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Items: 1 to 50 of 62

1.

Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples.

Jacobsen CS, Nielsen TK, Vester JK, Stougaard P, Nielsen JL, Voriskova J, Winding A, Baldrian P, Liu B, Frostegård Å, Pedersen D, Tveit AT, Svenning MM, Tebbe CC, Øvreås L, Jakobsen PB, Blazewicz SJ, Hubablek V, Bertilsson S, Hansen LH, Cary SC, Holben WE, Ekelund F, Bælum J.

Sci Rep. 2018 Apr 9;8(1):5711. doi: 10.1038/s41598-018-24082-y.

2.

High-resolution melt analysis for rapid comparison of bacterial community compositions.

Hjelmsø MH, Hansen LH, Baelum J, Feld L, Holben WE, Jacobsen CS.

Appl Environ Microbiol. 2014 Jun;80(12):3568-75.

3.

Functional response of a near-surface soil microbial community to a simulated underground CO2 storage leak.

Morales SE, Holben WE.

PLoS One. 2013 Nov 26;8(11):e81742. doi: 10.1371/journal.pone.0081742. eCollection 2013.

4.

Bacterial endophytes enhance competition by invasive plants.

Rout ME, Chrzanowski TH, Westlie TK, DeLuca TH, Callaway RM, Holben WE.

Am J Bot. 2013 Sep;100(9):1726-37. doi: 10.3732/ajb.1200577. Epub 2013 Aug 8.

5.

Yersinia enterocolitica: an unlikely cause of positive brucellosis tests in greater yellowstone ecosystem bison (Bison bison).

See W, Edwards WH, Dauwalter S, Almendra C, Kardos MD, Lowell JL, Wallen R, Cain SL, Holben WE, Luikart G.

J Wildl Dis. 2012 Jul;48(3):537-41.

PMID:
22740518
6.

Microbial degradation of 2,4-dichlorophenoxyacetic acid on the Greenland ice sheet.

Stibal M, Bælum J, Holben WE, Sørensen SR, Jensen A, Jacobsen CS.

Appl Environ Microbiol. 2012 Aug;78(15):5070-6. doi: 10.1128/AEM.00400-12. Epub 2012 May 11.

7.

(±)-catechin, a root exudate of the invasive centaurea stoebe lam. (Spotted knapweed) exhibits bacteriostatic activity against multiple soil bacterial populations.

Pollock JL, Kogan LA, Thorpe AS, Holben WE.

J Chem Ecol. 2011 Sep;37(9):1044-53. doi: 10.1007/s10886-011-0005-6. Epub 2011 Sep 1.

PMID:
21882071
8.

Wildfire and charcoal enhance nitrification and ammonium-oxidizing bacterial abundance in dry montane forest soils.

Ball PN, MacKenzie MD, DeLuca TH, Holben WE.

J Environ Qual. 2010 Jul-Aug;39(4):1243-53.

PMID:
20830912
9.

Linking bacterial identities and ecosystem processes: can 'omic' analyses be more than the sum of their parts?

Morales SE, Holben WE.

FEMS Microbiol Ecol. 2011 Jan;75(1):2-16. doi: 10.1111/j.1574-6941.2010.00938.x. Review.

10.

Comparison of 16S rRNA gene phylogeny and functional tfdA gene distribution in thirty-one different 2,4-dichlorophenoxyacetic acid and 4-chloro-2-methylphenoxyacetic acid degraders.

Baelum J, Jacobsen CS, Holben WE.

Syst Appl Microbiol. 2010 Mar;33(2):67-70. doi: 10.1016/j.syapm.2010.01.001. Epub 2010 Mar 5.

PMID:
20206455
11.

Bacterial gene abundances as indicators of greenhouse gas emission in soils.

Morales SE, Cosart T, Holben WE.

ISME J. 2010 Jun;4(6):799-808. doi: 10.1038/ismej.2010.8. Epub 2010 Feb 25.

PMID:
20182521
12.

E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in Escherichia coli.

Kinnersley MA, Holben WE, Rosenzweig F.

PLoS Genet. 2009 Nov;5(11):e1000713. doi: 10.1371/journal.pgen.1000713. Epub 2009 Nov 6.

13.

Hyporheic microbial community development is a sensitive indicator of metal contamination.

Feris KP, Ramsey PW, Gibbons SM, Frazar C, Rillig MC, Moore JN, Gannon JE, Holben WE.

