Dr. Bernd Wemheuer 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: 3.115
Tel: ++49 (0)551 39 23910
E-Mail: bwemheu(at)gwdg.de

Curriculum Vitae

• 05/2016 - 06/2016  RV Sonne: Pacific Ocean (cruise: SO248)
• 05/2014 – 06/2014  RV Heincke: North Sea (cruise: HE425)
• 03/2012 – 04/2012  RV Polarstern: Southern Ocean (cruise: AntXXVIII-4)
• 07/2011       RV Heincke: North Sea (cruise: HE361)
• 05/2010       RV Heincke: North Sea (cruise: HE327)
• 09/2009       Research stay at the University of the Free State, Bloemfontein, South Africa

Major Research Interests

• Microbial Ecology
  The main focus of my research is microbial ecology and functioning. Together with my wife Franziska Wemheuer (Section of Agricultural Entomology, Department for Crop Sciences), I am investigating distribution patterns, diversity, and functions of microbial life in diverse environments including water, soil and plants. We would like to know what is out there, what they are doing and how they respond to changing environmental conditions. In addition, we are interested in plant-microbe interactions.
• The Roseobacter clade
  The Roseobacter clade is a globally distributed and abundant marine lineage. Although being frequently studied, still little is known about traits contributing to its success. Moreover, genomic features of abundant Roseobacter subclusters are still missing. As part of the CRC51 “Roseobacter”, I contribute to a better understanding of success and distribution of this clade in marine ecosystems.
  For detailed information follow the link: http://www.roseobacter.de/
• Extremophiles
  Sites inhabited by extremophile microorganisms such as hot springs are windows in the past of our planet. Hence, studying these sites and their microbial life shed new insights into the early life on our plant. Due to the low diversity, extreme sites are an ideal place for studying microbial interactions. Moreover, extremophilic archaea and bacteria are a rich source for novel biocatalysts.
• Bioinformatics/Biostatistics
  With the advent of next generation sequencing, the amount of data produced has dramatically increased. This data has to be processed and analyzed. For our collaboration partners, I offer advice in the analysis of especially metagenomic, metatranscriptomic, and amplicon data. Moreover, I am involved in the invention of novel bioinformatic tools and statistical solutions for analysis of NGS-derived data.
  See also my ResearchGate profile: https://www.researchgate.net/profile/Bernd_Wemheuer/

Research Project(s)

• Ecology, Physiology and Molecular Biology of the Roseobacter clade

Publications

Hollensteiner J, Wemheuer F, Schneider D, Pfeiffer B, Wemheuer B (2023) Extraction of total DNA and RNA from marine filter samples and generation of a universal cDNA as universal template for marker gene studies. Methods Mol Biol 2555:13-21 (doi:10.1007/978-1-0716-2795-2_2).

Rao S, Esvaran M, Chen L, Kok C, Keil AD, Gollow I, Simmer K, Wemheuer B, Conway P, Patole S (2023) Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: guidelines for future research. Pediatr Res 93:49–55 (doi:10.1038/s41390-022-02087-8).

Dlugosch L, Poehlein A, Wemheuer B, Pfeiffer B, Badewien TH, Daniel R, Simon M (2022) Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. Nat Commun 11:1186 (doi:10.1038/s41467-022-28128-8).

Rao S, Esvaran M, Chen L, Keil AD, Gollow I, Simmer K, Wemheuer B, Conway P, Patole S (2022) Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: a pilot randomised controlled trial. Pediatr Res 92:1122–1131 (doi:10.1038/s41390-021-01884-x).

Tebbe DA, Geihser S, Wemheuer B, Daniel R, Schäfer H, Engelen B (2022) Seasonal and zonal succession of bacterial communities in North Sea salt marsh sediments. Microorganisms 10:859 (doi:10.3390/ microorganisms10050859).

Nguyen M, Wemheuer B, Laffy PW, Webster NS, Thomas T (2021) Taxonomic, functional and expression analysis of viral communities associated with marine sponges. Peer J 9:e10715 (doi:10.7717/peerj.10715).

