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Items: 26

1.

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.

Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ.

Microbiome. 2019 Aug 14;7(1):114. doi: 10.1186/s40168-019-0727-1.

2.

Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants.

Wilschut RA, Geisen S, Martens H, Kostenko O, de Hollander M, Ten Hooven FC, Weser C, Snoek LB, Bloem J, Caković D, Čelik T, Koorem K, Krigas N, Manrubia M, Ramirez KS, Tsiafouli MA, Vreš B, van der Putten WH.

Glob Chang Biol. 2019 Aug;25(8):2714-2726. doi: 10.1111/gcb.14657. Epub 2019 May 20.

3.

The wild side of plant microbiomes.

Pérez-Jaramillo JE, Carrión VJ, de Hollander M, Raaijmakers JM.

Microbiome. 2018 Aug 16;6(1):143. doi: 10.1186/s40168-018-0519-z. No abstract available.

4.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

Ramirez KS, Knight CG, de Hollander M, Brearley FQ, Constantinides B, Cotton A, Creer S, Crowther TW, Davison J, Delgado-Baquerizo M, Dorrepaal E, Elliott DR, Fox G, Griffiths RI, Hale C, Hartman K, Houlden A, Jones DL, Krab EJ, Maestre FT, McGuire KL, Monteux S, Orr CH, van der Putten WH, Roberts IS, Robinson DA, Rocca JD, Rowntree J, Schlaeppi K, Shepherd M, Singh BK, Straathof AL, Bhatnagar JM, Thion C, van der Heijden MGA, de Vries FT.

Nat Microbiol. 2018 Feb;3(2):189-196. doi: 10.1038/s41564-017-0062-x. Epub 2017 Nov 20.

PMID:
29158606
5.

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function.

Mendes LW, Raaijmakers JM, de Hollander M, Mendes R, Tsai SM.

ISME J. 2018 Jan;12(1):212-224. doi: 10.1038/ismej.2017.158. Epub 2017 Oct 13.

6.

Methanogens predominate in natural corrosion protective layers on metal sheet piles.

Kip N, Jansen S, Leite MFA, de Hollander M, Afanasyev M, Kuramae EE, Veen JAV.

Sci Rep. 2017 Sep 19;7(1):11899. doi: 10.1038/s41598-017-11244-7.

7.

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits.

Pérez-Jaramillo JE, Carrión VJ, Bosse M, Ferrão LFV, de Hollander M, Garcia AAF, Ramírez CA, Mendes R, Raaijmakers JM.

ISME J. 2017 Oct;11(10):2244-2257. doi: 10.1038/ismej.2017.85. Epub 2017 Jun 6.

8.

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture.

Hannula SE, Morriën E, de Hollander M, van der Putten WH, van Veen JA, de Boer W.

ISME J. 2017 Oct;11(10):2294-2304. doi: 10.1038/ismej.2017.90. Epub 2017 Jun 6.

9.

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

Dassen S, Cortois R, Martens H, de Hollander M, Kowalchuk GA, van der Putten WH, De Deyn GB.

Mol Ecol. 2017 Aug;26(15):4085-4098. doi: 10.1111/mec.14175. Epub 2017 Jun 2.

PMID:
28489329
10.

Soil networks become more connected and take up more carbon as nature restoration progresses.

Morriën E, Hannula SE, Snoek LB, Helmsing NR, Zweers H, de Hollander M, Soto RL, Bouffaud ML, Buée M, Dimmers W, Duyts H, Geisen S, Girlanda M, Griffiths RI, Jørgensen HB, Jensen J, Plassart P, Redecker D, Schmelz RM, Schmidt O, Thomson BC, Tisserant E, Uroz S, Winding A, Bailey MJ, Bonkowski M, Faber JH, Martin F, Lemanceau P, de Boer W, van Veen JA, van der Putten WH.

Nat Commun. 2017 Feb 8;8:14349. doi: 10.1038/ncomms14349.

11.

Successive DNA extractions improve characterization of soil microbial communities.

Dimitrov MR, Veraart AJ, de Hollander M, Smidt H, van Veen JA, Kuramae EE.

PeerJ. 2017 Feb 1;5:e2915. doi: 10.7717/peerj.2915. eCollection 2017.

12.

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System.

Lupatini M, Korthals GW, de Hollander M, Janssens TK, Kuramae EE.

