https://doi.org/10.1128/mSphere.00085-21.
@article{osti_1818172,
title = {Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil},
author = {Starr, Evan P. and Shi, Shengjing and Blazewicz, Steven J. and Koch, Benjamin J. and Probst, Alexander J. and Hungate, Bruce A. and Pett-Ridge, Jennifer and Firestone, Mary K. and Banfield, Jillian F. and Young, ed., Vincent B.},
abstractNote = {The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several 13C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily 13C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil. Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO2-derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.},
doi = {10.1128/mSphere.00085-21},
journal = {mSphere},
number = 5,
volume = 6,
place = {United States},
year = {Wed Oct 27 00:00:00 EDT 2021},
month = {Wed Oct 27 00:00:00 EDT 2021}
}
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Works referenced in this record:
NO way to live; the various roles of nitric oxide in plant–pathogen interactions
journal, December 2005
- Mur, Luis A. J.; Carver, Tim L. W.; Prats, Elena
- Journal of Experimental Botany, Vol. 57, Issue 3
The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent
journal, January 2017
- Nazir, Rashid; Mazurier, Sylvie; Yang, Pu
- Frontiers in Microbiology, Vol. 8
Salicylic Acid Inhibits Pathogen Growth in Plants through Repression of the Auxin Signaling Pathway
journal, October 2007
- Wang, Dong; Pajerowska-Mukhtar, Karolina; Culler, Angela Hendrickson
- Current Biology, Vol. 17, Issue 20
Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil
journal, May 2014
- Blazewicz, Steven J.; Schwartz, Egbert; Firestone, Mary K.
- Ecology, Vol. 95, Issue 5
Host-linked soil viral ecology along a permafrost thaw gradient
journal, July 2018
- Emerson, Joanne B.; Roux, Simon; Brum, Jennifer R.
- Nature Microbiology, Vol. 3, Issue 8
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
journal, October 2018
- Trubl, Gareth; Jang, Ho Bin; Roux, Simon
- mSystems, Vol. 3, Issue 5
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
journal, August 2012
- Sharon, I.; Morowitz, M. J.; Thomas, B. C.
- Genome Research, Vol. 23, Issue 1
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
journal, May 2018
- Zhang, Han; Yohe, Tanner; Huang, Le
- Nucleic Acids Research, Vol. 46, Issue W1
Mechanisms of action of plant growth promoting bacteria
journal, October 2017
- Olanrewaju, Oluwaseyi Samuel; Glick, Bernard R.; Babalola, Olubukola Oluranti
- World Journal of Microbiology and Biotechnology, Vol. 33, Issue 11
A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses
journal, December 2015
- Weinmaier, Thomas; Probst, Alexander J.; La Duc, Myron T.
- Microbiome, Vol. 3, Issue 1
InterProScan - an integration platform for the signature-recognition methods in InterPro
journal, September 2001
- Zdobnov, E. M.; Apweiler, R.
- Bioinformatics, Vol. 17, Issue 9, p. 847-848
Rhizosphere Carbon Turnover from Cradle to Grave: The Role of Microbe–Plant Interactions
book, August 2020
- Pett-Ridge, Jennifer; Shi, Shengjing; Estera-Molina, Katerina
- Rhizosphere Biology: Interactions Between Microbes and Plants
Effect of mechanical damage on vigor, physiological parameters, and susceptibility of oat (Avena sativa) to Fusarium culmorum infection
journal, September 2011
- Warzecha, Tomasz; Zieliński, Andrzej; Skrzypek, Edyta
- Phytoparasitica, Vol. 40, Issue 1
Who's your neighbor? New computational approaches for functional genomics
journal, June 2000
- Galperin, Michael Y.; Koonin, Eugene V.
- Nature Biotechnology, Vol. 18, Issue 6
Microbial extracellular polysaccharide production and aggregate stability controlled by switchgrass (Panicum virgatum) root biomass and soil water potential
journal, April 2020
- Sher, Yonatan; Baker, Nameer R.; Herman, Don
- Soil Biology and Biochemistry, Vol. 143
Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups
journal, June 2012
- Placella, S. A.; Brodie, E. L.; Firestone, M. K.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 27
Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients: Quantitative analysis of SIP gradients
journal, December 2003
- Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W.
- Environmental Microbiology, Vol. 6, Issue 1
Biochemistry and genetics of ACC deaminase: a weapon to “stress ethylene” produced in plants
journal, September 2015
- Singh, Rajnish P.; Shelke, Ganesh M.; Kumar, Anil
- Frontiers in Microbiology, Vol. 6
Strong succession in arbuscular mycorrhizal fungal communities
journal, August 2018
- Gao, Cheng; Montoya, Liliam; Xu, Ling
- The ISME Journal, Vol. 13, Issue 1
Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil: Ciliate diversity in soils
journal, December 2007
- Lara, Enrique; Berney, Cédric; Harms, Hauke
- FEMS Microbiology Ecology, Vol. 62, Issue 3
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
VirSorter: mining viral signal from microbial genomic data
journal, January 2015
- Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
- PeerJ, Vol. 3
Graph Clustering Via a Discrete Uncoupling Process
journal, January 2008
- Van Dongen, Stijn
- SIAM Journal on Matrix Analysis and Applications, Vol. 30, Issue 1
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
journal, June 2011
- Medema, Marnix H.; Blin, Kai; Cimermancic, Peter
- Nucleic Acids Research, Vol. 39, Issue suppl_2
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
journal, April 2017
- Blin, Kai; Wolf, Thomas; Chevrette, Marc G.
- Nucleic Acids Research, Vol. 45, Issue W1
Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis
journal, July 2010
- Bonfante, Paola; Genre, Andrea
- Nature Communications, Vol. 1, Issue 1
Notes on Methods for the Extraction of Small Soil Arthropods
journal, May 1953
- Macfadyen, A.
- The Journal of Animal Ecology, Vol. 22, Issue 1
Quantitative Microbial Ecology through Stable Isotope Probing
journal, August 2015
- Hungate, Bruce A.; Mau, Rebecca L.; Schwartz, Egbert
- Applied and Environmental Microbiology, Vol. 81, Issue 21
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999
- Ogata, H.; Goto, S.; Sato, K.
- Nucleic Acids Research, Vol. 27, Issue 1
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013
- Katoh, K.; Standley, D. M.
- Molecular Biology and Evolution, Vol. 30, Issue 4
Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil
journal, November 2019
- Starr, Evan P.; Nuccio, Erin E.; Pett-Ridge, Jennifer
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 51
Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons
journal, August 2015
- Shi, Shengjing; Nuccio, Erin; Herman, Donald J.
- mBio, Vol. 6, Issue 4
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
journal, July 2018
- Kroeger, Marie E.; Delmont, Tom O.; Eren, A. M.
- Frontiers in Microbiology, Vol. 9
Stable isotope probing of bacterial community structure and gene expression in the rhizosphere of Arabidopsis thaliana
journal, March 2012
- Haichar, Feth el Zahar; Roncato, Marie-Anne; Achouak, Wafa
- FEMS Microbiology Ecology, Vol. 81, Issue 2
Microbial Phosphorus Solubilization and Its Potential for Use in Sustainable Agriculture
journal, June 2017
- Alori, Elizabeth T.; Glick, Bernard R.; Babalola, Olubukola O.
- Frontiers in Microbiology, Vol. 8
Migratory Response of Soil Bacteria to Lyophyllum sp. Strain Karsten in Soil Microcosms
journal, March 2009
- Warmink, J. A.; van Elsas, J. D.
- Applied and Environmental Microbiology, Vol. 75, Issue 9
Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences
journal, August 2000
- Huynen, M.
