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Items: 38

1.

A Bioinformatics Guide to Plant Microbiome Analysis.

Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T.

Front Plant Sci. 2019 Oct 23;10:1313. doi: 10.3389/fpls.2019.01313. eCollection 2019. Review.

2.

Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity.

Zheng Q, Hu Y, Zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichorst SA, Woebken D, Richter A, Wanek W.

Soil Biol Biochem. 2019 Sep;136:107521. doi: 10.1016/j.soilbio.2019.107521. Epub 2019 Jun 26.

3.

Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons.

Wang B, Qin W, Ren Y, Zhou X, Jung MY, Han P, Eloe-Fadrosh EA, Li M, Zheng Y, Lu L, Yan X, Ji J, Liu Y, Liu L, Heiner C, Hall R, Martens-Habbena W, Herbold CW, Rhee SK, Bartlett DH, Huang L, Ingalls AE, Wagner M, Stahl DA, Jia Z.

ISME J. 2019 Aug 28. doi: 10.1038/s41396-019-0493-x. [Epub ahead of print]

PMID:
31462715
4.

Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon "Candidatus Nitrosotenuis uzonensis" at Different Growth Temperatures.

Bale NJ, Palatinszky M, Rijpstra WIC, Herbold CW, Wagner M, Sinninghe Damsté JS.

Appl Environ Microbiol. 2019 Oct 1;85(20). pii: e01332-19. doi: 10.1128/AEM.01332-19. Print 2019 Oct 15.

5.

Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6FT, Isolated from Marine Sediment in the Baltic Sea.

Hausmann B, Vandieken V, Pjevac P, Schreck K, Herbold CW, Loy A.

Microbiol Resour Announc. 2019 Aug 1;8(31). pii: e00427-19. doi: 10.1128/MRA.00427-19.

6.

Diversity decoupled from sulfur isotope fractionation in a sulfate-reducing microbial community.

Colangelo-Lillis J, Pelikan C, Herbold CW, Altshuler I, Loy A, Whyte LG, Wing BA.

Geobiology. 2019 Nov;17(6):660-675. doi: 10.1111/gbi.12356. Epub 2019 Jul 21.

PMID:
31328364
7.

Draft Genome Sequence of Desulfosporosinus sp. Strain Sb-LF, Isolated from an Acidic Peatland in Germany.

Hausmann B, Pjevac P, Huemer M, Herbold CW, Pester M, Loy A.

Microbiol Resour Announc. 2019 Jul 18;8(29). pii: e00428-19. doi: 10.1128/MRA.00428-19.

8.

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta.

Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M.

Environ Microbiol. 2019 Oct;21(10):3831-3854. doi: 10.1111/1462-2920.14732. Epub 2019 Jul 25.

9.

Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon.

Jung MY, Gwak JH, Rohe L, Giesemann A, Kim JG, Well R, Madsen EL, Herbold CW, Wagner M, Rhee SK.

ISME J. 2019 Oct;13(10):2633-2638. doi: 10.1038/s41396-019-0460-6. Epub 2019 Jun 21.

10.

Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment.

Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA.

Nat Microbiol. 2019 Feb;4(2):234-243. doi: 10.1038/s41564-018-0316-2. Epub 2018 Dec 10.

11.

Microbial temperature sensitivity and biomass change explain soil carbon loss with warming.

Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, Janssens IA, Sigurdsson BD, Richter A.

Nat Clim Chang. 2018 Oct;8(10):885-889. doi: 10.1038/s41558-018-0259-x. Epub 2018 Sep 17.

12.

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.

Nguyen NL, Yu WJ, Gwak JH, Kim SJ, Park SJ, Herbold CW, Kim JG, Jung MY, Rhee SK.

Front Microbiol. 2018 Aug 27;9:1982. doi: 10.3389/fmicb.2018.01982. eCollection 2018.

13.

Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources.

Matheus Carnevali PB, Herbold CW, Hand KP, Priscu JC, Murray AE.

Front Microbiol. 2018 Jun 7;9:1192. doi: 10.3389/fmicb.2018.01192. eCollection 2018.

14.

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data.

Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold CW, Eichorst SA, Woebken D.

Front Microbiol. 2018 Apr 30;9:703. doi: 10.3389/fmicb.2018.00703. eCollection 2018.

15.

Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.

Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, Kirkegaard RH, de la Torre JR, Daims H, Wagner M.

Front Microbiol. 2018 Feb 14;9:193. doi: 10.3389/fmicb.2018.00193. eCollection 2018.

16.

Peatland Acidobacteria with a dissimilatory sulfur metabolism.

Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A.

ISME J. 2018 Jun;12(7):1729-1742. doi: 10.1038/s41396-018-0077-1. Epub 2018 Feb 23.

17.

Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.

Hausmann B, Pjevac P, Schreck K, Herbold CW, Daims H, Wagner M, Loy A.

Genome Announc. 2018 Jan 25;6(4). pii: e01524-17. doi: 10.1128/genomeA.01524-17.

18.

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C.

