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Amino Acids and Ribose: Drivers of Protein and RNA Fermentation by Ingested Bacteria of a Primitive Gut Ecosystem.

Zeibich L, Staege M, Schmidt O, Drake HL.

Appl Environ Microbiol. 2019 Sep 17;85(19). pii: e01297-19. doi: 10.1128/AEM.01297-19. Print 2019 Oct 1.


Dietary polysaccharides: fermentation potentials of a primitive gut ecosystem.

Zeibich L, Schmidt O, Drake HL.

Environ Microbiol. 2019 Apr;21(4):1436-1451. doi: 10.1111/1462-2920.14556.


Fermenters in the earthworm gut: do transients matter?

Zeibich L, Schmidt O, Drake HL.

FEMS Microbiol Ecol. 2019 Feb 1;95(2). doi: 10.1093/femsec/fiy221.


Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris.

Zeibich L, Schmidt O, Drake HL.

Appl Environ Microbiol. 2018 May 17;84(11). pii: e00657-18. doi: 10.1128/AEM.00657-18. Print 2018 Jun 1.


Differential Engagement of Fermentative Taxa in Gut Contents of the Earthworm Lumbricus terrestris.

Meier AB, Hunger S, Drake HL.

Appl Environ Microbiol. 2018 Feb 14;84(5). pii: e01851-17. doi: 10.1128/AEM.01851-17. Print 2018 Mar 1.


Disentangling the influence of earthworms in sugarcane rhizosphere.

Braga LP, Yoshiura CA, Borges CD, Horn MA, Brown GG, Drake HL, Tsai SM.

Sci Rep. 2016 Dec 15;6:38923. doi: 10.1038/srep38923.


Formate-derived H2 , a driver of hydrogenotrophic processes in the root-zone of a methane-emitting fen.

Hunger S, Schmidt O, Gößner AS, Drake HL.

Environ Microbiol. 2016 Sep;18(9):3106-19. doi: 10.1111/1462-2920.13301. Epub 2016 Apr 28.


Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens.

Schmidt O, Hink L, Horn MA, Drake HL.

ISME J. 2016 Aug;10(8):1954-66. doi: 10.1038/ismej.2015.256. Epub 2016 Jan 15.


PilZ Domain Proteins of the Plant Pathogen Xanthomonas oryzae pv. oryzae Function Differentially in Virulence.

Drake HL.

Appl Environ Microbiol. 2015 Jul;81(13):4233-4. doi: 10.1128/AEM.01322-15. Epub 2015 Apr 24. No abstract available.


Anaerobic trophic interactions of contrasting methane-emitting mire soils: processes versus taxa.

Hunger S, Gößner AS, Drake HL.

FEMS Microbiol Ecol. 2015 May;91(5). pii: fiv045. doi: 10.1093/femsec/fiv045. Epub 2015 Apr 14.


Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil.

Schulz K, Hunger S, Brown GG, Tsai SM, Cerri CC, Conrad R, Drake HL.

ISME J. 2015 Aug;9(8):1778-92. doi: 10.1038/ismej.2014.262. Epub 2015 Jan 23.


Botulinum Neurotoxin Subtype A4 Originating from Nontoxigenic Clostridium botulinum.

Schaffner DW, Drake HL.

Appl Environ Microbiol. 2014 Dec;80(23):7131-2. doi: 10.1128/AEM.03001-14. Epub 2014 Sep 19. No abstract available.


Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil.

Schmidt O, Horn MA, Kolb S, Drake HL.

Environ Microbiol. 2015 Mar;17(3):720-34. doi: 10.1111/1462-2920.12507. Epub 2014 Jun 9.


Consumers of 4-chloro-2-methylphenoxyacetic acid from agricultural soil and drilosphere harbor cadA, r/sdpA, and tfdA-like gene encoding oxygenases.

Liu YJ, Liu SJ, Drake HL, Horn MA.

FEMS Microbiol Ecol. 2013 Oct;86(1):114-29. doi: 10.1111/1574-6941.12144. Epub 2013 May 23.


Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs.

Stacheter A, Noll M, Lee CK, Selzer M, Glowik B, Ebertsch L, Mertel R, Schulz D, Lampert N, Drake HL, Kolb S.

ISME J. 2013 May;7(5):1051-64. doi: 10.1038/ismej.2012.167. Epub 2012 Dec 20.


Microbiology of Lonar Lake and other soda lakes.

Antony CP, Kumaresan D, Hunger S, Drake HL, Murrell JC, Shouche YS.

ISME J. 2013 Mar;7(3):468-76. doi: 10.1038/ismej.2012.137. Epub 2012 Nov 22. Review. Erratum in: ISME J. 2013 Jun;7(6):1252.


Emission of nitrous oxide and dinitrogen by diverse earthworm families from Brazil and resolution of associated denitrifying and nitrate-dissimilating taxa.

Depkat-Jakob PS, Brown GG, Tsai SM, Horn MA, Drake HL.

