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Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis.

Challacombe JF, Hesse CN, Bramer LM, McCue LA, Lipton M, Purvine S, Nicora C, Gallegos-Graves V, Porras-Alfaro A, Kuske CR.

BMC Genomics. 2019 Dec 12;20(1):976. doi: 10.1186/s12864-019-6358-x.


Presence and distribution of insect-associated and entomopathogenic fungi in a temperate pine forest soil: An integrated approach.

Deaver NR, Hesse C, Kuske CR, Porras-Alfaro A.

Fungal Biol. 2019 Dec;123(12):864-874. doi: 10.1016/j.funbio.2019.09.006. Epub 2019 Sep 23.


Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing.

Steven B, Belnap J, Kuske CR.

Front Microbiol. 2018 Oct 8;9:2382. doi: 10.3389/fmicb.2018.02382. eCollection 2018.


Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil.

Albright MBN, Johansen R, Lopez D, Gallegos-Graves V, Steven B, Kuske CR, Dunbar J.

Appl Environ Microbiol. 2018 Jul 17;84(15). pii: e00598-18. doi: 10.1128/AEM.00598-18. Print 2018 Aug 1.


Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.

Torres-Cruz TJ, Billingsley Tobias TL, Almatruk M, Hesse CN, Kuske CR, Desirò A, Benucci GMN, Bonito G, Stajich JE, Dunlap C, Arnold AE, Porras-Alfaro A.

Mycologia. 2017 May-Jun;109(3):363-378. doi: 10.1080/00275514.2017.1364958. Epub 2017 Aug 8.


Shared features of cryptic plasmids from environmental and pathogenic Francisella species.

Challacombe JF, Pillai S, Kuske CR.

PLoS One. 2017 Aug 24;12(8):e0183554. doi: 10.1371/journal.pone.0183554. eCollection 2017.


Correction for Challacombe et al., Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection.

Challacombe JF, Petersen JM, Gallegos-Graves V, Hodge D, Pillai S, Kuske CR.

Appl Environ Microbiol. 2017 Mar 2;83(6). pii: e00174-17. doi: 10.1128/AEM.00174-17. Print 2017 Mar 15. No abstract available.


Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland.

McHugh TA, Morrissey EM, Mueller RC, Gallegos-Graves V, Kuske CR, Reed SC.

Environ Microbiol. 2017 Apr;19(4):1600-1611. doi: 10.1111/1462-2920.13678. Epub 2017 Mar 13.


Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau.

Yeager CM, Gallegos-Graves V, Dunbar J, Hesse CN, Daligault H, Kuske CR.

Appl Environ Microbiol. 2017 Mar 2;83(6). pii: e03020-16. doi: 10.1128/AEM.03020-16. Print 2017 Mar 15.


Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection.

Challacombe JF, Petersen JM, Gallegos-Graves V, Hodge D, Pillai S, Kuske CR.

Appl Environ Microbiol. 2017 Jan 17;83(3). pii: e02589-16. doi: 10.1128/AEM.02589-16. Print 2017 Feb 1. Erratum in: Appl Environ Microbiol. 2017 Mar 2;83(6):.


Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

Hesse CN, Torres-Cruz TJ, Tobias TB, Al-Matruk M, Porras-Alfaro A, Kuske CR.

Mycologia. 2016 Nov/Dec;108(6):1082-1090. doi: 10.3852/16-086.


A new fungal large subunit ribosomal RNA primer for high-throughput sequencing surveys.

Mueller RC, Gallegos-Graves LV, Kuske CR.

FEMS Microbiol Ecol. 2016 Feb;92(2). pii: fiv153. doi: 10.1093/femsec/fiv153. Epub 2015 Dec 9.


Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences.

Deshpande V, Wang Q, Greenfield P, Charleston M, Porras-Alfaro A, Kuske CR, Cole JR, Midgley DJ, Tran-Dinh N.

Mycologia. 2016 Jan-Feb;108(1):1-5. doi: 10.3852/14-293. Epub 2015 Nov 9.


Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland.

Mueller RC, Belnap J, Kuske CR.

Front Microbiol. 2015 Sep 4;6:891. doi: 10.3389/fmicb.2015.00891. eCollection 2015.


Soil microbial responses to nitrogen addition in arid ecosystems.

Sinsabaugh RL, Belnap J, Rudgers J, Kuske CR, Martinez N, Sandquist D.

Front Microbiol. 2015 Aug 14;6:819. doi: 10.3389/fmicb.2015.00819. eCollection 2015.


Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient.

Mueller RC, Gallegos-Graves L, Zak DR, Kuske CR.

Microb Ecol. 2016 Jan;71(1):57-67. doi: 10.1007/s00248-015-0655-y. Epub 2015 Aug 18.


Climate change and physical disturbance manipulations result in distinct biological soil crust communities.