Song W, Wemheuer B, Steinberg PD, Marzinelli EM, Thomas T (2021) Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. ISME J 15:807–817 (doi:10.1038/s41396-020-00815-8).

Taylor JA, Palladino G, Wemheuer B, Steinert G, Sipkema D, Williams TJ, Thomas T (2021) Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME J 15:503–519 (doi:10.1038/s41396-020-00791-z).

Coffey MJ, Low I, Stelzer-Braid S, Wemheuer B, Garg M, Thomas T, Jaffe A, Rawlinson WD, Ooi CY (2020) The intestinal virome in children with cystic fibrosis differs from healthy controls. PLoS ONE 15(5):e0233557 (doi:10.1371/journal.pone.0233557).

Coffey MJ, Low I, Stelzer-Braid S, Wemheuer B, Garg M, Thomas T, Jaffe A, Rawlinson WD, Ooi CY (2020) The intestinal virome in children with cystic fibrosis differs from healthy controls. PLoS One 15(5):e0233557 (doi:10.1371/journal.pone.0233557).

Eze MO, Lütgert SA, Neubauer H, Balouri A, Kraft AA, Sieven A, Daniel R, Wemheuer B (2020) Metagenome assembly and metagenome-assembled genome sequences from a historical oil field located in Wietze, Germany. Microbiol Resour Announc 9(21):e00333-20 (doi:10.1128/MRA.00333-20).

Heinrichs ME, Tebbe DA, Wemheuer B, Niggemann J, Engelen B (2020) Impact of viral lysis on the composition of bacterial communities and dissolved organic matter in deep-sea sediments. Viruses 12(9):922 (doi:10.3390/v12090922).

Rao SC, Esvaran M, Patole SK, Simmer KN, Gollow I, Keil A, Wemheuer B, Chen L, Conway PL (2020) Gut microbiota in neonates with congenital gastrointestinal surgical conditions: a prospective study. Pediatr Res 88:878-886 (doi:10.1038/s41390-020-0824-7).

Taylor JA, Palladino G, Wemheuer B, Steinert G, Sipkema D, Williams TJ, Thomas T (2020) Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME J (doi:10.1038/s41396-020-00791-z).

Tiede J, Diepenbruck M, Gadaub J, Wemheuer B, Daniel R, Scherber C (2020) Seasonal variation in the diet of the serotine bat (Eptesicus serotinus): A high-resolution analysis using DNA metabarcoding. Basic Appl Ecol 49:1-12 (doi:10.1016/j.baae.2020.09.004).

Vendl C, Slavich E, Wemheuer B, Nelson T, Ferrari B, Thomas T, Rogers T (2020) Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast. Sci Rep 10:12645 (doi:10.1038/s41598-020-69602-x).

Wemheuer F, Berkelmann D, Wemheuer B, Daniel R, Vidal S, Bisseleua Daghela HB, (2020) Agroforestry management systems drive the composition, diversity, and function of fungal and bacterial endophyte communities in Theobroma cacao leaves. Microorganisms 8(3):405 (doi:10.3390/microorganisms8030405).

Wemheuer, F., Taylor, J.A., Daniel, R, Johnston E, Meinicke P, Thomas T, Wemheuer B (2020) Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environ Microbiome 15:11 (doi:10.1186/s40793-020-00358-7).

Bakenhus I, Wemheuer B, Akyol P, Giebel HA, Dlugosch L, Daniel R, Simon M (2019) Distinct relationships between fluorescence in situ hybridization and 16S rRNA gene- and amplicon-based sequencing data of bacterioplankton lineages. Syst Appl Microbiol 42(5):126000 (doi:10.1016/j.syapm.2019.06.005).

Langer SG, Gabris C, Einfalt D, Wemheuer B, Kazda M, Bengelsdorf FR (2019) Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters. Microb Biotechnol 12(6):1210-1225 (doi:10.1111/1751-7915.13409).

Lurgi M, Thomas T, Wemheuer B, Webster NS, Montoya JM (2019) Modularity and predicted functions of the global sponge-microbiome network. Nat Commun 10(1):992 (doi:10.1038/s41467-019-08925-4).

