@article{KellerBrandelBeckeretal.2018, author = {Keller, Alexander and Brandel, Annette and Becker, Mira C. and Balles, Rebecca and Abdelmohsen, Usama Ramadan and Ankenbrand, Markus J. and Sickel, Wiebke}, title = {Wild bees and their nests host Paenibacillus bacteria with functional potential of avail}, series = {Microbiome}, volume = {6}, journal = {Microbiome}, number = {229}, doi = {10.1186/s40168-018-0614-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177554}, year = {2018}, abstract = {Background: In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either secondary invaders of European foulbrood or considered a threat to honey bees. We thus investigated whether Paenibacillus is a common bacterium associated with various wild bees and hence poses a latent threat to honey bees visiting the same flowers. Results: We collected 202 samples from 82 individuals or nests of 13 bee species at the same location and screened each for Paenibacillus using high-throughput sequencing-based 16S metabarcoding. We then isolated the identified strain Paenibacillus MBD-MB06 from a solitary bee nest and sequenced its genome. We did find conserved toxin genes and such encoding for chitin-binding proteins, yet none specifically related to foulbrood virulence or chitinases. Phylogenomic analysis revealed a closer relationship to strains of root-associated Paenibacillus rather than strains causing foulbrood or other accompanying diseases. We found anti-microbial evidence within the genome, confirmed by experimental bioassays with strong growth inhibition of selected fungi as well as gram-positive and gram-negative bacteria. Conclusions: The isolated wild bee associate Paenibacillus MBD-MB06 is a common, but irregularly occurring part of wild bee microbiomes, present on adult body surfaces and guts and within nests especially in megachilids. It was phylogenetically and functionally distinct from harmful members causing honey bee colony diseases, although it shared few conserved proteins putatively toxic to insects that might indicate ancestral predisposition for the evolution of insect pathogens within the group. By contrast, our strain showed anti-microbial capabilities and the genome further indicates abilities for chitin-binding and biofilm-forming, suggesting it is likely a useful associate to avoid fungal penetration of the bee cuticula and a beneficial inhabitant of nests to repress fungal threats in humid and nutrient-rich environments of wild bee nests.}, language = {en} } @article{KoetschanFoersterKelleretal.2010, author = {Koetschan, Christian and Foerster, Frank and Keller, Alexander and Schleicher, Tina and Ruderisch, Benjamin and Schwarz, Roland and Mueller, Tobias and Wolf, Matthias and Schultz, Joerg}, title = {The ITS2 Database III-sequences and structures for phylogeny}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-68390}, year = {2010}, abstract = {The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps .biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160 000 correct full ength and more than 50 000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses.}, subject = {Biologie}, language = {en} } @article{VillalobosWieseImhoffetal.2019, author = {Villalobos, Alvaro S. and Wiese, Jutta and Imhoff, Johannes F. and Dorador, Cristina and Keller, Alexander and Hentschel, Ute}, title = {Systematic affiliation and genome analysis of Subtercola vilae DB165T with particular emphasis on cold adaptation of an isolate from a high-altitude cold volcano lake}, series = {Microorganisms}, volume = {7}, journal = {Microorganisms}, number = {4}, issn = {2076-2607}, doi = {10.3390/microorganisms7040107}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197394}, year = {2019}, abstract = {Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of Agreia and Subtercola species. In order to gain insight into the ability of S. vilae to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of S. vilae DB165\(^T\) linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, S. vilae DB165\(^T\) is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to S. vilae DB165\(^T\). These results indicate that S. vilae has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake.}, language = {en} } @article{VoulgariKokotaSteffanDewenterKeller2020, author = {Voulgari-Kokota, Anna and Steffan-Dewenter, Ingolf and Keller, Alexander}, title = {Susceptibility of Red Mason Bee Larvae to Bacterial Threats Due to Microbiome Exchange with Imported Pollen Provisions}, series = {Insects}, volume = {11}, journal = {Insects}, number = {6}, issn = {2075-4450}, doi = {10.3390/insects11060373}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-207948}, year = {2020}, abstract = {Solitary bees are subject to a variety of pressures that cause severe population declines. Currently, habitat loss, temperature shifts, agrochemical exposure, and new parasites are identified as major threats. However, knowledge about detrimental bacteria is scarce, although they may disturb natural microbiomes, disturb nest environments, or harm the larvae directly. To address this gap, we investigated 12 Osmia bicornis nests with deceased larvae and 31 nests with healthy larvae from the same localities in a 16S ribosomal RNA (rRNA) gene metabarcoding study. We sampled larvae, pollen provisions, and nest material and then contrasted bacterial community composition and diversity in healthy and deceased nests. Microbiomes of pollen provisions and larvae showed similarities for healthy larvae, whilst this was not the case for deceased individuals. We identified three bacterial taxa assigned to Paenibacillus sp. (closely related to P. pabuli/amylolyticus/xylanexedens), Sporosarcina sp., and Bacillus sp. as indicative for bacterial communities of deceased larvae, as well as Lactobacillus for corresponding pollen provisions. Furthermore, we performed a provisioning experiment, where we fed larvae with untreated and sterilized pollens, as well as sterilized pollens inoculated with a Bacillus sp. isolate from a deceased larva. Untreated larval microbiomes were consistent with that of the pollen provided. Sterilized pollen alone did not lead to acute mortality, while no microbiome was recoverable from the larvae. In the inoculation treatment, we observed that larval microbiomes were dominated by the seeded bacterium, which resulted in enhanced mortality. These results support that larval microbiomes are strongly determined by the pollen provisions. Further, they underline the need for further investigation of the impact of detrimental bacterial acquired via pollens and potential buffering by a diverse pollen provision microbiome in solitary bees.}, language = {en} } @article{DeğirmenciRogeFerreiraVukosavljevicetal.2023, author = {Değirmenci, Laura and Rog{\´e} Ferreira, Fabio Luiz and Vukosavljevic, Adrian and Heindl, Cornelia and Keller, Alexander and Geiger, Dietmar and Scheiner, Ricarda}, title = {Sugar perception in honeybees}, series = {Frontiers in Physiology}, volume = {13}, journal = {Frontiers in Physiology}, issn = {1664-042X}, doi = {10.3389/fphys.2022.1089669}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-302284}, year = {2023}, abstract = {Honeybees (Apis mellifera) need their fine sense of taste to evaluate nectar and pollen sources. Gustatory receptors (Grs) translate taste signals into electrical responses. In vivo experiments have demonstrated collective responses of the whole Gr-set. We here disentangle the contributions of all three honeybee sugar receptors (AmGr1-3), combining CRISPR/Cas9 mediated genetic knock-out, electrophysiology and behaviour. We show an expanded sugar spectrum of the AmGr1 receptor. Mutants lacking AmGr1 have a reduced response to sucrose and glucose but not to fructose. AmGr2 solely acts as co-receptor of AmGr1 but not of AmGr3, as we show by electrophysiology and using bimolecular fluorescence complementation. Our results show for the first time that AmGr2 is indeed a functional receptor on its own. Intriguingly, AmGr2 mutants still display a wildtype-like sugar taste. AmGr3 is a specific fructose receptor and is not modulated by a co-receptor. Eliminating AmGr3 while preserving AmGr1 and AmGr2 abolishes the perception of fructose but not of sucrose. Our comprehensive study on the functions of AmGr1, AmGr2 and AmGr3 in honeybees is the first to combine investigations on sugar perception at the receptor level and simultaneously in vivo. We show that honeybees rely on two gustatory receptors to sense all relevant sugars.}, language = {en} } @phdthesis{Keller2010, author = {Keller, Alexander}, title = {Secondary (and tertiary) structure of the ITS2 and its application for phylogenetic tree reconstructions and species identification}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-56151}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {Biodiversity may be investigated and explored by the means of genetic sequence information and molecular phylogenetics. Yet, with ribosomal genes, information for phylogenetic studies may not only be retained from the primary sequence, but also from the secondary structure. Software that is able to cope with two dimensional data and designed to answer taxonomic questions has been recently developed and