Steven B, Kuske CR, Gallegos-Graves LV, Reed SC, Belnap J.

Appl Environ Microbiol. 2015 Nov;81(21):7448-59. doi: 10.1128/AEM.01443-15. Epub 2015 Aug 14.


Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests.

Hesse CN, Mueller RC, Vuyisich M, Gallegos-Graves LV, Gleasner CD, Zak DR, Kuske CR.

Front Microbiol. 2015 Apr 23;6:337. doi: 10.3389/fmicb.2015.00337. eCollection 2015.


Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker.

Mueller RC, Balasch MM, Kuske CR.

Mol Ecol. 2014 Sep;23(17):4406-17. doi: 10.1111/mec.12858. Epub 2014 Aug 7.


Comparative analyses of a putative Francisella conjugative element.

Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Kuske CR.

Genome. 2014 Mar;57(3):137-44. doi: 10.1139/gen-2013-0231. Epub 2014 Mar 17.


Elevated atmospheric CO2 stimulates soil fungal diversity through increased fine root production in a semiarid shrubland ecosystem.

Lipson DA, Kuske CR, Gallegos-Graves LV, Oechel WC.

Glob Chang Biol. 2014 Aug;20(8):2555-65. doi: 10.1111/gcb.12609. Epub 2014 May 26.


Nitrogen fertilization has a stronger effect on soil nitrogen-fixing bacterial communities than elevated atmospheric CO2.

Berthrong ST, Yeager CM, Gallegos-Graves L, Steven B, Eichorst SA, Jackson RB, Kuske CR.

Appl Environ Microbiol. 2014 May;80(10):3103-12. doi: 10.1128/AEM.04034-13. Epub 2014 Mar 7.


Ribosomal Database Project: data and tools for high throughput rRNA analysis.

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42. doi: 10.1093/nar/gkt1244. Epub 2013 Nov 27.


From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition.

Porras-Alfaro A, Liu KL, Kuske CR, Xie G.

Appl Environ Microbiol. 2014 Feb;80(3):829-40. doi: 10.1128/AEM.02894-13. Epub 2013 Nov 15.


High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert.

Steven B, Lionard M, Kuske CR, Vincent WF.

PLoS One. 2013 Aug 13;8(8):e71489. doi: 10.1371/journal.pone.0071489. eCollection 2013.


Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon.

Weber CF, Vilgalys R, Kuske CR.

Front Microbiol. 2013 Apr 9;4:78. doi: 10.3389/fmicb.2013.00078. eCollection 2013.


Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material.

Steven B, Gallegos-Graves LV, Belnap J, Kuske CR.

FEMS Microbiol Ecol. 2013 Oct;86(1):101-13. doi: 10.1111/1574-6941.12143. Epub 2013 May 20.


Analysis of stomach and gut microbiomes of the eastern oyster (Crassostrea virginica) from coastal Louisiana, USA.

King GM, Judd C, Kuske CR, Smith C.

PLoS One. 2012;7(12):e51475. doi: 10.1371/journal.pone.0051475. Epub 2012 Dec 12.


Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long-term elevated CO2.

Steven B, Gallegos-Graves LV, Yeager CM, Belnap J, Evans RD, Kuske CR.

Environ Microbiol. 2012 Dec;14(12):3247-58. doi: 10.1111/1462-2920.12011. Epub 2012 Nov 1.


Response of biological soil crust diazotrophs to season, altered summer precipitation, and year-round increased temperature in an arid grassland of the colorado plateau, USA.

Yeager CM, Kuske CR, Carney TD, Johnson SL, Ticknor LO, Belnap J.

Front Microbiol. 2012 Oct 11;3:358. doi: 10.3389/fmicb.2012.00358. eCollection 2012.


Rapid phylogenetic and functional classification of short genomic fragments with signature peptides.

Berendzen J, Bruno WJ, Cohn JD, Hengartner NW, Kuske CR, McMahon BH, Wolinsky MA, Xie G.

BMC Res Notes. 2012 Aug 28;5:460. doi: 10.1186/1756-0500-5-460.


Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources.

Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Kuske CR.

BMC Genomics. 2012 Aug 24;13:422. doi: 10.1186/1471-2164-13-422.


Soil fungal cellobiohydrolase I gene (cbhI) composition and expression in a loblolly pine plantation under conditions of elevated atmospheric CO2 and nitrogen fertilization.

Weber CF, Balasch MM, Gossage Z, Porras-Alfaro A, Kuske CR.

Appl Environ Microbiol. 2012 Jun;78(11):3950-7. doi: 10.1128/AEM.08018-11. Epub 2012 Mar 30.


Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study.

Steven B, Gallegos-Graves LV, Starkenburg SR, Chain PS, Kuske CR.

Environ Microbiol Rep. 2012 Apr;4(2):248-56. doi: 10.1111/j.1758-2229.2012.00328.x. Epub 2012 Feb 10.


