Molecular Biodiversity (moved to LMU)
Molecular Biodiversity Research
We recently moved to the LMU in München!
Until we have a new homepage there, please check the lab website here: https://www.molecular.eco
Our research projects focus on a combination of field ecology with bioinformatics and new sequencing technologies. Conceptually, we are interested in patterns and structuring forces of communities, where organisms are not easily identifiable or distinguishable from each other. This interest applies to various levels, starting with abundance and diversity of taxa, over phylogenetic reconstructions, towards environmental and spatial influences and lastly regarding organisms' molecular interactions with each other on a genomic level. Methodologically, the workgroup is developing computational workflows and databases as well as laboratory protocols to analyse ecological samples with next-generation sequencing technologies.
Biologically, the focus of current projects is the dynamics of bacteria-host associations in changing environments. Regarding this, we currently consider changes in microbiota induced by
- symbiotic host-host interactions,
- the host's development,
- geographic intra-specific variability,
- climatic changes,
- prey capturing,
- as well as general variation between tissues and species of hosts.
To answer these questions, we conduct field work, analyse samples in our molecular laboratory and apply computational approaches. We have successfully developed methods to simultaneously assess biodiversity of bacteria and plants (here: mixed pollen samples) through next-generation sequencing allowing a very fine scaled interpretation of plant-bee-microbe interactions. Usually we start with descriptive studies, investigating the status-quo, which are followed by experimental designs manipulating the associations by (e.g. antibiotic) exclusion and bioassays. Lastly, for prospective bacteria with interesting distributions and activity, we are also engaged into genomics, studying the genetic possibilities that bacteria bring into the associations with their respective hosts.
Publications
- [ 2024 ]
- [ 2023 ]
- [ 2022 ]
- [ 2021 ]
- [ 2020 ]
- [ 2019 ]
- [ 2018 ]
- [ 2017 ]
- [ 2016 ]
- [ 2015 ]
- [ 2014 ]
- [ 2013 ]
- [ 2012 ]
- [ 2011 ]
- [ 2010 ]
- [ 2009 ]
- [ 2008 ]
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Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. . In Scientific Data, 11(1), bl 129. 2024.
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{Opportunistic Bacteria of Grapevine Crown Galls Are Equipped with the Genomic Repertoire for Opine Utilization}. . In Genome Biology and Evolution, 15(12), bl evad228. 2023.
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Ten (mostly) simple rules to future-proof trait data in ecological and evolutionary sciences. . In Methods in Ecology and Evolution, 14(2), K. Bacon (red.), bll 444–458. 2023.
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Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities. . In Environmental Microbiology. Wiley, 2023.
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Decreased efficiency of pollen collection due to Sulfoxaflor exposure leads to a reduction in the size of bumble bee workers in late European summer. . In Frontiers in Ecology and Evolution, 10. 2022.
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Critical links between biodiversity, nutrition and health in wild bee conservation. . In Trends in Ecology and Evolution, bl in press. 2022.
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Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding. . In Molecular Ecology, n/a(n/a). 2022.
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Do amino and fatty acid profiles of pollen provisions correlate with bacterial microbiomes in the mason bee Osmia bicornis?. . In Philosophical Transactions of the Royal Society B, bl in press. 2022.
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Phylogenetic relatedness of food plants reveals highest insect herbivore specialisation at intermediate temperatures along a broad climatic gradient. . In Global Change Biology, bl in press. 2022.
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Wild bee larval food composition in five European cities. . In Ecology, bl in press. 2022.
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Forest landscapes increase diversity of honeybee diets in the tropics. . In Forest Ecology and Management, bl in press. 2022.
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Pollinator-flower interactions in gardens during the COVID-19 pandemic lockdown of 2020. . In Journal of Pollination Ecology, bl in press. 2022.
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Diets maintained in a changing world: Does land-use intensification alter wild bee communities by selecting for flexible generalists?. . In Ecology and Evolution, bl in press. 2022.
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Osmotic adaptation and compatible solute biosynthesis of phototrophic bacteria as revealed from genome analyses. . In Microorganisms, 9(1), bl 46. 2021.
