@article{BalintMartonSchatzetal.2018,
  author    = {Balint, Miklos and Marton, Orsolya and Schatz, Marlene and D{\"u}ring, Rolf-Alexander and Grossart, Hans-Peter},
  title     = {Proper experimental design requires randomization/balancing of molecular ecology experiments},
  series = {Ecology and evolution},
  volume    = {8},
  journal   = {Ecology and evolution},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.3687},
  pages     = {1786 -- 1793},
  year      = {2018},
  abstract  = {Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.},
  language  = {en}
}
@article{GoeritzBergerGegeetal.2018,
  author    = {G{\"o}ritz, Anna and Berger, Stella A. and Gege, Peter and Grossart, Hans-Peter and Nejstgaard, Jens C. and Riedel, Sebastian and R{\"o}ttgers, R{\"u}diger and Utschig, Christian},
  title     = {Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover},
  series = {Remote sensing / Molecular Diversity Preservation International (MDPI)},
  volume    = {10},
  journal   = {Remote sensing / Molecular Diversity Preservation International (MDPI)},
  number    = {2},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2072-4292},
  doi       = {10.3390/rs10020181},
  pages     = {19},
  year      = {2018},
  abstract  = {Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring.},
  language  = {en}
}
@article{CuadratIonescuDavilaetal.2018,
  author    = {Cuadrat, Rafael R. C. and Ionescu, Danny and Davila, Alberto M. R. and Grossart, Hans-Peter},
  title     = {Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics},
  series = {Frontiers in microbiology},
  volume    = {9},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2018.00251},
  pages     = {13},
  year      = {2018},
  abstract  = {Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.},
  language  = {en}
}
@article{LeachBeisnerCareyetal.2018,
  author    = {Leach, Taylor H. and Beisner, Beatrix E. and Carey, Cayelan C. and Pernica, Patricia and Rose, Kevin C. and Huot, Yannick and Brentrup, Jennifer A. and Domaizon, Isabelle and Grossart, Hans-Peter and Ibelings, Bastiaan W. and Jacquet, Stephan and Kelly, Patrick T. and Rusak, James A. and Stockwell, Jason D. and Straile, Dietmar and Verburg, Piet},
  title     = {Patterns and drivers of deep chlorophyll maxima structure in 100 lakes},
  series = {Limnology and oceanography},
  volume    = {63},
  journal   = {Limnology and oceanography},
  number    = {2},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0024-3590},
  doi       = {10.1002/lno.10656},
  pages     = {628 -- 646},
  year      = {2018},
  abstract  = {The vertical distribution of chlorophyll in stratified lakes and reservoirs frequently exhibits a maximum peak deep in the water column, referred to as the deep chlorophyll maximum (DCM). DCMs are ecologically important hot spots of primary production and nutrient cycling, and their location can determine vertical habitat gradients for primary consumers. Consequently, the drivers of DCM structure regulate many characteristics of aquatic food webs and biogeochemistry. Previous studies have identified light and thermal stratification as important drivers of summer DCM depth, but their relative importance across a broad range of lakes is not well resolved. We analyzed profiles of chlorophyll fluorescence, temperature, and light during summer stratification from 100 lakes in the Global Lake Ecological Observatory Network (GLEON) and quantified two characteristics of DCM structure: depth and thickness. While DCMs do form in oligotrophic lakes, we found that they can also form in eutrophic to dystrophic lakes. Using a random forest algorithm, we assessed the relative importance of variables associated with light attenuation vs. thermal stratification for predicting DCM structure in lakes that spanned broad gradients of morphometry and transparency. Our analyses revealed that light attenuation was a more important predictor of DCM depth than thermal stratification and that DCMs deepen with increasing lake clarity. DCM thickness was best predicted by lake size with larger lakes having thicker DCMs. Additionally, our analysis demonstrates that the relative importance of light and thermal stratification on DCM structure is not uniform across a diversity of lake types.},
  language  = {en}
}
@article{SchulzeMakuchWagnerKounavesetal.2018,