Environ Sci Technol. 2009 Aug 15;43(16):6158-63.

PMID:
19746707
14.

Tri-trophic linkages in disease: pathogen transmission to rainbow trout through stonefly prey.

Adams SM, Adams AS, Holben WE.

Environ Entomol. 2009 Aug;38(4):1022-7.

PMID:
19689880
15.

Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil.

Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE.

Int J Syst Evol Microbiol. 2009 Jul;59(Pt 7):1720-6. doi: 10.1099/ijs.0.000158-0. Epub 2009 Jun 19.

PMID:
19542109
16.

Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path.

Lowell JL, Gordon N, Engstrom D, Stanford JA, Holben WE, Gannon JE.

Microb Ecol. 2009 Oct;58(3):611-20. doi: 10.1007/s00248-009-9525-9. Epub 2009 May 22.

PMID:
19462196
17.

Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis.

Morales SE, Holben WE.

Appl Environ Microbiol. 2009 May;75(9):2677-83. doi: 10.1128/AEM.02166-08. Epub 2009 Feb 27.

18.

Ecology of sulfate-reducing bacteria in an iron-dominated, mining-impacted freshwater sediment.

Ramamoorthy S, Piotrowski JS, Langner HW, Holben WE, Morra MJ, Rosenzweig RF.

J Environ Qual. 2009 Feb 25;38(2):675-84. doi: 10.2134/jeq2007.0577. Print 2009 Mar-Apr.

PMID:
19244488
19.
20.

Supplemental programs for enhanced recovery of data from the DOTUR application.

Morales SE, Cosart T, Johnson JV, Holben WE.

J Microbiol Methods. 2008 Dec;75(3):572-5. doi: 10.1016/j.mimet.2008.07.017. Epub 2008 Jul 25.

PMID:
18703094
21.

Phytotoxic effects of (+/-)-catechin in vitro, in soil, and in the field.

Inderjit, Pollock JL, Callaway RM, Holben W.

PLoS One. 2008 Jul 2;3(7):e2536. doi: 10.1371/journal.pone.0002536.

22.

Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil.

Baelum J, Nicolaisen MH, Holben WE, Strobel BW, Sørensen J, Jacobsen CS.

ISME J. 2008 Jun;2(6):677-87. doi: 10.1038/ismej.2008.21. Epub 2008 Mar 20.

PMID:
18356824
23.

In vitro interactions between yeasts and bacteria and the fungal symbionts of the mountain pine beetle (Dendroctonus ponderosae).

Adams AS, Six DL, Adams SM, Holben WE.

Microb Ecol. 2008 Oct;56(3):460-6. doi: 10.1007/s00248-008-9364-0. Epub 2008 Mar 6.

PMID:
18322728
24.

Use of a PNA probe to block DNA-mediated PCR product formation in prokaryotic RT-PCR.

Bender M, Holben WE, Sørensen SJ, Jacobsen CS.

Biotechniques. 2007 May;42(5):609-10, 612-4.

25.

Quantification of mRNA in Salmonella sp. seeded soil and chicken manure using magnetic capture hybridization RT-PCR.

Jacobsen CS, Holben WE.

J Microbiol Methods. 2007 May;69(2):315-21. Epub 2007 Feb 20.

PMID:
17383760
26.

Spatial stratification of soil bacterial populations in aggregates of diverse soils.

Mummey D, Holben W, Six J, Stahl P.

Microb Ecol. 2006 Apr;51(3):404-11. Epub 2006 Apr 6.

PMID:
16598640
27.

Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment.

Kovacik WP Jr, Takai K, Mormile MR, McKinley JP, Brockman FJ, Fredrickson JK, Holben WE.

Environ Microbiol. 2006 Jan;8(1):141-55.

PMID:
16343329
28.

Relationship between communities and processes; new insights from a field study of a contaminated ecosystem.

Ramsey PW, Rillig MC, Feris KP, Gordon NS, Moore JN, Holben WE, Gannon JE.

Ecol Lett. 2005 Nov;8(11):1201-10. doi: 10.1111/j.1461-0248.2005.00821.x.

PMID:
21352444
29.
30.

Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient.

Feris KP, Ramsey PW, Frazar C, Rillig M, Moore JN, Gannon JE, Holben WE.

Appl Environ Microbiol. 2004 Apr;70(4):2323-31.

31.
32.

Soil biota and exotic plant invasion.