Environ Microbiol. 2017 Dec;19(12):4939-4952. doi: 10.1111/1462-2920.13971. Epub 2017 Dec 4.

19.

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters.

Lesaulnier CC, Herbold CW, Pelikan C, Berry D, Gérard C, Le Coz X, Gagnot S, Niggemann J, Dittmar T, Singer GA, Loy A.

Microbiome. 2017 Sep 22;5(1):126. doi: 10.1186/s40168-017-0344-9.

20.

AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment.

Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Lücker S, Wagner M, Daims H.

Front Microbiol. 2017 Aug 4;8:1508. doi: 10.3389/fmicb.2017.01508. eCollection 2017.

21.

Corrigendum: A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.

Herbold CW, Pelikan C, Kuzyk O, Hausmann B, Angel R, Berry D, Loy A.

Front Microbiol. 2016 Jun 6;7:870. doi: 10.3389/fmicb.2016.00870. eCollection 2016.

22.

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics.

Pelikan C, Herbold CW, Hausmann B, Müller AL, Pester M, Loy A.

Environ Microbiol. 2016 Sep;18(9):2994-3009. doi: 10.1111/1462-2920.13139. Epub 2016 Jan 26.

PMID:
26625892
23.

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.

Herbold CW, Pelikan C, Kuzyk O, Hausmann B, Angel R, Berry D, Loy A.

Front Microbiol. 2015 Jul 16;6:731. doi: 10.3389/fmicb.2015.00731. eCollection 2015. Erratum in: Front Microbiol. 2016;7:870.

24.

Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds.

Archer SD, McDonald IR, Herbold CW, Lee CK, Cary CS.

Front Microbiol. 2015 May 27;6:485. doi: 10.3389/fmicb.2015.00485. eCollection 2015.

25.

Characterisation of bacterioplankton communities in the meltwater ponds of Bratina Island, Victoria Land, Antarctica.

Archer SD, McDonald IR, Herbold CW, Cary SC.

FEMS Microbiol Ecol. 2014 Aug;89(2):451-64. doi: 10.1111/1574-6941.12358. Epub 2014 Jun 17.

26.

Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica.

Herbold CW, Lee CK, McDonald IR, Cary SC.

Nat Commun. 2014 May 20;5:3875. doi: 10.1038/ncomms4875.

PMID:
24846491
27.

Influence of soil properties on archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica.

Richter I, Herbold CW, Lee CK, McDonald IR, Barrett JE, Cary SC.

FEMS Microbiol Ecol. 2014 Aug;89(2):347-59. doi: 10.1111/1574-6941.12322. Epub 2014 Apr 16.

28.

Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions.

Lee KC, Herbold CW, Dunfield PF, Morgan XC, McDonald IR, Stott MB.

Appl Environ Microbiol. 2013 Apr;79(7):2484-7. doi: 10.1128/AEM.03333-12. Epub 2013 Feb 1.

29.

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, Cary SC.

PLoS One. 2012;7(9):e44224. doi: 10.1371/journal.pone.0044224. Epub 2012 Sep 6.

30.

Genome beginnings: rooting the tree of life.

Lake JA, Skophammer RG, Herbold CW, Servin JA.

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2177-85. doi: 10.1098/rstb.2009.0035. Review.

31.

Evidence for a new root of the tree of life.

Lake JA, Servin JA, Herbold CW, Skophammer RG.

Syst Biol. 2008 Dec;57(6):835-43. doi: 10.1080/10635150802555933.

PMID:
19085327
32.

Evidence excluding the root of the tree of life from the actinobacteria.

Servin JA, Herbold CW, Skophammer RG, Lake JA.

Mol Biol Evol. 2008 Jan;25(1):1-4. Epub 2007 Nov 13.

PMID:
18003601
33.

Evidence for a gram-positive, eubacterial root of the tree of life.

Skophammer RG, Servin JA, Herbold CW, Lake JA.

Mol Biol Evol. 2007 Aug;24(8):1761-8. Epub 2007 May 19.

PMID:
17513883
34.

Rooting the tree of life using nonubiquitous genes.

Lake JA, Herbold CW, Rivera MC, Servin JA, Skophammer RG.

Mol Biol Evol. 2007 Jan;24(1):130-6. Epub 2006 Oct 5.

PMID:
17023560
35.

Evidence that the root of the tree of life is not within the Archaea.

Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA.

Mol Biol Evol. 2006 Sep;23(9):1648-51. Epub 2006 Jun 26.

PMID:
16801395
36.

Decoding the genomic tree of life.

Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA.

Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6608-13. Epub 2005 Apr 25.

37.

Dissolved iron cycling in the subterranean estuary of a coastal bay: Waquoit Bay, Massachusetts.

Testa JM, Charette MA, Sholkovitz ER, Allen MC, Rago A, Herbold CW.

Biol Bull. 2002 Oct;203(2):255-6. No abstract available.

PMID:
12414608
38.

Cytochrome c unfolding on an anionic surface.

Herbold CW, Miller JH, Goheen SC.

J Chromatogr A. 1999 Nov 26;863(2):137-46.

PMID:
10593494

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