  author    = {Schulze-Makuch, Dirk and Wagner, Dirk and Kounaves, Samuel P. and Mangelsdorf, Kai and Devine, Kevin G. and de Vera, Jean-Pierre and Schmitt-Kopplin, Philippe and Grossart, Hans-Peter and Parro, Victor and Kaupenjohann, Martin and Galy, Albert and Schneider, Beate and Airo, Alessandro and Froesler, Jan and Davila, Alfonso F. and Arens, Felix L. and Caceres, Luis and Cornejo, Francisco Solis and Carrizo, Daniel and Dartnell, Lewis and DiRuggiero, Jocelyne and Flury, Markus and Ganzert, Lars and Gessner, Mark O. and Grathwohl, Peter and Guan, Lisa and Heinz, Jacob and Hess, Matthias and Keppler, Frank and Maus, Deborah and McKay, Christopher P. and Meckenstock, Rainer U. and Montgomery, Wren and Oberlin, Elizabeth A. and Probst, Alexander J. and Saenz, Johan S. and Sattler, Tobias and Schirmack, Janosch and Sephton, Mark A. and Schloter, Michael and Uhl, Jenny and Valenzuela, Bernardita and Vestergaard, Gisle and Woermer, Lars and Zamorano, Pedro},
  title     = {Transitory microbial habitat in the hyperarid Atacama Desert},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {115},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  number    = {11},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1714341115},
  pages     = {2670 -- 2675},
  year      = {2018},
  language  = {en}
}
@article{MantzoukiLurlingFastneretal.2018,
  author    = {Mantzouki, Evanthia and Lurling, Miquel and Fastner, Jutta and Domis, Lisette Nicole de Senerpont and Wilk-Wozniak, Elzbieta and Koreiviene, Judita and Seelen, Laura and Teurlincx, Sven and Verstijnen, Yvon and Krzton, Wojciech and Walusiak, Edward and Karosiene, Jurate and Kasperoviciene, Jurate and Savadova, Ksenija and Vitonyte, Irma and Cillero-Castro, Carmen and Budzynska, Agnieszka and Goldyn, Ryszard and Kozak, Anna and Rosinska, Joanna and Szelag-Wasielewska, Elzbieta and Domek, Piotr and Jakubowska-Krepska, Natalia and Kwasizur, Kinga and Messyasz, Beata and Pelechata, Aleksandra and Pelechaty, Mariusz and Kokocinski, Mikolaj and Garcia-Murcia, Ana and Real, Monserrat and Romans, Elvira and Noguero-Ribes, Jordi and Parreno Duque, David and Fernandez-Moran, Elisabeth and Karakaya, Nusret and Haggqvist, Kerstin and Demir, Nilsun and Beklioglu, Meryem and Filiz, Nur and Levi, Eti E. and Iskin, Ugur and Bezirci, Gizem and Tavsanoglu, Ulku Nihan and Ozhan, Koray and Gkelis, Spyros and Panou, Manthos and Fakioglu, Ozden and Avagianos, Christos and Kaloudis, Triantafyllos and Celik, Kemal and Yilmaz, Mete and Marce, Rafael and Catalan, Nuria and Bravo, Andrea G. and Buck, Moritz and Colom-Montero, William and Mustonen, Kristiina and Pierson, Don and Yang, Yang and Raposeiro, Pedro M. and Goncalves, Vitor and Antoniou, Maria G. and Tsiarta, Nikoletta and McCarthy, Valerie and Perello, Victor C. and Feldmann, Tonu and Laas, Alo and Panksep, Kristel and Tuvikene, Lea and Gagala, Ilona and Mankiewicz-Boczek, Joana and Yagci, Meral Apaydin and Cinar, Sakir and Capkin, Kadir and Yagci, Abdulkadir and Cesur, Mehmet and Bilgin, Fuat and Bulut, Cafer and Uysal, Rahmi and Obertegger, Ulrike and Boscaini, Adriano and Flaim, Giovanna and Salmaso, Nico and Cerasino, Leonardo and Richardson, Jessica and Visser, Petra M. and Verspagen, Jolanda M. H. and Karan, Tunay and Soylu, Elif Neyran and Maraslioglu, Faruk and Napiorkowska-Krzebietke, Agnieszka and Ochocka, Agnieszka and Pasztaleniec, Agnieszka and Antao-Geraldes, Ana M. and Vasconcelos, Vitor and Morais, Joao and Vale, Micaela and Koker, Latife and Akcaalan, Reyhan and Albay, Meric and Maronic, Dubravka Spoljaric and Stevic, Filip and Pfeiffer, Tanja Zuna and Fonvielle, Jeremy Andre and Straile, Dietmar and Rothhaupt, Karl-Otto and Hansson, Lars-Anders and Urrutia-Cordero, Pablo and Blaha, Ludek and Geris, Rodan and Frankova, Marketa and Kocer, Mehmet Ali Turan and Alp, Mehmet Tahir and Remec-Rekar, Spela and Elersek, Tina and Triantis, Theodoros and Zervou, Sevasti-Kiriaki and Hiskia, Anastasia and Haande, Sigrid and Skjelbred, Birger and Madrecka, Beata and Nemova, Hana and Drastichova, Iveta and Chomova, Lucia and Edwards, Christine and Sevindik, Tugba Ongun and Tunca, Hatice and OEnem, Burcin and Aleksovski, Boris and Krstic, Svetislav and Vucelic, Itana Bokan and Nawrocka, Lidia and Salmi, Pauliina and Machado-Vieira, Danielle and de Oliveira, Alinne Gurjao and Delgado-Martin, Jordi and Garcia, David and Cereijo, Jose Luis and Goma, Joan and Trapote, Mari Carmen and Vegas-Vilarrubia, Teresa and Obrador, Biel and Grabowska, Magdalena and Karpowicz, Maciej and Chmura, Damian and Ubeda, Barbara and Angel Galvez, Jose and Ozen, Arda and Christoffersen, Kirsten Seestern and Warming, Trine Perlt and Kobos, Justyna and Mazur-Marzec, Hanna and Perez-Martinez, Carmen