Wemheuer, Bernd

[["dc.bibliographiccitation.artnumber","14183"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Scientific Reports"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Wemheuer, Franziska"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Vidal, Stefan"],["dc.date.accessioned","2020-03-12T08:51:55Z"],["dc.date.available","2020-03-12T08:51:55Z"],["dc.date.issued","2019"],["dc.description.abstract","Green islands (the re-greening of senescent leaf tissues) are particularly evident on leaves infected with fungal pathogens. To date, there is only a limited number of studies investigating foliar endophytic microorganisms in phytopathogen-infected leaves. Here, we analysed bacterial and fungal endophyte communities in leaves without green islands (control leaves; CL), within green island areas (GLA) and the surrounding yellow leaf areas (YLA) of leaves with green islands of Acer campestre and A. platanoides. GLA samples of A. campestre and A. platanoides were dominated by Sawadaea polyfida and S. bicornis, respectively, suggesting that these fungi might be responsible for the green islands. We detected a higher fungal richness and diversity in CL compared to GLA samples of A. campestre. Leaf status (CL, GLA, YLA) significantly altered the composition of fungal communities of A. campestre. This was related to differences in fungal community composition between YLA and GLA samples. Site was the main driver of bacterial communities, suggesting that bacterial and fungal endophytes are shaped by different factors. Overall, we observed Acer species-specific responses of endophyte communities towards the presence of green islands and/or leaf type, which might be attributed to several fungi and bacteria specifically associated with one Acer species."],["dc.identifier.doi","10.1038/s41598-019-50540-2"],["dc.identifier.pmid","31578453"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16477"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63324"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.eissn","2045-2322"],["dc.relation.issn","2045-2322"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","922"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Viruses"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Heinrichs, Mara E."],["dc.contributor.author","Tebbe, Dennis A."],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Niggemann, Jutta"],["dc.contributor.author","Engelen, Bert"],["dc.date.accessioned","2021-04-14T08:32:27Z"],["dc.date.available","2021-04-14T08:32:27Z"],["dc.date.issued","2020"],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft"],["dc.identifier.doi","10.3390/v12090922"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/83928"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.publisher","MDPI"],["dc.relation.eissn","1999-4915"],["dc.rights","https://creativecommons.org/licenses/by/4.0/"],["dc.title","Impact of Viral Lysis on the Composition of Bacterial Communities and Dissolved Organic Matter in Deep-Sea Sediments"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e106707"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","PLoS One"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Ilmberger, Nele"],["dc.contributor.author","Güllert, Simon"],["dc.contributor.author","Dannenberg, Joana"],["dc.contributor.author","Rabausch, Ulrich"],["dc.contributor.author","Torres, Jeremy"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Alawi, Malik"],["dc.contributor.author","Poehlein, Anja"],["dc.contributor.author","Chow, Jennifer"],["dc.contributor.author","Turaev, Dimitrij"],["dc.contributor.author","Rattei, Thomas"],["dc.contributor.author","Schmeisser, Christel"],["dc.contributor.author","Salomon, Jesper"],["dc.contributor.author","Olsen, Peter B."],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Grundhoff, Adam"],["dc.contributor.author","Borchert, Martin S."],["dc.contributor.author","Streit, Wolfgang R."],["dc.date.accessioned","2018-11-07T09:35:20Z"],["dc.date.available","2018-11-07T09:35:20Z"],["dc.date.issued","2014"],["dc.description.abstract","A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal. The microbial diversity was examined via 16S rRNA gene analysis. We generated more than 44,000 GS-FLX+454 reads for each animal. For the baby elephant, 380 operational taxonomic units (OTUs) were identified at 97% sequence identity level; in the six-years-old animal, close to 3,000 OTUs were identified, suggesting high microbial diversity in the older animal. In both animals most OTUs belonged to Bacteroidetes and Firmicutes. Additionally, for the baby elephant a high number of Proteobacteria was detected. A metagenomic sequencing approach using Illumina technology resulted in the generation of 1.1 Gbp assembled DNA in contigs with a maximum size of 0.6 Mbp. A KEGG pathway analysis suggested high metabolic diversity regarding the use of polymers and aromatic and non-aromatic compounds. In line with the high phylogenetic diversity, a surprising and not previously described biodiversity of glycoside hydrolase (GH) genes was found. Enzymes of 84 GH families were detected. Polysaccharide utilization loci (PULs), which are found in Bacteroidetes, were highly abundant in the dataset; some of these comprised cellulase genes. Furthermore the highest coverage for GH5 and GH9 family enzymes was detected for Bacteroidetes, suggesting that bacteria of this phylum are mainly responsible for the degradation of cellulose in the Asian elephant. Altogether, this study delivers insight into the biomass conversion by one of the largest plant-fed and land-living animals."],["dc.identifier.doi","10.1371/journal.pone.0106707"],["dc.identifier.isi","000342030300036"],["dc.identifier.pmid","25208077"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/10859"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/32360"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1932-6203"],["dc.rights","CC BY 3.