Dr. Heiko Nacke Postdoc
Address
Georg-August University of Göttingen   Institute of Microbiology and Genetics   Department of Genomic and Applied Microbiology   Grisebachstr. 8, 37077 Göttingen, Germany
Office
Room: 3.127
Tel: ++49 (0)551 39 23841
E-Mail: hnacke(at)gwdg.de

Curriculum Vitae

Major Research Interests

• Analysis of factors controlling soil microbial diversity and community composition
  Soil harbors an enormous pool of microorganisms with probably the highest level of prokaryotic diversity among Earth’s habitats. The impact of different environmental factors such as land use on soil microbial diversity and community composition is explored by applying appropriate culture-independent and bioinformatics methods. Besides total microbial community analyses, specific groups such as nitrifiers or antibiotic-resistant bacteria are analyzed.
• Investigation of habitat-specific characteristics and activities of soil microorganisms
  Microorganisms mediate nearly all biogeochemical cycles in terrestrial ecosystems, play a key role in soil formation and are responsible for most nutrient transformations in soil. Based on e.g. metatranscriptomic approaches the manifold activities of microorganisms in soil are investigated. In addition, target soil microbes are cultured using appropriate enrichment medium and analyzed within physiological experiments.
• Metagenomic identification of novel genes and gene products hidden in soil ecosystems
  The mainly unexplored pool of microorganisms in soil represents an almost unlimited source for the discovery of genes encoding e.g. antibiotic resistance or enzymes with industrially relevant characteristics. To identify target genes and gene products, screening of soil-derived small-insert and large-insert metagenomic libraries is performed, and molecular analyses as well as biochemical characterization of identified biomolecules are carried out.

Research Project(s)

• Assessment of the functional diversity of soil microbial communities in the German Biodiversity Exploratories by metagenomics

Publications

Castillo Villamizar GA, Nacke H, Daniel R (2023) Functional metagenomics approach for the discovery of novel genes encoding phosphatase activity. Methods Mol Biol 2555:103-114 (doi:10.1007/978-1-0716-2795-2_7).

Arif S, Nacke H, Hoppert M (2021) Metagenome-assembled genome sequences of a biofilm derived from Marsberg copper mine. Microbiol Resour Announc 10(2):e01253-20 (doi:10.1128/MRA.01253-20).

Arif S, Willenberg C, Dreyer A, Nacke H, Hoppert M (2021) Sasso Pisano geothermal field environment harbours diverse Ktedonobacteria representatives and illustrates habitat-specific adaptations. Microorganisms 9(7):1402 (doi:10.3390/microorganisms9071402).

Willms IM, Grote M, Kocatürk M, Singhoff L, Kraft AA, Bolz SH, Nacke H (2021) Novel soil-derived beta-lactam, chloramphenicol, fosfomycin and trimethoprim resistance genes revealed by functional metagenomics. Antibiotics 10(4):378 (doi:10.3390/antibiotics10040378).

Willms IM, Bolz SH, Yuan J, Krafft L, Schneider D, Schöning I, Schrumpf M, Nacke H (2021) The ubiquitous soil verrucomicrobial clade ‘Candidatus Udaeobacter’ shows preferences for acidic pH. Environ Microbiol Rep 13(6):878-883 (doi:10.1111/1758-2229.13006).

Nacke H, Kirck LL,Schwarz S, Schneider D, Poehlein A, Daniel R (2020) Metagenome sequences of a wastewater treatment plant digester sludge-derived enrichment culture. Microbiol Resour Announc 9(32):e00712-20 (doi:10.1128/MRA.00712-20).

Willms IM, Yuan J, Penone C, Goldmann K, Vogt J, Wubet T, Schöning I, Schrumpf M, Buscot F, Nacke H (2020) Distribution of medically relevant antibiotic resistance genes and mobile genetic elements in soils of temperate forests and grasslands varying in land use. Genes 11(2):150 (doi:10.3390/genes11020150).

Willms IM, Rudolph AY, Göschel I, Bolz SH, Schneider D, Penone C, Poehlein A, Schöning I, Nacke H (2020) Globally abundant “Candidatus Udaeobacter” benefits from release of antibiotics in soil and potentially performs trace gas scavenging. mSphere 5(4):e00186-20 (doi:10.1128/mSphere.00186-20).

Winkler L, Münker MF, Brunotte S, Rohlmann L, Alfageme AD, Poehlein A, Hoppert M, Reitner J, Nacke H (2020) Metagenome-assembled genome sequences from an anoxygenic photosynthetic consortium involved in sulfur cycling. Microbiol Resour Announc 9(38):e00819-20 (doi:10.1128/MRA.00819-20).