Ozkan J, Willcox M, Wemheuer B, Wilcsek G, Coroneo M, Thomas T (2019) Biogeography of the human ocular microbiota. Ocul Surf 17(1):111-118 (doi:10.1016/j.jtos.2018.11.005).

Pohlner M, Dlugosch L, Wemheuer B, Mills H, Engelen B, Reese BK (2019) The majority of active Rhodobacteraceae in marine sediments belong to uncultured genera: a molecular approach to link their distribution to environmental conditions. Front Microbiol 10:659 (doi:10.3389/fmicb.2019.00659).

Schröter K, Wemheuer B, Pena R, Schöning I, Ehbrecht M, Schall P, Ammer C, Daniel R, Polle A (2019) Assembly processes of trophic guilds in the root mycobiome of temperate forests. Mol Ecol 28:348-364 (doi:10.1111/mec.14887).

Song W, Wemheuer B, Zhang S, Steensen K, Thomas T (2019) MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches. Microbiome 7(1):36 (doi:10.1186/s40168-019-0649-y).

Steinert G, Wemheuer B, Janussen D, Erpenbeck D, Daniel R, Simon M, Brinkhoff T, Schupp PJ (2019) Prokaryotic diversity and community patterns in Antarctic continental shelf sponges. Front Mar Sci 6:297 (doi:10.3389/fmars.2019.00297).

Wemheuer F, von Hoyningen-Huene AJE, Pohlner M, Degenhardt J, Engelen B, Daniel R, Wemheuer B (2019) Primary production in the water column as major structuring element of the biogeographical distribution and function of Archaea in deep-sea sediments of the Central Pacific Ocean. Archaea 2019:ID 3717239 (doi:10.1155/2019/3717239).

Wemheuer F, Wemheuer B, Daniel R, Vidal S (2019) Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands. Sci Rep 9:14183 (doi:10.1038/s41598-019-50540-2).

Wemheuer B, Thomas T, Wemheuer F (2019) Fungal endophyte communities of three agricultural important grass species differ in their response towards management regimes. Microorganisms 7(2):37 (doi:10.3390/microorganisms7020037).

Wilkes Walburn J, Wemheuer B, Thomas T, Copeland E, O'Connor W, Booth M, Fielder S, Egan S (2019) Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi). Microb Biotechnol 12(2):275-288 (doi:10.1111/1751-7915.13323).

Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T (2019) Comparative genomics reveals ecological and evolutionary insights into sponge-associated Thaumarchaeota. mSystems 4(4):288 (doi:10.1128/mSystems.00288-19).

Daniel R, Simon M, Wemheuer B (2018) Editorial: Molecular ecology and genetic diversity of the Roseobacter clade. Front Microbiol 9:1185 (doi:10.3389/fmicb.2018.01185).

Ozkan J, Coroneo M, Willcox M, Wemheuer B, Thomas T (2018) Identification and visualization of a distinct microbiome in ocular surface conjunctival tissue. Invest Ophthalmol Vis Sci 59(10):4268-4276 (doi:10.1167/iovs.18-24651).

Poehlein A, Hollensteiner J, Granzow S, Wemheuer B, Vidal S, Wemheuer F (2018) First insights into the draft genome sequence of the endophyte Paenibacillus sp. strain GM1FR, isolated from Festuca rubra. Genome Announc 6(4):e01516 (doi:10.1128/genomeA.01516-17).

Wemheuer F, Hollensteiner J, Poehlein A, Liesegang H, Daniel R, Wemheuer B (2018) Draft genome sequence of the endophyte Bacillus mycoides strain GM6LP isolated from Lolium perenne. Genome Announc 6(5):e00011 (doi:10.1128/genomeA.00011-18).

Wemheuer F, Wemheuer B, Hollensteiner J, Daniel R, Poehlein A (2018) Draft genome sequence of the endophyte Paenibacillus sp. strain GM2FR isolated from Festuca rubra. Genome Announc 6(6):e00017 (doi:10.1128/genomeA.00017-18).

