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Publications

Dan gives a video abstract of a recent Buckley Lab paper:

 

Other recent publications:

Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M., Stahl, D. A. (2017) Brock Biology of Microorganisms, 15th edition. Pearson, New York.

Youngblut, N., Buckley, D. H. (2017) Evaluating the accuracy of DNA stable isotope probing. Environmental Microbiology. BioRxiv. https://doi.org/10.1101/138719

Gaby, J. C. and Buckley, D. H. (2017) The use of degenerate primers in qPCR analysis of functional genes can cause dramatic quantification bias as revealed by investigation of nifH primer performance. Microbial Ecology. doi: 10.1007/s00248-017-0968-0

Choudoir, M. J., Panke-Buisse, K., Andam, C. P., Buckley, D. H. (2017) Genome surfing as driver of microbial genomic diversity. Trends in Microbiology. doi: 10.1016/j.tim.2017.02.006

Choudoir, M. J. and Buckley, D. H. (2016) Latitude delineates patterns of genetic diversity and dispersal in terrestrial Streptomyces. Environmental Microbiology. 18:4931-4945. doi: 10.1111/1462-2920.13420

Pepe-Ranney, C., Campbell, A. N., Koechli, C., Berthrong, S. T., Buckley, D. H. (2016) Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil. Frontiers in Microbiology. 7:703. doi: 10.3389/fmicb.2016.00703

Andam, C. P., Doroghazi, J. R., Campbell, A.N., Kelly, P. J. Choudoir, M. J., Buckley, D. H. (2016) A latitudinal diversity gradient in terrestrial bacteria of the genus Streptomyces. mBio. 7:e02200-15. doi:10.1128/mBio.02200-15

Whitman, T., Pepe-Ranney C., Enders, A., Koechli, C., Campbell, A. N., Buckley, D. H., Lehmann, J. (2016) Pyrogenic organic matter, soil organic matter, and plant root interactions determined using three-part partitioning with stable C isotopes and microbial community analysis. International Society for Microbial Ecology 10:2918-2930. doi: 10.1038/ismej.2016.68

Andam, C. P., Choudoir, M. J., Nguyen, V. A., Buckley, D.H. (2016) Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces International Society for Microbial Ecology Journal. 10:1731-1741. doi:10.1038/ismej.2015.230

Pepe-Ranney, C., Koechli, C., Potrafka, R., Andam, C., Eggleston, E., Garcia-Pichel, F., Buckley, D.H. (2016) Non-cyanobacterial diazotrophs dominate dinitrogen fixation in biological soil crusts at the early stage of crust formation. International Society for Microbial Ecology Journal. 10: 287–298. doi:10.1038/ismej.2015.106

Gaby, J. C. and Buckley, D. H. (2015) Assessment of nitrogenase diversity in the environment. In J. de Bruijn (ed.). Biological Nitrogen Fixation. Wiley/Blackwell, New York.

Doroghazi, J. R. and Buckley, D. H. (2014) Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin. BMC Genomics. 15:970. doi: 10.1186/1471-2164-15-970

Youngblut, N. D. and Buckley, H. (2014) Intra-genomic variation in G+C content and its implications for DNA Stable Isotope Probing (DNA-SIP). Environmental Microbiology Reports. 6: 767-775. doi: 10.1111/1758-2229.12201

Doroghazi, J. R. and Buckley, D. H. (2014) Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin. BMC Genomics. 15 :970.

Gaby, J. C., D. H. Buckley (2014) A comprehensive, aligned nifH gene database: a multi-purpose tool for studies of nitrogen-fixing bacteria. Database. 2014:bauoo1. doi: 10.1093/database/bau001

Madigan, M. T., Martinko J. M., Bender, K., Buckley, D. H., Stahl, D. A. (2014) Brock Biology of Microorganisms, Fourteenth Edition. Pearson, New York.

Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, Buckley DH , Zinder SH, Druschel GK, Fike DA, Orphan VJ (2014) A sulfurous symbiosis: microscale sulfur cycling in the pink berry consortia of the Sippewissett salt marsh. Environmnetal Microbiology. 16:3398-3415. doi: 10.1111/1462-2920.12388

Bräuer SL, Carmichael MJ, Vuono D, Strom A, Pepe-Ranney C, Rabinowitz E, Buckley DH, and Zinder SH (2014) Microbial sequencing analyses suggest the presence of a fecal veneer on indoor climbing wall holds. Current Microbiology. 69 :681-689. doi: 10.1007/s00284-014-0643-3

Blasiak, L.C., Zinder, S.Z., Buckley, D.H. , Hill R.T. (2013) Specific and conserved tunic bacterial community in the model chordate Ciona intestinalis. ISMEJ . doi:10.1038/ismej.2013.156.