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Open Science principles for accelerating trait-based science across the Tree of Life. . In Nature Ecology & Evolution, bll 294–303. Nature Publishing Group, 2021.
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Many small rather than few large sources identified in long-term bee pollen diets in agroecosystems. . In Agriculture, Ecosystems and Environment. 2021.
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Effects of three flower field types on bumblebees and their pollen diets. . In Basic and Applied Ecology, 52, bll 95–108. 2021.
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Pollen diets and niche overlap of honey bees and native bees in protected areas. . In Basic and Applied Ecology, Special issue: Sequence based molecular ecology. 2021.
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Functional resin use in solitary bees. . In Ecological Entomology, bl in press. 2021.
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How bees find a way in European cities: pollen metabarcoding unravels multiple feeding strategies and their effects on distribution patterns in four wild bee species. . In Journal of Applied Ecology, bl in press. 2021.
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Inferring core genome phylogenies for bacteria. . In Bacterial Pangenomics (in press), A. Mengoni, M. Fondi, G. Bacci (reds.). Springer Verlag, Heidelberg, Germany, 2021.
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DNA sequence-based biodiversity and interaction ecology. . In Basic and Applied Ecology. 2021.
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Preservation methods of honey-bee collected pollen are not a source of bias in ITS2 metabarcoding. . In Environmental Monitoring and Assessment, bl in press. 2021.
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Cryptic species and hidden ecological interactions of halictine bees along an elevational gradient. . In Ecology and Evolution. 2021.
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Species richness is more important for ecosystem functioning than species turnover along an elevational gradient. . In Nature Ecology and Evolution, bl in press. 2021.
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Standard methods for pollen research. . In Journal of Apicultural Research, 60(4), bll 1–109. Taylor & Francis, 2021.
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Putative roles of bacteria in the carbon and nitrogen cycles in a tropical peat swamp forest. . In Basic and Applied Ecology, Special issue: Predictors of microbiomes. 2021.
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Changes amid constancy: flower and leaf microbiomes along land use gradients and between bioregions. . In Basic and Applied Ecology, 50, bll 1–15. Elsevier {BV}, 2021.
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Transmission of Bacterial Symbionts With and Without Genome Erosion Between a Beetle Host and the Plant Environment. . In Frontiers in Microbiology, 12. Frontiers Media {SA}, 2021.
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Tracking beekeepers in floristic regions of Iran: employing DNA metabarcoding to determine the geographical origin of honey. . In Heliyon. 2020.
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The genus Micromonospora as a model microorganism for bioactive natural product discovery. . In Royal Society of Chemistry Advances, 10(35), bll 20939–20959. The Royal Society of Chemistry, 2020.
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BCdatabaser: on-the-fly reference database creation for DNA (meta-)barcoding. . In Bioinformatics, bl in press. 2020.
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Floral Species Richness Correlates with Changes in the Nutritional Quality of Larval Diets in a Stingless Bee. . In Insects, 11(2). 2020.
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Introduced bees (Osmia cornifrons) collect pollen from both coevolved and novel host-plant species within their family-level phylogenetic preferences. . In Royal Society Open Science, bl in press. 2020.
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Susceptibility of red mason bee larvae to bacterial threats due to microbiome exchange with imported pollen provisions. . In Insects, 11(6). 2020.
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Strong phylogenetic constraint on transition metal incorporation in the mandibles of the hyper-diverse Hymenoptera (Insecta). . In Organisms, Diversity and Evolution, bl in press. 2020.
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CRISPR/Cas 9 mediated mutations as a new tool for studying taste in honeybees. . In Chemical Senses, bl bjaa063. 2020.
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Honey bee waggle dance communication increases diversity of pollen diets in intensively managed agricultural landscapes. . In Molecular Ecology, bl in press. 2019.
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Venus flytrap microbiota withstand harsh conditions during prey digestion. . In FEMS Microbiology Ecology, bl fiz010. 2019.
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Bacterial community structure and succession in nests of two megachilid bee genera. . In FEMS Microbiology Ecology, 95(1), bl fiy218. 2019.
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Linking the foraging patterns of megachilid bee species to nest bacteria. . In Ecology and Evolution, bl in press. 2019.
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Drivers, diversity and functions of solitary bee microbiota. . In Trends in Microbiology, bl in press. 2019.
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Climate–land-use interactions shape tropical mountain biodiversity and ecosystem functions. . In Nature. 2019.
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Cold-adaptation of Subtercola vilae DB165T, an isolate from a high-altitude cold volcano lake, as revealed by its genome analysis. . 2019.
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FENNEC - Functional Exploration of Natural Networks and Ecological Communities. . In Methods in Ecology and Evolution, bll 2028–2033. 2018.
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Draft Genome Sequence of Klebsiella sp. Strain C31 Isolated from a Malaysian Tropical Peat Swamp Forest. . In Genome announcements, 6(25), bll e00560–18. Am Soc Microbiol, 2018.
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Draft Genome Sequence of Dyella sp. Strain C9, Isolated from a Malaysian Tropical Peat Swamp Forest. . In Microbiol Res Announc, 7(12), bll e01083–18. Am Soc Microbiol, 2018.
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Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest. . In Genome announcements, 6(25), bll e00459–18. Am Soc Microbiol, 2018.
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Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest. . In Genome Announcements, 6(25). American Society for Microbiology Journals, 2018.
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Wild bees and their nests host Paenibacillus bacteria with functional potential of avail. . In Microbiome, (6), bl 229. 2018.
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Physical contact between mesenchymal stem cells and endothelial precursors induces distinct signatures with relevance to the very early phase of regeneration. . In Journal of Cellular Biochemistry. 2018.
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Microbial community structure in a Malaysian tropical peat swamp forest: the influence of tree species and depth. . In Frontiers in Microbiology, 9, bl 2859. 2018.
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The characterization of the circadian clock in the olive fly Bactrocera oleae (Diptera: Tephritidae) reveals a Drosophila-like organization. . In Scientific Reports, 8(1), bl 816. 2018.
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Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. . In PloS one, 12(8), bl e0183716. Public Library of Science, 2017.
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Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. . In PLoS one, in press. 2017.
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Generalist social bees maximize diversity intake in plant species-rich and resource-abundant environments. . In Ecosphere, 8(3), bl e01758-n/a. 2017.
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Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps. . In Evolution, in press. 2017.
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Crown galls of grapevine (Vitis vinifera) host distinct microbiota. . In Applied and Environmental Microbiology, 82, bll 5542–5552. 2016.
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Pollen DNA barcoding: current applications and future prospects. . In Genome, 59, bll 629–640. 2016.
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Laboratory rearing of solitary bees and wasps. . In Insect Science, 23, bl 918. 2016.
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DNA-Metabarcoding – ein neuer Blick auf organismische Diversität. . In BioSpektrum, 22, bll 147–150. 2016.
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Silent listeners: Can preferences of eavesdropping midges predict the parasitism risk of their host?. . In Behavioral Ecology, 27, bll 995–1003. 2016.
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Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1. . In Standards in Genomic Sciences. 2016.
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TBro: visualization and management of de novo transcriptomes. . In Database, 2016. 2016.
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biojs-io-biom, a {BioJS} component for handling data in Biological Observation Matrix ({BIOM}) format. . In F1000Research, 5, bl 2348. F1000 Research, Ltd., 2016.
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bcgTree: automatized phylogenetic tree building from bacterial core genomes. . In Genome, 59, bll 783–791. 2016.
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Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies. . In Microbial Ecology, 71, bll 938–953. 2016.
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Contact of myeloma cells induces a characteristic transcriptome signature in skeletal precursor cells--Implications for myeloma bone disease. . In Bone, 93, bll 155–166. Elsevier, 2016.
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Reptiles as reservoirs of bacterial infections: real threat or methodological bias?. . In Microbial Ecology, 70(3), bll 579–84. 2015.
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DNA-analyses of Venerupis philippinarum (Adams and Reeve, 1850) with a new and constant shell-pattern from Italy, Emilia Romagna. . In Malacologia, 86(1), bll 30–32. 2015.
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Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. . In BMC Ecology, 15, bl 20. 2015.
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ITS2 Database V: Twice as Much. . In Molecular Biology and Evolution, 32(11), bll 3030–3032. 2015.
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Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples. . In Plant Biology, 17, bll 558–566. 2015.
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Monophyletic clades of Macaranga pollinating thrips with high specificity to host plant taxonomic sections. . In Biological Journal of the Linnean Society, 116(3), bll 558–570. 2015.
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Functional and phylogenetic diversities of plant communities differently affect the structure of flower-visitor interactions and reveal convergences in floral traits. . In Evolutionary Ecology, 29, bll 437–450. 2015.
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Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity. . In FEMS Microbiology Ecology, 91(1), bl fiv09. 2015.
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Confirmation of warfarin resistance of naturally occurring VKORC1 variants by coexpression with coagulation factor IX and in silico protein modelling. . In BMC Genetics, 15, bl 17. 2014.
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Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6. . In European Journal of Human Genetics, (22), bll 208–215. Nature Publishing Group, 2014.
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Identification of WISP1 as an important survival factor in human mesenchymal stem cells. . In Gene, 551(2), bll 243–54. 2014.
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Density-dependent responses by bumblebees to flower dwelling bacteria. . In Apidologie, 45, bll 467–477. 2014.
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Pollen DNA barcoding using next-generation sequencing. . In Barcode Bulletin, 5(3), bl 8. 2014.
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Diverse microbiota identified in whole intact nest chambers of the red mason bee Osmia bicornis (Linnaeus 1758). . In PloS one, 8(10), bl e78296. Public Library of Science, 2013.
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Only distance matters--non-choosy females in a poison frog population. . In Frontiers in Zoology, 10(1), bl 29. BioMed Central Ltd, 2013.
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Common ancestry or environmental trait filters: cross-continental comparisons of trait--habitat relationships in tropical anuran amphibian assemblages. . In Global Ecology and Biogeography, 21(7), bll 704–715. Wiley Online Library, 2012.
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Hawaiian ant-flower networks: nectar-thieving ants prefer undefended native over introduced plants with floral defenses. . In Ecological Monographs, 81(2), bll 295–311. Eco Soc America, 2011.
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Composition of epiphytic bacterial communities differs on petals and leaves. . In Plant Biology, 13(6), bll 918–924. Wiley Online Library, 2011.
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Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. . In PLoS One, 6(2), bl e16931. Public Library of Science, 2011.
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Ribosomal RNA phylogenetics: the third dimension. . In Biologia, 65(3), bll 388–391. Springer, 2010.
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ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to em Coelastrum em (Chlorophyta, Chlorophyceae), including the new genera em Comasiella em and em Pectinodesmusem. . In Phycologia, 49(4), bll 325–335. The International Phycological Society Phycologia Business Office, Allen Press, 810 East 10th Street, PO Box 1897, Lawrence, KS 66044-8897, 2010.
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Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. . In Biology Direct, 5, bl 4. BioMed Central Ltd, 2010.
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The ITS2 Database III—sequences and structures for phylogeny. . In Nucleic Acids Research, 38(Suppl 1), bll D275-D279. Oxford Univ Press, 2010.
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ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus em Agrodiaetus em (Lepidoptera: Lycaenidae: \em Polyommatus\em ). . In BMC Evolutionary Biology, 9(1), bl 300. BioMed Central Ltd, 2009.
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Die Artenvielfalt der Amphibien in einem Tieflandregenwald auf Borneo. . bll 80–83. 2009.
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The importance of environmental heterogeneity for species diversity and assemblage structure in Bornean stream frogs. . In Journal of Animal Ecology, 78(2), bll 305–314. 2009.
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ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). . In BMC Evolutionary Biology, 8(1), bl 218. 2008.
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Geographic distribution: Parias sumatranus (Short Note). . In Herpetological Review, 39, bl 373. 2008.
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Geographic distribution: Xenodermus javanicus (Short Note). . In Herpetological Review, 39, bl 373. 2008.