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/3.0"],["dc.title","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"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","UNSP 695826"],["dc.bibliographiccitation.journal","Archaea"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Wemheuer, Franziska"],["dc.contributor.author","Daniel, Rolf"],["dc.date.accessioned","2018-11-07T09:14:45Z"],["dc.date.available","2018-11-07T09:14:45Z"],["dc.date.issued","2012"],["dc.description.abstract","Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these marine archaeal communities is largely unknown. To assess diversity and composition of active archaeal communities in the German Bight, seven marine water samples were taken and studied by RNA-based analysis of ribosomal 16S rRNA. For this purpose, total RNA was extracted from the samples and converted to cDNA. Archaeal community structures were investigated by pyrosequencing-based analysis of 16S rRNA amplicons generated from cDNA. To our knowledge, this is the first study combining next-generation sequencing and metatranscriptomics to study archaeal communities in marine habitats. The pyrosequencing-derived dataset comprised 62,045 archaeal 16S rRNA sequences. We identified Halobacteria as the predominant archaeal group across all samples with increased abundance in algal blooms. Thermoplasmatales (Euryarchaeota) and the Marine Group I (Thaumarchaeota) were identified in minor abundances. It is indicated that archaeal community patterns were influenced by environmental conditions."],["dc.identifier.doi","10.1155/2012/695826"],["dc.identifier.isi","000311574700001"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/8395"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/27493"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1472-3646"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","RNA-Based Assessment of Diversity and Composition of Active Archaeal Communities in the German Bight"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","121"],["dc.bibliographiccitation.journal","Biotechnology for Biofuels"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Güllert, Simon"],["dc.contributor.author","Fischer, Martin A."],["dc.contributor.author","Turaev, Dmitrij"],["dc.contributor.author","Noebauer, Britta"],["dc.contributor.author","Ilmberger, Nele"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Alawi, Malik"],["dc.contributor.author","Rattei, Thomas"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Schmitz, Ruth A."],["dc.contributor.author","Grundhoff, Adam"],["dc.contributor.author","Streit, Wolfgang R."],["dc.date.accessioned","2018-11-07T10:12:53Z"],["dc.date.available","2018-11-07T10:12:53Z"],["dc.date.issued","2016"],["dc.description.abstract","Background: The diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood. Results: In this paper, we show that a typical industrial biogas reactor fed with maize silage, cow manure, and chicken manure has relatively lower hydrolysis rates compared to feces samples from herbivores. We provide evidence that on average, 2.5 genes encoding cellulolytic GHs/Mbp were identified in the biogas fermenter compared to 3.8 in the elephant feces and 3.2 in the cow rumen data sets. The ratio of genes coding for cellulolytic GH enzymes affiliated with the Firmicutes versus the Bacteroidetes was 2.8:1 in the biogas fermenter compared to 1:1 in the elephant feces and 1.4:1 in the cow rumen sample. Furthermore, RNA-Seq data indicated that highly transcribed cellulases in the biogas fermenter were four times more often affiliated with the Firmicutes compared to the Bacteroidetes, while an equal distribution of these enzymes was observed in the elephant feces sample. Conclusions: Our data indicate that a relatively lower abundance of bacteria affiliated with the phylum of Bacteroidetes and, to some extent, Fibrobacteres is associated with a decreased richness of predicted lignocellulolytic enzymes in biogas fermenters. This difference can be attributed to a partial lack of genes coding for cellulolytic GH enzymes derived from bacteria which are affiliated with the Fibrobacteres and, especially, the Bacteroidetes. The partial deficiency of these genes implies a potentially important limitation in the biogas fermenter with regard to the initial hydrolysis of biomass. Based on these findings, we speculate that increasing the members of Bacteroidetes and Fibrobacteres in biogas fermenters will most likely result in an increased hydrolytic performance."],["dc.description.sponsorship","German Federal Ministry of Education and Research [03SF0421H]"],["dc.identifier.doi","10.1186/s13068-016-0534-x"],["dc.identifier.isi","000377260600001"],["dc.identifier.pmid","27279900"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13327"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/40325"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1754-6834"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","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"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","405"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Microorganisms"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Wemheuer, Franziska"],["dc.contributor.author","Berkelmann, Dirk"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Vidal, Stefan"],["dc.contributor.author","Bisseleua Daghela, Hervé Bertin"],["dc.date.accessioned","2020-04-28T12:39:40Z"],["dc.date.available","2020-04-28T12:39:40Z"],["dc.date.issued","2020"],["dc.description.abstract","Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of T.cacao. To close this knowledge gap, we investigated the diversity, community composition, and function of bacterial and fungal endophytes in the leaves of T.cacao trees growing in five major cacao-growing regions in the central region of Cameroon using DNA metabarcoding. Fungal but not bacterial alpha diversity measures differed significantly between the agroforestry management systems. Interestingly, less managed home-garden cacao forests harbored the lowest fungal richness and diversity. Our results suggest that the composition of bacterial and fungal endophyte communities is predominantly affected by agroforestry management systems and, to a lesser extent, by environmental properties. The core microbiome detected comprised important fungal phytopathogens, such as Lasiodiplodia species. Several predicted pathways of bacterial endophytes and functional guilds of fungal endophytes differed between the agroforest systems which might be attributed to bacteria and fungi specifically associated with a single agroforest. Our results provide the basis for future studies on foliar fungal and bacterial endophytes of T.cacao and their responsiveness towards agroforestry management systems."],["dc.description.sponsorship","Volkswagen Foundation"],["dc.identifier.doi","10.3390/microorganisms8030405"],["dc.identifier.pmid","32183118"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/17357"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64434"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.publisher","MDPI"],["dc.relation.eissn","2076-2607"],["dc.relation.issn","2076-2607"],["dc.rights","CC BY 4.0"],["dc.rights.uri","http://creativecommons.org/licenses/by/4.0/"],["dc.title","Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1210"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Microbial Biotechnology"],["dc.bibliographiccitation.lastpage","1225"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Langer, Susanne G."],["dc.contributor.author","Gabris, Christina"],["dc.contributor.author","Einfalt, Daniel"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Kazda, Marian"],["dc.contributor.author","Bengelsdorf, Frank R."],["dc.date.accessioned","2020-03-12T08:37:30Z"],["dc.date.available","2020-03-12T08:37:30Z"],["dc.date.issued","2019"],["dc.description.abstract","Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes."],["dc.identifier.doi","10.1111/1751-7915.13409"],["dc.identifier.pmid","30995692"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16668"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63318"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.eissn","1751-7915"],["dc.relation.issn","1751-7915"],["dc.relation.issn","1751-7915"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","136714"],["dc.bibliographiccitation.journal","Archaea"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Taube, Robert"],["dc.contributor.author","Akyol, Pinar"],["dc.contributor.author","Wemheuer, Franziska"],["dc.contributor.author","Daniel, Rolf"],["dc.date.accessioned","2018-11-07T09:30:11Z"],["dc.date.available","2018-11-07T09:30:11Z"],["dc.date.issued","2013"],["dc.description.abstract","Volcanic regions contain a variety of environments suitable for extremophiles. This study was focused on assessing and exploiting the prokaryotic diversity of two microbial communities derived from different Kamchatkian thermal springs by metagenomic approaches. Samples were taken from a thermoacidophilic spring near the Mutnovsky Volcano and from a thermophilic spring in the Uzon Caldera. Environmental DNA for metagenomic analysis was isolated from collected sediment samples by direct cell lysis. The prokaryotic community composition was examined by analysis of archaeal and bacterial 16S rRNA genes. A total number of 1235 16S rRNA gene sequences were obtained and used for taxonomic classification. Most abundant in the samples were members of Thaumarchaeota, Thermotogae, and Proteobacteria. The Mutnovsky hot spring was dominated by the Terrestrial Hot Spring Group, Kosmotoga, and Acidithiobacillus. The Uzon Caldera was dominated by uncultured members of the Miscellaneous Crenarchaeotic Group and Enterobacteriaceae. The remaining 16S rRNA gene sequences belonged to the Aquificae, Dictyoglomi, Euryarchaeota, Korarchaeota, Thermodesulfobacteria, Firmicutes, and some potential new phyla. In addition, the recovered DNA was used for generation of