- Genome Research, Vol. 10, Issue 8
CRISPRDetect: A flexible algorithm to define CRISPR arrays
journal, May 2016
- Biswas, Ambarish; Staals, Raymond H. J.; Morales, Sergio E.
- BMC Genomics, Vol. 17, Issue 1
Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development
journal, January 2016
- Deveau, Aurélie; Antony-Babu, Sanjay; Le Tacon, François
- Mycorrhiza, Vol. 26, Issue 5
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development
journal, March 2015
- Raveh-Sadka, Tali; Thomas, Brian C.; Singh, Andrea
- eLife, Vol. 4
Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method
journal, April 2012
- Lee, Chol Gyu; Watanabe, Takeshi; Fujita, Yuichi
- Soil Science and Plant Nutrition, Vol. 58, Issue 2
Creating the CIPRES Science Gateway for inference of large phylogenetic trees
conference, November 2010
- Miller, Mark A.; Pfeiffer, Wayne; Schwartz, Terri
- 2010 Gateway Computing Environments Workshop (GCE)
UniProt Knowledgebase: a hub of integrated protein data
journal, January 2011
- Magrane, M.; Consortium, U.
- Database, Vol. 2011, Issue 0
Structure and function of the global topsoil microbiome
journal, August 2018
- Bahram, Mohammad; Hildebrand, Falk; Forslund, Sofia K.
- Nature, Vol. 560, Issue 7717
Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design
journal, August 2020
- Sieradzki, Ella T.; Koch, Benjamin J.; Greenlon, Alex
- mSystems, Vol. 5, Issue 4
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon
journal, July 2018
- Starr, Evan P.; Shi, Shengjing; Blazewicz, Steven J.
- Microbiome, Vol. 6, Issue 1
Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters
journal, October 2014
- Haig, Sarah-Jane; Schirmer, Melanie; D'Amore, Rosalinda
- The ISME Journal, Vol. 9, Issue 4
Characterization of an Insecticidal Toxin and Pathogenicity of Pseudomonas taiwanensis against Insects
journal, August 2014
- Chen, Wen-Jen; Hsieh, Feng-Chia; Hsu, Fu-Chiun
- PLoS Pathogens, Vol. 10, Issue 8
HMMER web server: interactive sequence similarity searching
journal, May 2011
- Finn, R. D.; Clements, J.; Eddy, S. R.
- Nucleic Acids Research, Vol. 39, Issue suppl
A global atlas of the dominant bacteria found in soil
journal, January 2018
- Delgado-Baquerizo, Manuel; Oliverio, Angela M.; Brewer, Tess E.
- Science, Vol. 359, Issue 6373
Nematicidal Bacteria Associated to Pinewood Nematode Produce Extracellular Proteases
journal, November 2013
- Paiva, Gabriel; Proença, Diogo Neves; Francisco, Romeu
- PLoS ONE, Vol. 8, Issue 11
A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
journal, August 2018
- Wylezich, Claudia; Papa, Anna; Beer, Martin
- Scientific Reports, Vol. 8, Issue 1
Steady-state dissolution kinetics of mineral ferric phosphate in the presence of desferrioxamine-B and oxalate ligands at pH=4–6 and T=24±0.6°C
journal, August 2012
- Cervini-Silva, Javiera; Kearns, Josh; Banfield, Jillian
- Chemical Geology, Vol. 320-321
Diverse effect of phosphatidylcholine biosynthetic genes on phospholipid homeostasis, cell autophagy and fungal developments in Metarhizium robertsii: PC biosynthetic genes effect fungal physiology
journal, December 2017
- Chen, Yixiong; Li, Bing; Cen, Kai
- Environmental Microbiology, Vol. 20, Issue 1
Bacterial volatiles promote growth in Arabidopsis
journal, April 2003
- Ryu, C. -M.; Farag, M. A.; Hu, C. -H.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 8
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
journal, April 2012
- Kearse, M.; Moir, R.; Wilson, A.