Callaway RM, Thelen GC, Rodriguez A, Holben WE.

Nature. 2004 Feb 19;427(6976):731-3.

PMID:
14973484
33.

Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the western United States.

Feris KP, Ramsey PW, Frazar C, Rillig MC, Gannon JE, Holben WE.

Microb Ecol. 2003 Aug;46(2):200-15.

PMID:
14708745
34.

Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces.

Apajalahti JH, Kettunen A, Nurminen PH, Jatila H, Holben WE.

Appl Environ Microbiol. 2003 Sep;69(9):5731-5.

35.

Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient.

Feris K, Ramsey P, Frazar C, Moore JN, Gannon JE, Holben WE.

Appl Environ Microbiol. 2003 Sep;69(9):5563-73.

36.

Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock.

Takai K, Mormile MR, McKinley JP, Brockman FJ, Holben WE, Kovacik WP Jr, Fredrickson JK.

Environ Microbiol. 2003 Apr;5(4):309-20.

PMID:
12662178
37.

Culture-independent microbial community analysis reveals that inulin in the diet primarily affects previously unknown bacteria in the mouse cecum.

Apajalahti JH, Kettunen H, Kettunen A, Holben WE, Nurminen PH, Rautonen N, Mutanen M.

Appl Environ Microbiol. 2002 Oct;68(10):4986-95.

38.

Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon.

Holben WE, Williams P, Gilbert M, Saarinen M, Särkilahti LK, Apajalahti JH.

Microb Ecol. 2002 Aug;44(2):175-85. Epub 2002 Jun 26. Erratum in: Microb Ecol. 2003 Aug;46(2):289.

PMID:
12082453
39.

Percent G+C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens.

Apajalahti JH, Kettunen A, Bedford MR, Holben WE.

Appl Environ Microbiol. 2001 Dec;67(12):5656-67.

40.

Comparison of methods for monitoring bacterial transport in the subsurface.

DeFlaun MF, Fuller ME, Zhang P, Johnson WP, Mailloux BJ, Holben WE, Kovacik WP, Balkwill DL, Onstott TC.

J Microbiol Methods. 2001 Nov;47(2):219-31.

PMID:
11576686
41.

Ferrographic tracking of bacterial transport in the field at the narrow channel focus area, Oyster, VA.

Johnson WP, Zhang P, Fuller ME, Scheibe TD, Mailloux BJ, Onstott TC, Deflaun MF, Hubbard SS, Radtke J, Kovacik WP, Holben W.

Environ Sci Technol. 2001 Jan 1;35(1):182-91.

PMID:
11352009
42.

Monitoring bacterial transport by stable isotope enrichment of cells.

Holben WE, Ostrom PH.

Appl Environ Microbiol. 2000 Nov;66(11):4935-9.

43.

Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms.

Di Meo CA, Wilbur AE, Holben WE, Feldman RA, Vrijenhoek RC, Cary SC.

Appl Environ Microbiol. 2000 Feb;66(2):651-8.

44.

Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments.

Kieft TL, Murphy EM, Haldeman DL, Amy PS, Bjornstad BN, McDonald EV, Ringelberg DB, White DC, Stair J, Griffiths RP, Gsell TC, Holben WE, Boone DR.

Microb Ecol. 1998 Nov;36(3):336-348.

PMID:
9852513
45.

Effective recovery of bacterial DNA and percent-guanine-plus-cytosine-based analysis of community structure in the gastrointestinal tract of broiler chickens.

Apajalahti JH, Särkilahti LK, Mäki BR, Heikkinen JP, Nurminen PH, Holben WE.

Appl Environ Microbiol. 1998 Oct;64(10):4084-8.

47.
48.

Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments.

Schleper C, Holben W, Klenk HP.

Appl Environ Microbiol. 1997 Jan;63(1):321-3.

49.

Evidence for Acquisition in Nature of a Chromosomal 2,4-Dichlorophenoxyacetic Acid/(alpha)-Ketoglutarate Dioxygenase Gene by Different Burkholderia spp.

Matheson VG, Forney LJ, Suwa Y, Nakatsu CH, Sexstone AJ, Holben WE.

Appl Environ Microbiol. 1996 Jul;62(7):2457-63.

50.

Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. strain RASC.

Suwa Y, Wright AD, Fukimori F, Nummy KA, Hausinger RP, Holben WE, Forney LJ.

Appl Environ Microbiol. 1996 Jul;62(7):2464-9.

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