published as a new scientific pipeline. This thesis is concerned with expanding this pipeline by a tool that facialiates the annotation of a ribosomal region, namely the ITS2. We were also able to show that this states a crucial step for secondary structure phylogenetics and for data allocation of the ITS2-database. This resulting freely available tool determines high quality annotations. In a further study, the complete phylogenetic pipeline has been evaluated on a theoretical basis in a comprehensive simulation study. We were able to show that both, the accuracy and the robustness of phylogenetic trees are largely improved by the approach. The second major part of this thesis concentrates on case studies that applied this pipeline to resolve questions in taxonomy and ecology. We were able to determine several independent phylogenies within the green algae that further corroborate the idea that secondary structures improve the obtainable phylogenetic signal, but now from a biological perspective. This approach was applicable in studies on the species and genus level, but due to the conservation of the secondary structure also for investigations on the deeper level of taxonomy. An additional case study with blue butterflies indicates that this approach is not restricted to plants, but may also be used for metazoan phylogenies. The importance of high quality phylogenetic trees is indicated by two ecological studies that have been conducted. By integrating secondary structure phylogenetics, we were able to answer questions about the evolution of ant-plant interactions and of communities of bacteria residing on different plant tissues. Finally, we speculate how phylogenetic methods with RNA may be further enhanced by integration of the third dimension. This has been a speculative idea that was supplemented with a small phylogenetic example, however it shows that the great potential of structural phylogenetics has not been fully exploited yet. Altogether, this thesis comprises aspects of several different biological disciplines, which are evolutionary biology and biodiversity research, community and invasion ecology as well as molecular and structural biology. Further, it is complemented by statistical approaches and development of informatical software. All these different research areas are combined by the means of bioinformatics as the central connective link into one comprehensive thesis.}, subject = {Phylogenie}, language = {en} } @article{KoenigKraussKelleretal.2022, author = {K{\"o}nig, Sebastian and Krauss, Jochen and Keller, Alexander and Bofinger, Lukas and Steffan-Dewenter, Ingolf}, title = {Phylogenetic relatedness of food plants reveals highest insect herbivore specialization at intermediate temperatures along a broad climatic gradient}, series = {Global Change Biology}, volume = {28}, journal = {Global Change Biology}, number = {13}, doi = {10.1111/gcb.16199}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-276441}, pages = {4027 -- 4040}, year = {2022}, abstract = {The composition and richness of herbivore and plant assemblages change along climatic gradients, but knowledge about associated shifts in specialization is scarce and lacks controlling for the abundance and phylogeny of interaction partners. Thus, we aimed to test whether the specialization of phytophagous insects in insect-plant interaction networks decreases toward cold habitats as predicted by the 'altitude niche-breadth hypothesis' to forecast possible consequences of interaction rewiring under climate change. We used a non-invasive, standardized metabarcoding approach to reconstruct dietary relationships of Orthoptera species as a major insect herbivore taxon along a broad temperature gradient (~12°C) in Southern Germany. Based on Orthoptera surveys, feeding observations, collection of fecal pellets from >3,000 individuals of 54 species, and parallel vegetation surveys on 41 grassland sites, we quantified plant resource availability and its use by herbivores. Herbivore assemblages were richer in species and individuals at sites with high summer temperatures, while plant richness peaked at intermediate temperatures. Corresponding interaction networks were most specialized in warm habitats. Considering phylogenetic relationships of plant resources, however, the specialization pattern was not linear but peaked at intermediate temperatures, mediated by herbivores feeding on a narrow range of phylogenetically related resources. Our study provides empirical evidence of resource specialization of insect herbivores along a climatic gradient, demonstrating that resource phylogeny, availability, and temperature interactively shape the specialization of herbivore assemblages. Instead of low specialization levels only in cold, harsh habitats, our results suggest increased generalist feeding due to intraspecific changes and compositional differences at both ends of the microclimatic gradient. We conclude that this nonlinear change of phylogeny-based resource specialization questions predictions derived from the 'altitude-niche breadth hypothesis' and highlights the currently limited understanding of how plant-herbivore interactions will change under future climatic conditions.