Rong, X. Doroghazi, J.R., Cheng, K., Zhang, L., Buckley, D.H. , Huang, Y. (2013) Classification of Streptomyces phylogroup pratensis based on genetic and phenotypic evidence, and proposal of Streptomyces pratensis sp. nov. Systematic and Applied Microbiology . 36: 401-407. doi: 10.1016/j.syapm.2013.03.010.

Falbo, K., Schneider, R.L., Buckley , D.H ., Walter, M.T., Bergholtz, P.W., Buchanan, B.P. (2013) The role of roadside ditches as conduits of fecal indicator organisms and sediment to downstream drinking and recreational waters . Journal of Environmental Management. 128:1050-1059.

Berthrong, S. T., D. H. Buckley , L. E. Drinkwater (2013) Microbial controls on soil C and N cycling in agroecosystems, Microbial Ecology. 66 : 158-170. doi: 10.1007/s00248-013-0225-0

Gaby, J. C., D. H. Buckley (2012) A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase . PloS ONE. 7 (7): e42149 . doi:10.1371/journal.pone.0042149

Choudoir, M J., Campbell, A. N., Buckley, D. H. (2012) Grappling with Proteus: Population level approaches to understanding microbial diversity . Frontiers in Microbiology. 3 :336. doi: 10.3389/fmicb.2012.00336

Armitage, D. W., Gallager, K. L., Youngblut, N. D., Buckley D. H., Zinder S. H. (2012) Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat . Frontiers in Microbiology. 3: 293. doi: 10.3389/fmicb.2012.00293

Doroghazi, J. R., D. H. Buckley (2011) A neutral model for the effect of homologous recombination on microbial diversification. Genome Biology and Evolution. 3:1349-1356 . doi: 10.1093/gbe/evr110

Gaby, J. C., D. H. Buckley (2011) A global census of diazotroph diversity. Environmental Microbiology. 13 :1790.

Bergholz, P. W., J. D. Noar, D. H. Buckley (2011) Environmental patterns are imposed on the spatial structure of E. coli in Topsoil. Applied and Environmental Microbiology. 77:211-219.

Doroghazi, J. R, and D. H. Buckley (2010) Widespread homologous recombination within and between Streptomyces species. International Society for Microbial Ecology Journal. 4:1136-1143.

Buckley, D. H. (2010) Stable Isotope Probing Techniques Using 15N. In J. C. Murrell and A. S. Whiteley (eds.). Stable Isotope Probing and Related Technologies. ASM Press, Washington , D.C.

Shapiro, O. H., R. Hatzenpichler, D. H. Buckley, S. H. Zinder, V. J. Orphan (2010) Multicellular Photo-Magnetotactic Bacteria. Environmental Microbiology Reports. 3:233-238. doi:10.1111/j.1758-2229.2010.00215.x

Buckley, D. H. (2010) Assessing the Diversity of the Unseen Majority. In Sigurdur Greipsson (ed.). Restoration Ecology . Jones and Bartlett Publishers, Inc., Boston.

DuPont, S.T., S.W. Culman, H. Ferris, D. H. Buckley, J.D. Glover. (2010) No-tillage conversion of hayed perennial grassland to annual cropland reduces root biomass, decreases active carbon stocks, and impacts soil biota. Agriculture, Ecosystems and Environment. 137:25-32.

Glover, J. D., S. W. Culman, S.T. DuPont, W. Broussard , L. Young, M. E. Mangan, J. G. Mai1, T. E. Crews, L. R. DeHaan, D. H. Buckley, H. Ferris, R. E. Turner, H. L. Reynolds and D. L. Wyse (2010) Harvested perennial grasslands provide ecological benchmarks for agricultural sustainability. Agriculture, Ecosystems and Environment. 137:3-12.

Culman, S.W., DuPont, S.T., Glover, J.D., Buckley, D.H., Fick, G.W., Ferris, H., Crews, T.E. (2010) Long-term impacts of high-input annual cropping and unfertilized perennial grass production on soil properties and belowground food webs in Kansas, USA. Agriculture, Ecosystems and Environment. 137:13-24.

Hsu, S. and D. H. Buckley (2009) Correspondence between diazotroph diversity and rates of nitrogen fixation in soil. International Society for Microbial Ecology Journal. 3:124-136.

Noar, J. and D. H. Buckley (2009) Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella. International Journal of Systematic and Evolutionary Microbiology. 59:1941-1946.

Culman, S.W., R. Bukowski, H.G. Gauch, H. Cadillo-Quiroz, and D.H. Buckley. (2009) T-REX: Software for the labeling, processing, and analysis of T-RFLP data. BMC Bioinformatics. 10:171.

Baumgartner, L. K., J. R. Spear, D. H. Buckley, N. R. Pace, R. P. Reid, P. T. Visscher (2009) Microbial Diversity in Modern Marine Stromatolites, Highborne Cay, Bahamas. Environmental Microbiology. 11:2710–2719.