Castillo Villamizar GA, Nacke H, Boehning M, Herz K, Daniel R (2019) Functional metagenomics reveals an overlooked diversity and novel features of soil-derived bacterial phosphatases and phytases. mBio 10:e01966-18 (doi:10.1128/mBio.01966-18).

Castillo Villamizar GA, Nacke H, Griese L, Tabernero L, Funkner K, Daniel R (2019) Characteristics of the first protein tyrosine phosphatase with phytase activity from a soil metagenome. Genes 10:101 (doi:10.3390/genes10020101).

Castillo Villamizar GA, Funkner K, Nacke H, Foerster K, Daniel R (2019) Functional metagenomics reveals a new catalytic domain, the metallo-β-lactamase superfamily domain, associated with phytase activity. mSphere 4(3):e00167-19 (doi:10.1128/mSphere.00167-19).

Willms IM, Kamran A, Aßmann NF, Krone D, Bolz SH, Fiedler F, Nacke H (2019) Discovery of novel antibiotic resistance determinants in forest and grassland soil metagenomes. Front Microbiol 10:460 (doi:10.3389/fmicb.2019.00460).

Djukic M, Erler S, Leimbach A, Grossar D, Charrière J-D, Gauthier L, Hartken D, Dietrich S, Nacke H, Daniel R, Poehlein A (2018) Comparative genomics and description of putative virulence factors of Melissococcus plutonius, the causative agent of European foulbrood disease in honey bees. Genes 9:419 (doi:10.3390/genes9080419).

Köbke S, Senbayram M, Pfeiffer B, Nacke H, Dittert K (2018) Post-harvest N₂O and CO₂ emissions related to plant residue incorporation of oilseed rape and barley straw depend on soil NO₃^- content. Soil Till Res 179:105-113 (doi:10.1016/j.still.2018.01.013).

Nacke H, Daniel R, Poehlein A (2017) Genome sequence of creatinine-fermenting Tissierella creatinophila strain KRE 4^T (DSM 6911). Genome Announc 5(12):e00051-17 (doi:10.1128/genomeA.00051-17).

Nacke H, Schöning I, Schindler M, Schrumpf M, Daniel R, Nicol GW, Prosser JI (2017) Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity. FEMS Microbiol Ecol 93:11 (doi:10.1093/femsec/fix144).

Villamizar GA, Nacke H, Daniel R (2017) Function-based metagenomic library screening and heterologous expression strategy for genes encoding phosphatase activity. Methods Mol Biol 1539:249-260 (doi:10.1007/978-1-4939-6691-2_16).

Boch S, Allan E, Birkhofer B, Bossdorf O, Blüthgen N, Christ-Breulmann S, Diekötter T, Dormann CF, Gossner MM, Hallmann C, Hemp A, Hölzel N, Jung K, Klaus VH, Klein AM, Kleinebecker T, Lange M, Müller J, Nacke H, Prati D, Renner SC, Rothenwöhrer C, Schall P, Schulze E-D, Socher SA, Tscharntke T, Türke M, Weiner CN, Weisser WW, Westphal C, Wolters V, Wubet T, Fischer M (2016) Extensive und jährlich wechselnde Nutzungs-intensität fördert den Artenreichtum im Grünland. ANLiegen Natur 38/1: (abstract)

Kaiser K, Wemheuer B, Korolkow V , Wemheuer F, Nacke H, Schöning I, Schrumpf M, Daniel R (2016) Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests. Sci Rep 6:33696 (doi:10.1038/srep33696).

Nacke H, Goldmann K, Schöning I, Pfeiffer B, Kaiser K, Castillo-Villamizar GA, Schrumpf M, Buscot F, Daniel R, Wubet T (2016) Fine spatial scale variation of soil microbial communities under European beech and Norway spruce. Front Microbiol 7:2067 (doi:10.3389/fmicb.2016.02067).

Wüst PK, Nacke H, Kaiser K, Marhan S, Sikorski J, Kandeler E, Daniel R, Overmann J (2016) Estimates of soil bacterial ribosome content and diversity in soils are significantly affected by different nucleic acid extraction methods. Appl Environ Microbiol 82(9):2595-607 (doi:10.1128/AEM.00019-16).

Nacke H, Daniel R (2015) Approaches in metagenome research - progress and challenges. In: Encyclopedia of Metagenomics. SpringerReference (Ed: Nelson, K.). Springer-Verlag Berlin Heidelberg SpringerReference_363415 (doi:10.1007/978-1-4899-7478-5_790).