A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil.

Gans JD, Dunbar J, Eichorst SA, Gallegos-Graves LV, Wolinsky M, Kuske CR.

Nucleic Acids Res. 2012 Jul;40(12):e96. doi: 10.1093/nar/gks238. Epub 2012 Mar 20.


Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing.

Eichorst SA, Kuske CR.

Appl Environ Microbiol. 2012 Apr;78(7):2316-27. doi: 10.1128/AEM.07313-11. Epub 2012 Jan 27.


Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.

Dunbar J, Eichorst SA, Gallegos-Graves LV, Silva S, Xie G, Hengartner NW, Evans RD, Hungate BA, Jackson RB, Megonigal JP, Schadt CW, Vilgalys R, Zak DR, Kuske CR.

Environ Microbiol. 2012 May;14(5):1145-58. doi: 10.1111/j.1462-2920.2011.02695.x. Epub 2012 Jan 20.


Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes.

Liu KL, Porras-Alfaro A, Kuske CR, Eichorst SA, Xie G.

Appl Environ Microbiol. 2012 Mar;78(5):1523-33. doi: 10.1128/AEM.06826-11. Epub 2011 Dec 22.


Comparative assessment of fungal cellobiohydrolase I richness and composition in cDNA generated using oligo(dT) primers or random hexamers.

Weber CF, Kuske CR.

J Microbiol Methods. 2012 Feb;88(2):224-8. doi: 10.1016/j.mimet.2011.11.016. Epub 2011 Dec 8.


Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands.

Kuske CR, Yeager CM, Johnson S, Ticknor LO, Belnap J.

ISME J. 2012 Apr;6(4):886-97. doi: 10.1038/ismej.2011.153. Epub 2011 Nov 24.


Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076.

Challacombe JF, Eichorst SA, Hauser L, Land M, Xie G, Kuske CR.

PLoS One. 2011;6(9):e24882. doi: 10.1371/journal.pone.0024882. Epub 2011 Sep 15.


Responses of soil cellulolytic fungal communities to elevated atmospheric CO₂ are complex and variable across five ecosystems.

Weber CF, Zak DR, Hungate BA, Jackson RB, Vilgalys R, Evans RD, Schadt CW, Megonigal JP, Kuske CR.

Environ Microbiol. 2011 Oct;13(10):2778-93. doi: 10.1111/j.1462-2920.2011.02548.x. Epub 2011 Sep 1.


Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide.

Starkenburg SR, Reitenga KG, Freitas T, Johnson S, Chain PS, Garcia-Pichel F, Kuske CR.

J Bacteriol. 2011 Sep;193(17):4569-70. doi: 10.1128/JB.05138-11. Epub 2011 Jun 24.


Reverse transcription-PCR methods significantly impact richness and composition measures of expressed fungal cellobiohydrolase I genes in soil and litter.

Weber CF, Kuske CR.

J Microbiol Methods. 2011 Sep;86(3):344-50. doi: 10.1016/j.mimet.2011.06.011. Epub 2011 Jun 17.


Common ancestry and novel genetic traits of Francisella novicida-like isolates from North America and Australia as revealed by comparative genomic analyses.

Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Hogg G, Kuske CR.

Appl Environ Microbiol. 2011 Aug;77(15):5110-22. doi: 10.1128/AEM.00337-11. Epub 2011 Jun 10.


Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria.

Eichorst SA, Kuske CR, Schmidt TM.

Appl Environ Microbiol. 2011 Jan;77(2):586-96. doi: 10.1128/AEM.01080-10. Epub 2010 Nov 19.


Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR.

Appl Environ Microbiol. 2009 Apr;75(7):2046-56. doi: 10.1128/AEM.02294-08. Epub 2009 Feb 5.


Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).

Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS.

Nat Biotechnol. 2008 May;26(5):553-60. doi: 10.1038/nbt1403. Epub 2008 May 4. Erratum in: Nat Biotechnol. 2008 Oct;26(10):1193.. Barbote, Ravi [corrected to Barabote, Ravi].


A comparison of taxon co-occurrence patterns for macro- and microorganisms.

Horner-Devine MC, Silver JM, Leibold MA, Bohannan BJ, Colwell RK, Fuhrman JA, Green JL, Kuske CR, Martiny JB, Muyzer G, Ovreås L, Reysenbach AL, Smith VH.

Ecology. 2007 Jun;88(6):1345-53.


Three distinct clades of cultured heterocystous cyanobacteria constitute the dominant N2-fixing members of biological soil crusts of the Colorado Plateau, USA.

Yeager CM, Kornosky JL, Morgan RE, Cain EC, Garcia-Pichel F, Housman DC, Belnap J, Kuske CR.

FEMS Microbiol Ecol. 2007 Apr;60(1):85-97.

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