Baumgartner, L. K. , C. Dupraz, D. H. Buckley, J. R. Spear, N. R. Pace, P. T. Visscher (2009) Spatial and Temporal Changes in the Microbial Communities of Lithifying and Non-lithifying Microbial Mats. Astrobiology, 9:861-874.

Buckley, D. H., V. Huangyutitham, S-F. Hsu, T. A. Nelson (2008) 15N2-DNA-Stable isotope probing of diazotrophic methanotrophs in soil. Soil Biology and Biochemistry 40: 1272-1283.

Buckley D. H. , L. K. Baumgartner, and P. T. Visscher (2008) Vertical distribution of methane metabolism in microbial mats of the Great Sippewissett Salt Marsh. Environmental Microbiology. 10:967-977.

Buckley, D. H., V. Huangyutitham, S-F. Hsu, and T. A. Nelson. (2007). Stable isotope probing with 15N achieved by disentangling the effects of genome G + C content and isotope enrichment on DNA density. Applied and Environmental Microbiology . 73:3189-3195

Buckley, D. H., V. Huangyutitham, S-F. Hsu, and T. A. Nelson. (2007). Stable isotope probing with 15N2 reveals novel non-cultivated diazotrophs in soil . Applied and Environmental Microbiology . 73:3196-3204

Buckley, D. H. and T. M. Schmidt ( 2007 ) Measurement of ribosomal RNA abundance by hybridization with oligonucleotide probes. In Reddy, C. A., T. J. Beveridge, J. A. Breznak, G. A. Marzluf and T. M. Schmidt (eds.). Methods for General and Molecular Microbiology. American Society for Microbiology, Washington , D.C.

Buckley, D. H. , V. Huangyutitham, T. A. Nelson, A. Rumberger, and J. E. Thies (2006) Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity. Applied and Environmental Microbiology. 72:4522-4531.

Baumgartner, L. K., R. P. Reid, C. Dupraz, A. W. Decho, D. H. Buckley, J. R. Spear, K. M. Przekop, P. T. Visscher (2006) Sulfate reducing bacteria in microbial mats: changing paradigms, new discoveries. Sedimentary Geology. 185:131-145.

Buckley, D. H. and T. M. Schmidt (2003) The structure of microbial communities in soil: patterns of microbial distribution their dynamic nature and the lasting impact of cultivation. Environmental Microbiology. 5:441-452.

Visscher, P. T., L. K. Baumgartner, D. H. Buckley , D. R. Rogers, B. M. Bebout, M. Hogan, C. Raleigh, K. Turk and D. J. Des Marais (2003) Dimethyl sulfide and methanethiol as biogenic signatures in laminated microbial ecosystems. Environmental Microbiology. 5:296-308.

Buckley, D. H. and T. M. Schmidt (2001) Environmental factors influencing the distribution of Verrucomicrobia in soil. FEMS Microbial Ecology. 35:105-112.

Buckley, D. H. and T. M. Schmidt (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microbial Ecology. 42:11-21.

Buckley, D. H. and T. M. Schmidt (2001) Exploring the diversity of soil – a microbial rainforest. In J. T. Staley and A. L. Reysenbach (eds.). Biodiversity of Microbial Life: Foundation of Earth’s Biosphere. Wiley-Liss , New York , pp. 183-208.

Bruns, M. A. and D. H. Buckley ( 2001 ) Isolation and purification of microbial community nucleic acids from environmental samples. In C. J. Hurst, R. L. Crawford, G. R. Knudsen, M. McInerney and L. Stetzenbach (eds.). Manual of Environmental Microbiology, 2nd Edition . American Society for Microbiology, Washington, D.C, pp. 564-572.

Buckley, D. H., J. R. Graber, T. M. Schmidt (1998) Phylogenetic analysis of nonthermophilic members of the Kingdom Crenarchaeot a and their diversity and abundance in soils. Applied and Environmental Microbiology. 64:4333-4339.

Yanni, Y. G., R. Y. Rizk, V. Corich, A. Squartini, K. Ninke, S. Philip-Hollingsworth, G. Orgambide, F. DeBruijn, J. Stoltzfus, D. Buckley , T. Schmidt, P. F. Mateos, J. K. Ladha, and F. B. Dazzo (1997) Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assesment of its potential to promote rice growth. Plant & Soil. 194:99-114.

Hogan, D. A., D. H. Buckley , C. Nakatsu, T. M. Schmidt and R. P. Hausinger (1997) Distribution of tfd A in soil isolates that do not degrade 2,4-dichlorophenoxyacetic acid. Microbial Ecology. 34 :90-96.

Belli, W. A., D. H. Buckley and R. E. Marquis (1995) Weak acid effects and fluoride inhibition of glycolysis by Streptococcus mutans GS-5. Canadian Journal of Microbiology. 41:785-791.

Curran, T. M., D. H. Buckley and R. E. Marquis (1994) Quasi-irreversible inhibition of enolase of Streptococcus mutans by fluoride. FEMS Microbiology Letters. 119:283-288.

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