Schneider D, Engelhaupt M, Allen K, Kurniawan S, Krashevska V, Heinemann M, Nacke H, Wijayanti M, Meryandini A, Corre MD, Scheu S, Daniel R (2015) Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia). Front Microbiol 6:01339 (doi:10.3389/fmicb.2015.01339).

Allan E, Bossdorf O, Dormann CF, Prati D, Gossner MM, Tscharntke T, Blüthgen N, Bellach M, Birkhofer K, Boch S, Böhm S, Börschig C, Chatzinotas A, Christ S, Daniel R, Diekötter T, Fischer C, Friedl T, Glaser K, Hallmann C, Hodac L, Hölzel N, Jung K, Klein AM, Klaus VH, Kleinebecker T, Krauss J, Lange M, Morrisu EK, Müller J, Nacke H, Pašalic E, Rillig MC, Rothenwöhrer C, Schall P, Scherber C, Schulze W, Socher SA, Steckel J, Steffan-Dewenter I, Türke M, Weiner CN, Werner M, Westphal C, Wolters V, Wubet T, Gockel S, Gorke M, Hemp A, Renner SC, Schöning I, Pfeiffer S, König-Ries B, Buscot F, Linsenmair KE, Schulze E-D, Weisser WW, Fischer M (2014) Interannual variation in land-use intensity enhances grassland multidiversity. PNAS 111(1):308-313 (doi:10.1073/pnas.1312213111).

Broszat M, Nacke H, Blasi R, Siebe C , Huebner J, Daniel R, Grohmann E (2014) Wastewater irrigation increases abundance of potentially harmful Gammaproteobacteria in soils from Mezquital Valley, Mexico. Appl Environ Microbiol 80:5282-5291 (doi:10.1128/AEM.01295-14).

Nacke H, Fischer C, Thürmer A, Meinicke P, Daniel R (2014) Land use type significantly affects microbial gene transcription in soil. Microb Ecol 67:919–930 (doi:10.1007/s00248-014-0377-6).

Röske I, Sabra W, Nacke H, Daniel R, Zeng AP, Antranikian G, Sahm K (2014) Microbial community composition and dynamics in high-temperature biogas reactors using industrial bioethanol waste as substrate. Appl Microbiol Biotechnol 98(21):9095-9106 (doi:10.1007/s00253-014-5906-1).

Sahm K, John P, Nacke H, Wemheuer B, Grote R, Daniel R, Antranikian G (2013) High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods. Extremophiles 17:649-662 (doi:10.1007/s00792-013-0548-2).

Birkhofer K, Schöning I, Alt F, Herold N, Klarner B, Maraun M, Marhan S, Oelmann Y, Wubet T, Yurkov A, Begerow D, Berner D, Buscot F, Daniel R, Diekötter T, Ehnes RB, Erdmann G, Fischer C, Foesel B, Groh J, Gutknecht J, Kandeler E, Lang C, Lohaus G, Meyer A, Nacke H, Näther A, Overmann J, Polle A, Pollierer MM, Scheu S, Schloter M, Schulze ED, Schulze W, Weinert J, Weisser WW, Wolters V, Schrumpf M (2012) General relationships between abiotic soil properties and soil biota across spatial scales and different land-use types. PLoS One 7(8):e43292 (doi:10.1371/journal.pone.0043292).

Nacke H, Engelhaupt M, Brady S, Fischer C, Tautzt J, Daniel R (2012) Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes. Biotechnol Lett 34(4):663-75 (doi:10.1007/s10529-011-0830-2).

Pallmann P, Schaarschmidt F, Hothorn LA, Fischer C, Nacke H, Priesnitz KU, Schork NJ (2012) Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices. Mol Ecol Resour 12(6):1068-1078 (doi:10.1111/1755-0998.12004).

Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schöning I, Schrumpf M, Daniel R (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6(2):e17000 (doi:10.1371/journal.pone.0017000).

Nacke H, Will C, Herzog S, Nowka B, Engelhaupt M, Daniel R (2011) Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories. FEMS Microbiol Ecol 78(1):188-201 (doi:10.1111/j.1574-6941.2011.01088.x).

Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R (2010) Horizon-specific bacterial community composition of German grassland soils as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 76:6751-6759 (abstract)

Will C, Nacke H, Thürmer A, Daniel R (2010) Charakterisierung und Nutzung der bakteriellen Diversität in Bodenmetagenomen. GENOMXPRESS 1.10:9-11 (abstract)