Ammer C, Schall P, Gossner MM, Heinrichs S, Boch S, Prati D, Jung K, Baumgartner V, Blaser S, Böhm S, Buscot F, Daniel R, Goldmann K, Kaiser K, Kahl T, Lange M, Müller J, Overmann J, Renner S C, Schulze E-D, Sikorski J, Tschapka M, Türke M, Weisser WW, Wemheuer B, Wubet T, Fischer M (2017) Waldbewirtschaftung und Biodiversität: Vielfalt ist gefragt. Allgemeine Forstzeitschrift/Der Wald 72(17):20-25

Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T (2017) Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol 40(6):370-382 (doi:10.1016/j.syapm.2017.05.006).

Granzow S, Kaiser K, Wemheuer B, Pfeiffer B, Daniel R, Vidal S Wemheuer F (2017) The effects of cropping regimes on fungal and bacterial communities of wheat and faba bean in a greenhouse pot experiment differ between plant species and compartment. Front Microbiol 8:902 (doi:10.3389/fmicb.2017.00902).

Pohlner M, Degenhardt J, von Hoyningen-Huene AJE, Wemheuer B, Erlmann N, Schnetger B, Badewien TH, Engelen B (2017) The biogeographical distribution of benthic Roseobacter group members along a Pacific transect Is structured by nutrient availability within the sediments and pprimary production in different oceanic provinces. Front Microbiol 8:2550 (doi:10.3389/fmicb.2017.02550).

Schneider D, Wemheuer F, Pfeiffer B, Wemheuer B (2017) Extraction of total DNA and RNA from marine filter samples and generation of a cDNA as universal template for marker gene studies. Methods Mol Biol 1539:13-22 (doi:10.1007/978-1-4939-6691-2_2).

Wemheuer B, Wemheuer F (2017) Assessing bacterial and fungal diversity in the plant endosphere. Methods Mol Biol 1539:75-84 (doi:10.1007/978-1-4939-6691-2_6).

Wemheuer F, Kaiser K, Karlovsky P, Daniel R, Vidal S, Wemheuer B (2017) Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes. Sci Rep 7:40914 (doi:10.1038/srep40914).

Wemheuer F, Hollensteiner J, Poehlein A, Granzow S, Daniel R, Vidal S, Wemheuer B (2017) Draft genome sequence of Pseudomonas putida strain GM4FR, an endophytic bacterium isolated from Festuca rubra L. Genome Announc 5(13):e00086-17 (doi:10.1128/genomeA.00086-17).

Wemheuer B, Wemheuer F, Meier D, Billerbeck S, Giebel H-A, Simon M, Scherber C, Daniel R (2017) Linking compositional and functional predictions to decipher the biogeochemical significance in DFAA turnover of abundant bacterioplankton lineages in the North Sea. Microorganisms 5(4):68 (doi:10.3390/microorganisms5040068 ).

Wöhlbrand L, Wemheuer B, Feenders C, Ruppersberg HS, Hinrichs C, Blasius B, Daniel R, Rabus R (2017) Complementary metaproteomic approaches to assess the bacterioplankton response towards a phytoplankton spring bloom in the southern North Sea. Front Microbiol 8:442 (doi:10.3389/fmicb.2017.00442).

Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel H-A, Brinkhoff T, Gram L, Jeffrey WH, Daniel R, Simon M (2016) Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nature Microbiol 1:16063 (doi:10.1038/nmicrobiol.2016.63).

Güllert S, Fischer MA, Turaev D, Nöbauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR (2016) Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies. Biotechnol Biofuels 9:121 (doi:10.1186/s13068-016-0534-x).

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).

Kanukollu S, Wemheuer B, Herber J, Billerbeck S, Lucas J, Daniel R, Simon M, Cypionka H, Engelen B (2016) Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea. FEMS Microbiol Ecol 92(1):fiv137 (doi:10.1093/femsec/fiv145).