}, language = {en} } @article{MeucheBrusaLinsenmairetal.2013, author = {Meuche, Ivonne and Brusa, Oscar and Linsenmair, K. Eduard and Keller, Alexander and Pr{\"o}hl, Heike}, title = {Only distance matters - non-choosy females in a poison frog population}, series = {Frontiers in Zoology}, volume = {10}, journal = {Frontiers in Zoology}, number = {29}, issn = {1742-9994}, doi = {10.1186/1742-9994-10-29}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-122617}, year = {2013}, abstract = {Background: Females have often been shown to exhibit preferences for certain male traits. However, little is known about behavioural rules females use when searching for mates in their natural habitat. We investigated mate sampling tactics and related costs in the territorial strawberry poison frog (Oophaga pumilio) possessing a lek-like mating system, where both sequential and simultaneous sampling might occur. We continuously monitored the sampling pattern and behaviour of females during the complete period between two successive matings. Results: We found no evidence that females compared males by visiting them. Instead females mated with the closest calling male irrespective of his acoustic and physical traits, and territory size. Playback experiments in the natural home ranges of receptive females revealed that tested females preferred the nearest speaker and did not discriminate between low and high call rates or dominant frequencies. Conclusions: Our results suggest that females of O. pumilio prefer the closest calling male in the studied population. We hypothesize that the sampling tactic in this population is affected by 1) a strongly female biased sex ratio and 2) a low variance in traits of available males due to strong male-male competition, preventing low quality males from defending a territory and mating.}, language = {en} } @article{Voulgari‐KokotaAnkenbrandGrimmeretal.2019, author = {Voulgari-Kokota, Anna and Ankenbrand, Markus J. and Grimmer, Gudrun and Steffan-Dewenter, Ingolf and Keller, Alexander}, title = {Linking pollen foraging of megachilid bees to their nest bacterial microbiota}, series = {Ecology and Evolution}, volume = {2019}, journal = {Ecology and Evolution}, number = {9}, issn = {00}, doi = {10.1002/ece3.5599}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-201749}, pages = {10788-10800}, year = {2019}, abstract = {Solitary bees build their nests by modifying the interior of natural cavities, and they provision them with food by importing collected pollen. As a result, the microbiota of the solitary bee nests may be highly dependent on introduced materials. In order to investigate how the collected pollen is associated with the nest microbiota, we used metabarcoding of the ITS2 rDNA and the 16S rDNA to simultaneously characterize the pollen composition and the bacterial communities of 100 solitary bee nest chambers belonging to seven megachilid species. We found a weak correlation between bacterial and pollen alpha diversity and significant associations between the composition of pollen and that of the nest microbiota, contributing to the understanding of the link between foraging and bacteria acquisition for solitary bees. Since solitary bees cannot establish bacterial transmission routes through eusociality, this link could be essential for obtaining bacterial symbionts for this group of valuable pollinators.}, language = {en} } @article{BuchheimKellerKoetschanetal.2011, author = {Buchheim, Mark A. and Keller, Alexander and Koetschan, Christian and F{\"o}rster, Frank and Merget, Benjamin and Wolf, Matthias}, title = {Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {2}, doi = {10.1371/journal.pone.0016931}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-140866}, pages = {e16931}, year = {2011}, abstract = {Background: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. Methodology/Principal Findings: Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. Conclusions/Significance: Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.}, language = {en} }