- Bioinformatics, Vol. 28, Issue 12
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
journal, January 2016
- Butterfield, Cristina N.; Li, Zhou; Andeer, Peter F.
- PeerJ, Vol. 4
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
journal, February 2015
- Sharon, Itai; Kertesz, Michael; Hug, Laura A.
- Genome Research, Vol. 25, Issue 4
Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing
journal, October 2016
- Taylor, D. Lee; Walters, William A.; Lennon, Niall J.
- Applied and Environmental Microbiology, Vol. 82, Issue 24
Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda
journal, June 2015
- Wu, Shu; Xiong, Jie; Yu, Yuhe
- PLOS ONE, Vol. 10, Issue 6
Disentangling carbon flow across microbial kingdoms in the rhizosphere of maize
journal, July 2019
- Hünninghaus, Maike; Dibbern, Dörte; Kramer, Susanne
- Soil Biology and Biochemistry, Vol. 134
UniRef: comprehensive and non-redundant UniProt reference clusters
journal, March 2007
- Suzek, B. E.; Huang, H.; McGarvey, P.
- Bioinformatics, Vol. 23, Issue 10
Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs
journal, February 2015
- Schubotz, Florence; Hays, Lindsay E.; Meyer-Dombard, D'Arcy R.
- Frontiers in Microbiology, Vol. 6
Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO 2 concentrations : Genomic resolution of a high-CO
journal, July 2016
- Probst, Alexander J.; Castelle, Cindy J.; Singh, Andrea
- Environmental Microbiology, Vol. 19, Issue 2
Quantitative Analysis of Lysobacter Predation
journal, July 2015
- Seccareccia, Ivana; Kost, Christian; Nett, Markus
- Applied and Environmental Microbiology, Vol. 81, Issue 20
GC–MS SPME profiling of rhizobacterial volatiles reveals prospective inducers of growth promotion and induced systemic resistance in plants
journal, October 2006
- Farag, Mohamed A.; Ryu, Choong-Min; Sumner, Lloyd W.
- Phytochemistry, Vol. 67, Issue 20
Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers
journal, February 2014
- Hadziavdic, Kenan; Lekang, Katrine; Lanzen, Anders
- PLoS ONE, Vol. 9, Issue 2
Off the hook – how bacteria survive protozoan grazing
journal, July 2005
- Matz, Carsten; Kjelleberg, Staffan
- Trends in Microbiology, Vol. 13, Issue 7
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface
journal, January 2018
- Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.
- Nature Microbiology, Vol. 3, Issue 3
dbCAN: a web resource for automated carbohydrate-active enzyme annotation
journal, May 2012
- Yin, Yanbin; Mao, Xizeng; Yang, Jincai
- Nucleic Acids Research, Vol. 40, Issue W1
Estimating taxon‐specific population dynamics in diverse microbial communities
journal, January 2018
- Koch, Benjamin J.; McHugh, Theresa A.; Hayer, Michaela
- Ecosphere, Vol. 9, Issue 1
Bacterial quorum sensing and nitrogen cycling in rhizosphere soil: Bacterial QS and rhizosphere nitrogen cycling
journal, November 2008
- DeAngelis, Kristen M.; Lindow, Steven E.; Firestone, Mary K.
- FEMS Microbiology Ecology, Vol. 66, Issue 2
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
Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism
journal, April 2016
- Bouskill, Nicholas J.; Wood, Tana E.; Baran, Richard
- Frontiers in Microbiology, Vol. 7
RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro
journal, January 2017
- Herrmann, Elena; Young, Wayne; Rosendale, Douglas
- BioMed Research International, Vol. 2017
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing
journal, November 2011
- Murase, Jun; Shibata, Manami; Lee, Chol Gyu
- FEMS Microbiology Ecology, Vol. 79, Issue 2
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing
journal, October 2015
- Chen, Lin; Xu, Jianming; Feng, Youzhi
- Frontiers in Microbiology, Vol. 6
A high-efficiency, “low-technology” Tullgren-type extractor for soil microarthropods
journal, February 1991
- Crossley, D. A.; Blair, John M.