Osterholz H, Singer G, Wemheuer B, Daniel R, Simon M, Niggemann J, Dittmar T (2016) Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system. ISME J 10:1717–1730 (doi:10.1038/ismej.2015.231).

Tiede J, Wemheuer B, Traugott M, Daniel R, Tscharntke T, Ebeling A, Scherber C (2016) Trophic and non-trophic interactions in a biodiversity experiment assessed by Next-Generation Sequencing. PLOS One 11(2):e0148781 (doi:10.1371/journal.pone.0148781).

Wemheuer F, Wemheuer B, Kretzschmar D, Pfeiffer B, Herzog S, Daniel R, Vidal S (2016) Impact of grassland management regimes on bacterial endophyte diversity differs with grass species. Lett Appl Microbiol 62(4):323-329 (doi:10.1111/lam.12551).

Aßhauer KP, Wemheuer B, Daniel R, Meinicke P (2015) Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 31:2882-2884 (doi:10.1093/bioinformatics/btv287).

Gram L, Rasmussen BB, Wemheuer B, Bernbom N, Ng YY, Porsby CH, Breider S, Brinkhoff T (2015) Phaeobacter inhibens from the Roseobacter clade has an environmental niche as a surface colonizer in harbors. Syst Appl Microbiol 38(7):483-493 (doi:10.1016/j.syapm.2015.07.006).

Herzog S, Wemheuer F, Wemheuer B, Daniel R (2015) Effects of fertilization and sampling time on composition and diversity of entire and active bacterial communities in German grassland soils. PLOS One 10(3):e0145575 (doi:10.1371/journal.pone.0145575).

Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel H.-A., Beardsley C, Sardemann C, Bakenhus I, Billerbeck S, Daniel R, Simon M (2015) Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses. ISME J 9(2):371-384 (doi:10.1038/ismej.2014.134).

Wemheuer B, Wemheuer F, Hollensteiner J, Meyer F-D, Voget S, Daniel R (2015) The green impact: bacterioplankton response towards a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches. Front Microbiol 6:805 (doi:10.3389/fmicb.2015.00805).

Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, Brinkhoff T, Simon M (2015) Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. Environ Microbiol 17(10):3822-3831 (doi:10.1111/1462-2920.12842).

Ilmberger N, Güllert S, Dannenberg J, Rabausch U, Torres J, Wemheuer B, Alawi M, Poehlein A, Chow J, Turaev D, Rattei T, Schmeisser C, Salomon J, Olsen PB, Daniel R, Grundhoff A, Borchert MS, Streit WR (2014) A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes. PLOS One 9:e106707 (doi:10.1371/journal.pone.0106707).

Wemheuer B, Güllert S, Billerbeck S, Giebel H-A, Voget S, Simon M, Daniel R (2014) Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiology Ecology 87:378-389 (doi:10.1111/1574-6941.12230).

Krohn-Molt I, Wemheuer B, Alaw Mi, Poehlein A, Güllert S, Schmeisser C, Pommerening-Röser A, Grundhoff A, Daniel R, Hanelt D, Streit WR (2013) Metagenome survey of a multispecies and algae-associated biofilm reveals key elements of bacterial-algae interactions in photobioreactors. Appl Environ Microbiol 79(20):6196-6206 (doi:10.1128/AEM.01641-13).

Mientus M, Brady S, Angelov A, Zimmermann P, Wemheuer B, Schuldes J, Daniel R, Liebl W (2013) Thermostable xylanase and β-glucanase derived from the metagenome of the Avachinsky Crater in Kamchatka (Russia) . Current Biotechnology 2:284-293 (doi:10.2174/2211550102999131128150257).

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).

Wemheuer B, Taube R, Akyol P, Wemheuer F, Daniel R (2013) Microbial diversity and biochemical potential encoded by thermal spring metagenomes derived from the Kamchatka peninsula. Archaea 2013: Article ID 136714 (doi:10.1155/2013/136714).

Wemheuer B, Wemheuer F, Daniel R (2012) RNA-based assessment of diversity and composition of active archaeal communities in the German Bight. Archaea 2012: Article ID 695826 (doi:10.1155/2012/695826).