FEMS Microbiol Ecol. 2013 Feb;83(2):375-91. doi: 10.1111/j.1574-6941.2012.01476.x. Epub 2012 Sep 17.


Emission of methane by Eudrilus eugeniae and other earthworms from Brazil.

Depkat-Jakob PS, Hunger S, Schulz K, Brown GG, Tsai SM, Drake HL.

Appl Environ Microbiol. 2012 Apr;78(8):3014-9. doi: 10.1128/AEM.07949-11. Epub 2012 Feb 17.


Impairment of cellulose- and cellobiose-degrading soil Bacteria by two acidic herbicides.

Schellenberger S, Drake HL, Kolb S.

FEMS Microbiol Lett. 2012 Feb;327(1):60-5. doi: 10.1111/j.1574-6968.2011.02460.x. Epub 2011 Dec 5.


Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture.

Foesel BU, Drake HL, Schramm A.

Syst Appl Microbiol. 2011 Nov;34(7):498-502. doi: 10.1016/j.syapm.2011.08.006. Epub 2011 Sep 29.


Novel [NiFe]- and [FeFe]-hydrogenase gene transcripts indicative of active facultative aerobes and obligate anaerobes in earthworm gut contents.

Schmidt O, Wüst PK, Hellmuth S, Borst K, Horn MA, Drake HL.

Appl Environ Microbiol. 2011 Sep;77(17):5842-50. doi: 10.1128/AEM.05432-11. Epub 2011 Jul 22.


Trophic links between the acetogen Clostridium glycolicum KHa and the fermentative anaerobe Bacteroides xylanolyticus KHb, isolated from Hawaiian forest soil.

Hunger S, Gössner AS, Drake HL.

Appl Environ Microbiol. 2011 Sep;77(17):6281-5. doi: 10.1128/AEM.05519-11. Epub 2011 Jul 15.


Functionally redundant cellobiose-degrading soil bacteria respond differentially to oxygen.

Schellenberger S, Drake HL, Kolb S.

Appl Environ Microbiol. 2011 Sep;77(17):6043-8. doi: 10.1128/AEM.00564-11. Epub 2011 Jul 8.


Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil.

Hunger S, Schmidt O, Hilgarth M, Horn MA, Kolb S, Conrad R, Drake HL.

Appl Environ Microbiol. 2011 Jun;77(11):3773-85. doi: 10.1128/AEM.00282-11. Epub 2011 Apr 8.


Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs.

Wieczorek AS, Drake HL, Kolb S.

FEMS Microbiol Ecol. 2011 Jul;77(1):28-39. doi: 10.1111/j.1574-6941.2011.01080.x. Epub 2011 Apr 13.


Alphaproteobacteria dominate active 2-methyl-4-chlorophenoxyacetic acid herbicide degraders in agricultural soil and drilosphere.

Liu YJ, Liu SJ, Drake HL, Horn MA.

Environ Microbiol. 2011 Apr;13(4):991-1009. doi: 10.1111/j.1462-2920.2010.02405.x. Epub 2011 Jan 10.


The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders.

Liu YJ, Zaprasis A, Liu SJ, Drake HL, Horn MA.

ISME J. 2011 Mar;5(3):473-85. doi: 10.1038/ismej.2010.140. Epub 2010 Aug 26.


Effect of earthworm feeding guilds on ingested dissimilatory nitrate reducers and denitrifiers in the alimentary canal of the earthworm.

Depkat-Jakob PS, Hilgarth M, Horn MA, Drake HL.

Appl Environ Microbiol. 2010 Sep;76(18):6205-14. doi: 10.1128/AEM.01373-10. Epub 2010 Jul 23.


Clostridiaceae and Enterobacteriaceae as active fermenters in earthworm gut content.

Wüst PK, Horn MA, Drake HL.

ISME J. 2011 Jan;5(1):92-106. doi: 10.1038/ismej.2010.99. Epub 2010 Jul 8.


Different atmospheric methane-oxidizing communities in European beech and Norway spruce soils.

Degelmann DM, Borken W, Drake HL, Kolb S.

Appl Environ Microbiol. 2010 May;76(10):3228-35. doi: 10.1128/AEM.02730-09. Epub 2010 Mar 26.


Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen.

Schmidt O, Drake HL, Horn MA.

Appl Environ Microbiol. 2010 Mar;76(6):2027-31. doi: 10.1128/AEM.02895-09. Epub 2010 Jan 29.


Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen.

Schellenberger S, Kolb S, Drake HL.

Environ Microbiol. 2010 Apr;12(4):845-61. doi: 10.1111/j.1462-2920.2009.02128.x. Epub 2009 Dec 27.


Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen.

Palmer K, Drake HL, Horn MA.

Appl Environ Microbiol. 2010 Feb;76(4):1125-34. doi: 10.1128/AEM.02256-09. Epub 2009 Dec 18.


Abundance of novel and diverse tfdA-like genes, encoding putative phenoxyalkanoic acid herbicide-degrading dioxygenases, in soil.

Zaprasis A, Liu YJ, Liu SJ, Drake HL, Horn MA.