Front Microbiol. 2017 Jan 4;7:2064. doi: 10.3389/fmicb.2016.02064. eCollection 2016.

13.

Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere.

Yan Y, Kuramae EE, de Hollander M, Klinkhamer PG, van Veen JA.

ISME J. 2017 Jan;11(1):56-66. doi: 10.1038/ismej.2016.108. Epub 2016 Aug 2.

14.

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland.

Cassman NA, Leite MF, Pan Y, de Hollander M, van Veen JA, Kuramae EE.

Sci Rep. 2016 Mar 29;6:23680. doi: 10.1038/srep23680.

15.

Context dependency and saturating effects of loss of rare soil microbes on plant productivity.

Hol WH, de Boer W, de Hollander M, Kuramae EE, Meisner A, van der Putten WH.

Front Plant Sci. 2015 Jun 30;6:485. doi: 10.3389/fpls.2015.00485. eCollection 2015.

16.

Soil microbiome responses to the short-term effects of Amazonian deforestation.

Navarrete AA, Tsai SM, Mendes LW, Faust K, de Hollander M, Cassman NA, Raes J, van Veen JA, Kuramae EE.

Mol Ecol. 2015 May;24(10):2433-48. doi: 10.1111/mec.13172. Epub 2015 Apr 21.

PMID:
25809788
17.

Soil-borne microbiome: linking diversity to function.

Mendes LW, Tsai SM, Navarrete AA, de Hollander M, van Veen JA, Kuramae EE.

Microb Ecol. 2015 Jul;70(1):255-65. doi: 10.1007/s00248-014-0559-2. Epub 2015 Jan 14.

PMID:
25586384
18.

Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil.

Pan Y, Cassman N, de Hollander M, Mendes LW, Korevaar H, Geerts RH, van Veen JA, Kuramae EE.

FEMS Microbiol Ecol. 2014 Oct;90(1):195-205. doi: 10.1111/1574-6941.12384. Epub 2014 Aug 21.

19.

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy.

Hiltemann S, Mei H, de Hollander M, Palli I, van der Spek P, Jenster G, Stubbs A.

Gigascience. 2014 Jan 24;3(1):1. doi: 10.1186/2047-217X-3-1.

20.

Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing.

Kuramae EE, Verbruggen E, Hillekens R, de Hollander M, Röling WF, van der Heijden MG, Kowalchuk GA.

PLoS One. 2013 Jul 18;8(7):e69973. doi: 10.1371/journal.pone.0069973. Print 2013.

21.

Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf.

Kuramae EE, Hillekens RH, de Hollander M, van der Heijden MG, van den Berg M, van Straalen NM, Kowalchuk GA.

FEMS Microbiol Ecol. 2013 Jun;84(3):519-31. doi: 10.1111/1574-6941.12080. Epub 2013 Feb 19.

22.

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils.

Navarrete AA, Kuramae EE, de Hollander M, Pijl AS, van Veen JA, Tsai SM.

FEMS Microbiol Ecol. 2013 Mar;83(3):607-21. doi: 10.1111/1574-6941.12018. Epub 2012 Oct 19.

23.

Testing potential effects of maize expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) on mycorrhizal fungal communities via DNA- and RNA-based pyrosequencing and molecular fingerprinting.

Verbruggen E, Kuramae EE, Hillekens R, de Hollander M, Kiers ET, Röling WF, Kowalchuk GA, van der Heijden MG.

Appl Environ Microbiol. 2012 Oct;78(20):7384-92. Epub 2012 Aug 10.

24.

A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity.

Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA.

PLoS One. 2012;7(2):e30600. doi: 10.1371/journal.pone.0030600. Epub 2012 Feb 15.

25.

Mitochondrial proteome evolution and genetic disease.

Huynen MA, de Hollander M, Szklarczyk R.

Biochim Biophys Acta. 2009 Dec;1792(12):1122-9. doi: 10.1016/j.bbadis.2009.03.005. Epub 2009 Mar 26. Review.

26.

Can subtle changes in gene expression be consistently detected with different microarray platforms?

Pedotti P, 't Hoen PA, Vreugdenhil E, Schenk GJ, Vossen RH, Ariyurek Y, de Hollander M, Kuiper R, van Ommen GJ, den Dunnen JT, Boer JM, de Menezes RX.

BMC Genomics. 2008 Mar 10;9:124. doi: 10.1186/1471-2164-9-124.

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