• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4640408)   Today's Articles (188)   Subscriber (50354)
For: Youngblut ND, Buckley DH. Intra-genomic variation in G + C content and its implications for DNA stable isotope probing. Environ Microbiol Rep 2014;6:767-775. [PMID: 25139123 DOI: 10.1111/1758-2229.12201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Number Cited by Other Article(s)
1
Wang J, Yao H, Zhang X. The effect of the 13C abundance of soil microbial DNA on identifying labelled fractions after ultracentrifugation. Appl Microbiol Biotechnol 2024;108:318. [PMID: 38700733 PMCID: PMC11068677 DOI: 10.1007/s00253-024-13151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/17/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024]
2
Simpson A, Wood-Charlson EM, Smith M, Koch BJ, Beilsmith K, Kimbrel JA, Kellom M, Hunter CI, Walls RL, Schriml LM, Wilhelm RC. MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment. Gigascience 2024;13:giae071. [PMID: 39399973 PMCID: PMC11471955 DOI: 10.1093/gigascience/giae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/29/2024] [Accepted: 08/27/2024] [Indexed: 10/15/2024]  Open
3
Barnett SE, Youngblut ND, Koechli CN, Buckley DH. Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. Proc Natl Acad Sci U S A 2021;118:e2115292118. [PMID: 34799453 PMCID: PMC8617410 DOI: 10.1073/pnas.2115292118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/10/2021] [Indexed: 11/18/2022]  Open
4
Sieradzki ET, Morando M, Fuhrman JA. Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater. mSystems 2021;6:e00245-21. [PMID: 33975968 PMCID: PMC8125074 DOI: 10.1128/msystems.00245-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022]  Open
5
Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. mBio 2021;12:mBio.03099-20. [PMID: 33402535 PMCID: PMC8545098 DOI: 10.1128/mbio.03099-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
6
Liao H, Fan H, Li Y, Yao H. Influence of reductive soil disinfestation or biochar amendment on bacterial communities and their utilization of plant-derived carbon in the rhizosphere of tomato. Appl Microbiol Biotechnol 2021;105:815-825. [PMID: 33386895 DOI: 10.1007/s00253-020-11036-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/11/2020] [Accepted: 11/23/2020] [Indexed: 11/24/2022]
7
Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020;11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/03/2022]  Open
8
Wang J, Zhang X, Yao H. Optimizing ultracentrifugation conditions for DNA-based stable isotope probing (DNA-SIP). J Microbiol Methods 2020;173:105938. [PMID: 32360380 DOI: 10.1016/j.mimet.2020.105938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
9
Liao H, Li Y, Yao H. Biochar Amendment Stimulates Utilization of Plant-Derived Carbon by Soil Bacteria in an Intercropping System. Front Microbiol 2019;10:1361. [PMID: 31316475 PMCID: PMC6611431 DOI: 10.3389/fmicb.2019.01361] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 05/31/2019] [Indexed: 11/22/2022]  Open
10
Angel R. Experimental Setup and Data Analysis Considerations for DNA- and RNA-SIP Experiments in the Omics Era. Methods Mol Biol 2019;2046:1-15. [PMID: 31407292 DOI: 10.1007/978-1-4939-9721-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
11
Barnett SE, Youngblut ND, Buckley DH. Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP. Methods Mol Biol 2019;2046:109-128. [PMID: 31407300 DOI: 10.1007/978-1-4939-9721-3_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
12
Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME JOURNAL 2018;13:413-429. [PMID: 30258172 PMCID: PMC6331573 DOI: 10.1038/s41396-018-0279-6] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/20/2018] [Accepted: 08/11/2018] [Indexed: 11/19/2022]
13
Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. Environ Microbiol 2018;20:3543-3559. [PMID: 30051558 DOI: 10.1111/1462-2920.14309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
14
Youngblut ND, Barnett SE, Buckley DH. SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments. Front Microbiol 2018;9:570. [PMID: 29643843 PMCID: PMC5882788 DOI: 10.3389/fmicb.2018.00570] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/13/2018] [Indexed: 11/13/2022]  Open
15
Youngblut ND, Barnett SE, Buckley DH. HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. PLoS One 2018;13:e0189616. [PMID: 29298299 PMCID: PMC5751983 DOI: 10.1371/journal.pone.0189616] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]  Open
16
Amha YM, Anwar MZ, Brower A, Jacobsen CS, Stadler LB, Webster TM, Smith AL. Inhibition of anaerobic digestion processes: Applications of molecular tools. BIORESOURCE TECHNOLOGY 2018;247:999-1014. [PMID: 28918349 DOI: 10.1016/j.biortech.2017.08.210] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 05/25/2023]
17
A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting. Sci Data 2017;4:170092. [PMID: 28765786 PMCID: PMC5525643 DOI: 10.1038/sdata.2017.92] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/15/2017] [Indexed: 12/04/2022]  Open
18
Pepe-Ranney C, Koechli C, Potrafka R, Andam C, Eggleston E, Garcia-Pichel F, Buckley DH. Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation. THE ISME JOURNAL 2016;10:287-98. [PMID: 26114889 PMCID: PMC4737922 DOI: 10.1038/ismej.2015.106] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 11/08/2022]
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA