@article{NumbergerRiedelMcEwenetal.2019,
  author    = {Numberger, Daniela and Riedel, Thomas and McEwen, Gayle and N{\"u}bel, Ulrich and Frentrup, Martinique and Schober, Isabel and Bunk, Boyke and Spr{\"o}er, Cathrin and Overmann, J{\"o}rg and Grossart, Hans-Peter and Greenwood, Alex D.},
  title     = {Genomic analysis of three Clostridioides difficile isolates from urban water sources},
  series = {Anaerobe},
  volume    = {56},
  journal   = {Anaerobe},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1075-9964},
  doi       = {10.1016/j.anaerobe.2019.01.002},
  pages     = {22 -- 26},
  year      = {2019},
  abstract  = {We investigated inflow of a wastewater treatment plant and sediment of an urban lake for the presence of Clostridioides difficile by cultivation and PCR. Among seven colonies we sequenced the complete genomes of three: two non-toxigenic isolates from wastewater and one toxigenic isolate from the urban lake. For all obtained isolates, a close genomic relationship with human-derived isolates was observed. (C) 2019 Elsevier Ltd. All rights reserved.},
  language  = {en}
}
@article{NumbergerDreierVullioudetal.2019,
  author    = {Numberger, Daniela and Dreier, Carole and Vullioud, Colin and Gabriel, G{\"u}lsah and Greenwood, Alex D. and Grossart, Hans-Peter},
  title     = {Recovery of influenza a viruses from lake water and sediments by experimental inoculation},
  series = {PLoS one},
  volume    = {14},
  journal   = {PLoS one},
  number    = {5},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0216880},
  pages     = {13},
  year      = {2019},
  abstract  = {Influenza A viruses (IAV) are zoonotic pathogens relevant to human, domestic animal and wildlife health. Many avian IAVs are transmitted among waterfowl via a faecal-oral-route. Therefore, environmental water where waterfowl congregate may play an important role in the ecology and epidemiology of avian IAV. Water and sediment may sustain and transmit virus among individuals or species. It is unclear at what concentrations waterborne viruses are infectious or remain detectable. To address this, we performed lake water and sediment dilution experiments with varying concentrations or infectious doses of four IAV strains from seal, turkey, duck and gull. To test for infectivity of the IAV strains in a concentration dependent manner, we applied cultivation to specific pathogen free (SPF) embryonated chicken eggs and Madin-Darby Canine Kidney (MDCK) cells. IAV recovery was more effective from embryonated chicken eggs than MDCK cells for freshwater lake dilutions, whereas, MDCK cells were more effective for viral recovery from sediment samples. Low infectious dose (1 PFU/200 mu L) was sufficient in most cases to detect and recover IAV from lake water dilutions. Sediment required higher initial infectious doses (>= 100 PFU/200 mu L).},
  language  = {en}
}
@misc{NumbergerDreierVullioudetal.2019,
  author    = {Numberger, Daniela and Dreier, Carola and Vullioud, Colin and Gabriel, Guelsah and Greenwood, Alex D. and Grossart, Hans-Peter},
  title     = {Correction: Recovery of influenza A viruses from lake water and sediments by experimental inoculation (vol 14, e0216880, 2019)},
  series = {PLoS one},
  volume    = {14},
  journal   = {PLoS one},
  number    = {6},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0218882},
  pages     = {1},
  year      = {2019},
  language  = {en}
}
@article{NumbergerGanzertZoccaratoetal.2019,
  author    = {Numberger, Daniela and Ganzert, Lars and Zoccarato, Luca and M{\"u}hldorfer, Kristin and Sauer, Sascha and Grossart, Hans-Peter and Greenwood, Alex D.},
  title     = {Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing},
  series = {Scientific reports},
  volume    = {9},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-019-46015-z},
  pages     = {14},
  year      = {2019},
  abstract  = {Wastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk.},
  language  = {en}
}
@article{HegerBernardVerdierGessleretal.2019,
  author    = {Heger, Tina and Bernard-Verdier, Maud and Gessler, Arthur and Greenwood, Alex D. and Grossart, Hans-Peter and Hilker, Monika and Keinath, Silvia and Kowarik, Ingo and K{\"u}ffer, Christoph and Marquard, Elisabeth and Mueller, Johannes and Niemeier, Stephanie and Onandia, Gabriela and Petermann, Jana S. and Rillig, Matthias C. and Rodel, Mark-Oliver and Saul, Wolf-Christian and Schittko, Conrad and Tockner, Klement and Joshi, Jasmin Radha and Jeschke, Jonathan M.},
  title     = {Towards an Integrative, Eco-Evolutionary Understanding of Ecological Novelty: Studying and Communicating Interlinked Effects of Global Change},
  series = {Bioscience},
  volume    = {69},
  journal   = {Bioscience},
  number    = {11},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0006-3568},
  doi       = {10.1093/biosci/biz095},
  pages     = {888 -- 899},
  year      = {2019},
  abstract  = {Global change has complex eco-evolutionary consequences for organisms and ecosystems, but related concepts (e.g., novel ecosystems) do not cover their full range. Here we propose an umbrella concept of "ecological novelty" comprising (1) a site-specific and (2) an organism-centered, eco-evolutionary perspective. Under this umbrella, complementary options for studying and communicating effects of global change on organisms, ecosystems, and landscapes can be included in a toolbox. This allows researchers to address ecological novelty from different perspectives, e.g., by defining it based on (a) categorical or continuous measures, (b) reference conditions related to sites or organisms, and (c) types of human activities. We suggest striving for a descriptive, non-normative usage of the term "ecological novelty" in science. Normative evaluations and decisions about conservation policies or management are important, but require additional societal processes and engagement with multiple stakeholders.},
  language  = {en}
}
@article{CuiLoeberAlquezarPlanasetal.2016,
  author    = {Cui, Pin and L{\"o}ber, Ulrike and Alquezar-Planas, David E. and Ishida, Yasuko and Courtiol, Alexandre and Timms, Peter and Johnson, Rebecca N. and Lenz, Dorina and Helgen, Kristofer M. and Roca, Alfred L. and Hartman, Stefanie and Greenwood, Alex D.},
  title     = {Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome},
  series = {PeerJ},
  volume    = {4},
  journal   = {PeerJ},
  publisher = {PeerJ Inc.},
  address   = {London},
  issn      = {2167-8359},
  doi       = {10.7717/peerj.1847},
  pages     = {29},
  year      = {2016},
  abstract  = {Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.},
  language  = {en}
}
@article{HartmannHasenkampMayeretal.2015,
  author    = {Hartmann, Stefanie and Hasenkamp, Natascha and Mayer, Jens and Michaux, Johan and Morand, Serge and Mazzoni, Camila J. and Roca, Alfred L. and Greenwood, Alex D.},
  title     = {Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse},
  series = {BMC genomics},
  volume    = {16},
  journal   = {BMC genomics},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-015-1766-z},
  pages     = {13},
  year      = {2015},
  abstract  = {Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present. Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences. Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.},
  language  = {en}
}