- Agriculture, Ecosystems & Environment, Vol. 34, Issue 1-4
Bacterial Secretion Systems: An Overview
journal, February 2016
- Green, Erin R.; Mecsas, Joan
- Microbiology Spectrum, Vol. 4, Issue 1
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
journal, May 2018
- Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison
- Nature Microbiology, Vol. 3, Issue 7
Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes
journal, June 2016
- White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya
- mSystems, Vol. 1, Issue 3
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
Niche differentiation is spatially and temporally regulated in the rhizosphere
journal, January 2020
- Nuccio, Erin E.; Starr, Evan; Karaoz, Ulas
- The ISME Journal, Vol. 14, Issue 4
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 28, Issue 11
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis
journal, June 2018
- Crits-Christoph, Alexander; Diamond, Spencer; Butterfield, Cristina N.
- Nature, Vol. 558, Issue 7710
Adhesins Involved in Attachment to Abiotic Surfaces by Gram-Negative Bacteria
journal, August 2015
- Berne, Cécile; Ducret, Adrien; Hardy, Gail G.
- Microbiology Spectrum, Vol. 3, Issue 4
Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms
journal, May 2019
- Diamond, Spencer; Andeer, Peter F.; Li, Zhou
- Nature Microbiology, Vol. 4, Issue 8
Using stable isotopes to explore root-microbe-mineral interactions in soil
journal, June 2017
- Pett-Ridge, Jennifer; Firestone, Mary K.
- Rhizosphere, Vol. 3
Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing: RNA-SIP of human microbiota
journal, April 2007
- Egert, Markus; De Graaf, Albert A.; Maathuis, Annet
- FEMS Microbiology Ecology, Vol. 60, Issue 1
A View to a Kill: The Bacterial Type VI Secretion System
journal, January 2014
- Ho, Brian T.; Dong, Tao G.; Mekalanos, John J.
- Cell Host & Microbe, Vol. 15, Issue 1
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition
journal, August 2015
- Yang, An; Liu, Nana; Tian, Qiuying
- Frontiers in Microbiology, Vol. 6
Increased plant productivity and decreased microbial respiratory C loss by plant growth-promoting rhizobacteria under elevated CO2
journal, March 2015
- Nie, Ming; Bell, Colin; Wallenstein, Matthew D.
- Scientific Reports, Vol. 5, Issue 1
Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing
journal, March 2014
- Godwin, Scott; Kang, Alicia; Gulino, Lisa-Maree
- The ISME Journal, Vol. 8, Issue 9
The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria
journal, April 2017
- Tyc,, Olaf; Song, Chunxu; Dickschat, Jeroen S.
- Trends in Microbiology, Vol. 25, Issue 4
Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing
journal, September 2018
- Wilhelm, Roland C.; Singh, Rahul; Eltis, Lindsay D.
- The ISME Journal, Vol. 13, Issue 2
Control of Glucosylceramide Production and Morphogenesis by the Bar1 Ceramide Synthase in Fusarium graminearum
journal, April 2011
- Rittenour, William R.; Chen, Ming; Cahoon, Edgar B.
- PLoS ONE, Vol. 6, Issue 4
Metagenomic Analysis of the Bacterial Community Associated with the Taproot of Sugar Beet
journal, January 2015
- Tsurumaru, Hirohito; Okubo, Takashi; Okazaki, Kazuyuki
- Microbes and environments, Vol. 30, Issue 1
Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis
journal, April 2016
- Esmaeel, Qassim; Pupin, Maude; Kieu, Nam Phuong
- MicrobiologyOpen, Vol. 5, Issue 3
Microbial community assembly differs across minerals in a rhizosphere microcosm
journal, September 2018
- Whitman, Thea; Neurath, Rachel; Perera, Adele
- Environmental Microbiology, Vol. 20, Issue 12