metagenomic libraries, which were subsequently mined for genes encoding lipolytic and proteolytic enzymes. Three novel genes conferring lipolytic and one gene conferring proteolytic activity were identified."],["dc.description.sponsorship","Bundesministerium fur Bildung und Forschung (BMBF)"],["dc.identifier.doi","10.1155/2013/136714"],["dc.identifier.isi","000315875000001"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/9968"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/31245"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1472-3646"],["dc.title","Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2882"],["dc.bibliographiccitation.issue","17"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","2884"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Aßhauer, Kathrin Petra"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Meinicke, Peter"],["dc.date.accessioned","2018-11-07T09:52:22Z"],["dc.date.available","2018-11-07T09:52:22Z"],["dc.date.issued","2015"],["dc.description.abstract","Motivation: The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data. Results: Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [ME 3138, TRR51]"],["dc.identifier.doi","10.1093/bioinformatics/btv287"],["dc.identifier.isi","000361395700020"],["dc.identifier.pmid","25957349"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/12148"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/36110"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1460-2059"],["dc.relation.issn","1367-4803"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","442"],["dc.bibliographiccitation.journal","Frontiers in Microbiology"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Woehlbrand, Lars"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Feenders, Christoph"],["dc.contributor.author","Ruppersberg, Hanna S."],["dc.contributor.author","Hinrichs, Christina"],["dc.contributor.author","Blasius, Bernd"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Rabus, Ralf"],["dc.date.accessioned","2018-11-07T10:26:05Z"],["dc.date.available","2018-11-07T10:26:05Z"],["dc.date.issued","2017"],["dc.description.abstract","Annually recurring phytoplankton spring blooms are characteristic of temperate coastal shelf seas. During these blooms, environmental conditions, including nutrient availability, differ considerably from non-bloom conditions, affecting the entire ecosystem including the bacterioplankton. Accordingly, the emerging ecological niches during bloom transition are occupied by different bacterial populations, with Roseobacter RCA cluster and SAR92 clade members exhibiting high metabolic activity during bloom events. In this study, the functional response of the ambient bacterial community toward a Phaeocystis globosa bloom in the southern North Sea was studied using metaproteomic approaches. In contrast to other metaproteomic studies of marine bacterial communities, this is the first study comparing two different cell lysis and protein preparation methods [using trifluoroethanol (TFE) and in-solution digest as well as bead beating and SDS-based solubilization and in-gel digest (BB GeLC)]. In addition, two different mass spectrometric techniques (ESI-iontrap MS and MALDI-TOF MS) were used for peptide analysis. A total of 585 different proteins were identified, 296 of which were only detected using the TFE and 191 by the BB GeLC method, demonstrating the complementarity of these sample preparation methods. Furthermore, 158 proteins of the TFE cell lysis samples were exclusively detected by ESI-iontrap MS while 105 were only detected using MALDI-TOF MS, underpinning the value of using two different ionization and mass analysis methods. Notably, 12% of the detected proteins represent predicted integral membrane proteins, including the difficult to detect rhodopsin, indicating a considerable coverage of membrane proteins by this approach. This comprehensive approach verified previous metaproteomic studies of marine bacterioplankton, e.g., detection of many transport-related proteins (17% of the detected proteins). In addition, new insights into e.g., carbon and nitrogen metabolism were obtained. For instance, the C1 pathway was more prominent outside the bloom and different strategies for glucose metabolism seem to be applied under the studied conditions. Furthermore, a higher number of nitrogen assimilating proteins were present under non-bloom conditions, reflecting the competition for this limited macro nutrient under oligotrophic conditions. Overall, application of different sample preparation techniques as well as MS methods facilitated a more holistic picture of the marine bacterioplankton response to changing environmental conditions."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft (DFG) [TRR51]"],["dc.identifier.doi","10.3389/fmicb.2017.00442"],["dc.identifier.isi","000397175800001"],["dc.identifier.pmid","28392779"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14467"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/42967"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1664-302X"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Complementary Metaproteomic Approaches to Assess the Bacterioplankton Response toward a Phytoplankton Spring Bloom in the Southern North Sea"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]