Appl Environ Microbiol. 2010 Jan;76(1):119-28. doi: 10.1128/AEM.01727-09. Epub 2009 Oct 30.


Intermediary ecosystem metabolism as a main driver of methanogenesis in acidic wetland soil.

Drake HL, Horn MA, Wüst PK.

Environ Microbiol Rep. 2009 Oct;1(5):307-18. doi: 10.1111/j.1758-2229.2009.00050.x. Epub 2009 Jul 21.


Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers.

Palmer K, Drake HL, Horn MA.

Appl Environ Microbiol. 2009 Aug;75(15):5170-4. doi: 10.1128/AEM.00254-09. Epub 2009 Jun 5.


Enterobacteriaceae facilitate the anaerobic degradation of glucose by a forest soil.

Degelmann DM, Kolb S, Dumont M, Murrell JC, Drake HL.

FEMS Microbiol Ecol. 2009 Jun;68(3):312-9. doi: 10.1111/j.1574-6941.2009.00681.x.


Gut-associated denitrification and in vivo emission of nitrous oxide by the earthworm families megascolecidae and lumbricidae in new zealand.

Wüst PK, Horn MA, Henderson G, Janssen PH, Rehm BH, Drake HL.

Appl Environ Microbiol. 2009 Jun;75(11):3430-6. doi: 10.1128/AEM.00304-09. Epub 2009 Apr 3.


Trophic links between fermenters and methanogens in a moderately acidic fen soil.

Wüst PK, Horn MA, Drake HL.

Environ Microbiol. 2009 Jun;11(6):1395-409. doi: 10.1111/j.1462-2920.2009.01867.x. Epub 2009 Feb 13.


In situ hydrogen and nitrous oxide as indicators of concomitant fermentation and denitrification in the alimentary canal of the earthworm Lumbricus terrestris.

Wüst PK, Horn MA, Drake HL.

Appl Environ Microbiol. 2009 Apr;75(7):1852-9. doi: 10.1128/AEM.02745-08. Epub 2009 Feb 5.


Carbon metabolism of the moderately acid-tolerant acetogen Clostridium drakei isolated from peat.

Gössner AS, Picardal F, Tanner RS, Drake HL.

FEMS Microbiol Lett. 2008 Oct;287(2):236-42. doi: 10.1111/j.1574-6968.2008.01313.x. Epub 2008 Aug 15.


Corynebacterium glutamicum contains 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases that display novel biochemical features.

Liu YJ, Li PP, Zhao KX, Wang BJ, Jiang CY, Drake HL, Liu SJ.

Appl Environ Microbiol. 2008 Sep;74(17):5497-503. doi: 10.1128/AEM.00262-08. Epub 2008 Jul 11.


Anaerobic consumers of monosaccharides in a moderately acidic fen.

Hamberger A, Horn MA, Dumont MG, Murrell JC, Drake HL.

Appl Environ Microbiol. 2008 May;74(10):3112-20. doi: 10.1128/AEM.00193-08. Epub 2008 Mar 31.


Old acetogens, new light.

Drake HL, Gössner AS, Daniel SL.

Ann N Y Acad Sci. 2008 Mar;1125:100-28. doi: 10.1196/annals.1419.016. Review.


Catabolic pathway for the production of skatole and indoleacetic acid by the acetogen Clostridium drakei, Clostridium scatologenes, and swine manure.

Whitehead TR, Price NP, Drake HL, Cotta MA.

Appl Environ Microbiol. 2008 Mar;74(6):1950-3. doi: 10.1128/AEM.02458-07. Epub 2008 Jan 25.


Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm.

Foesel BU, Gieseke A, Schwermer C, Stief P, Koch L, Cytryn E, de la Torré JR, van Rijn J, Minz D, Drake HL, Schramm A.

FEMS Microbiol Ecol. 2008 Feb;63(2):192-204. Epub 2007 Dec 15.


pH gradient-induced heterogeneity of Fe(III)-reducing microorganisms in coal mining-associated lake sediments.

Blöthe M, Akob DM, Kostka JE, Göschel K, Drake HL, Küsel K.

Appl Environ Microbiol. 2008 Feb;74(4):1019-29. Epub 2007 Dec 14. Erratum in: Appl Environ Microbiol. 2008 Nov,74(22):7100.


Simultaneous biodegradation of nitrogen-containing aromatic compounds in a sequencing batch bioreactor.

Liu XY, Wang BJ, Jiang CY, Zhao KX, Drake HL, Liu SJ.

J Environ Sci (China). 2007;19(5):530-5.


Geminicoccus roseus gen. nov., sp. nov., an aerobic phototrophic Alphaproteobacterium isolated from a marine aquaculture biofilter.

Foesel BU, Gössner AS, Drake HL, Schramm A.

Syst Appl Microbiol. 2007 Dec;30(8):581-6. Epub 2007 Jul 23.


As the worm turns: the earthworm gut as a transient habitat for soil microbial biomes.

Drake HL, Horn MA.

Annu Rev Microbiol. 2007;61:169-89. Review.


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