and Ramos-Rodriguez, Eloisa and Arvola, Lauri and Alcaraz-Parraga, Pablo and Toporowska, Magdalena and Pawlik-Skowronska, Barbara and Niedzwiecki, Michal and Peczula, Wojciech and Leira, Manel and Hernandez, Armand and Moreno-Ostos, Enrique and Maria Blanco, Jose and Rodriguez, Valeriano and Juan Montes-Perez, Jorge and Palomino, Roberto L. and Rodriguez-Perez, Estela and Carballeira, Rafael and Camacho, Antonio and Picazo, Antonio and Rochera, Carlos and Santamans, Anna C. and Ferriol, Carmen and Romo, Susana and Miguel Soria, Juan and Dunalska, Julita and Sienska, Justyna and Szymanski, Daniel and Kruk, Marek and Kostrzewska-Szlakowska, Iwona and Jasser, Iwona and Zutinic, Petar and Udovic, Marija Gligora and Plenkovic-Moraj, Andelka and Frak, Magdalena and Bankowska-Sobczak, Agnieszka and Wasilewicz, Michal and Ozkan, Korhan and Maliaka, Valentini and Kangro, Kersti and Grossart, Hans-Peter and Paerl, Hans W. and Carey, Cayelan C. and Ibelings, Bas W.},
  title     = {Temperature effects explain continental scale distribution of cyanobacterial toxins},
  series = {Toxins},
  volume    = {10},
  journal   = {Toxins},
  number    = {4},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2072-6651},
  doi       = {10.3390/toxins10040156},
  pages     = {24},
  year      = {2018},
  abstract  = {Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.},
  language  = {en}
}
@article{HartmanGentzSchilleretal.2018,
  author    = {Hartman, Jan F. and Gentz, Torben and Schiller, Amanda and Greule, Markus and Grossart, Hans-Peter and Ionescu, Danny and Keppler, Frank and Martinez-Cruz, Karla and Sepulveda-Jauregui, Armando and Isenbeck-Schroeter, Margot},
  title     = {A f ast and sensitive method for the continuous in situ determination of dissolved methane and its delta C-13-isotope ratio in surface waters},
  series = {Limnology and Oceanography-methods},
  volume    = {16},
  journal   = {Limnology and Oceanography-methods},
  number    = {5},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1541-5856},
  doi       = {10.1002/lom3.10244},
  pages     = {273 -- 285},
  year      = {2018},
  abstract  = {A fast and sensitive method for the continuous determination of methane (CH4) and its stable carbon isotopic values (delta C-13-CH4) in surface waters was developed by applying a vacuum to a gas/liquid exchange membrane and measuring the extracted gases by a portable cavity ring-down spectroscopy analyser (M-CRDS). The M-CRDS was calibrated and characterized for CH4 concentration and delta C-13-CH4 with synthetic water standards. The detection limit of the M-CRDS for the simultaneous determination of CH4 and delta C-13-CH4 is 3.6 nmol L-1 CH4. A measurement precision of CH4 concentrations and delta C-13-CH4 in the range of 1.1\%, respectively, 1.7 parts per thousand (1 sigma) and accuracy (1.3\%, respectively, 0.8 parts per thousand [1 sigma]) was achieved for single measurements and averaging times of 10 min. The response time tau of 57 +/- 5 s allow determination of delta C-13-CH4 values more than twice as fast than other methods. The demonstrated M-CRDS method was applied and tested for Lake Stechlin (Germany) and compared with the headspace-gas chromatography and fast membrane CH4 concentration methods. Maximum CH4 concentrations (577 nmol L-1) and lightest delta C-13-CH4 (-35.2 parts per thousand) were found around the thermocline in depth profile measurements. The M-CRDS-method was in good agreement with other methods. Temporal variations in CH4 concentration and delta C-13-CH4 obtained in 24 h measurements indicate either local methane production/oxidation or physical variations in the thermocline. Therefore, these results illustrate the need of fast and sensitive analyses to achieve a better understanding of different mechanisms and pathways of CH4 formation in aquatic environments.},
  language  = {en}
}
@article{GarciaBuckHamiltonetal.2018,
  author    = {Garcia, Sarahi L. and Buck, Moritz and Hamilton, Joshua J. and Wurzbacher, Christian and Grossart, Hans-Peter and McMahon, Katherine D. and Eiler, Alexander},
  title     = {Model communities hint at promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria},
  series = {mSphere},
  volume    = {3},
  journal   = {mSphere},
  number    = {3},
  publisher = {American Society for Microbiology},
  address   = {Washington},
  issn      = {2379-5042},
  doi       = {10.1128/mSphere.00202-18},
  pages     = {8},
  year      = {2018},
  abstract  = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.},
  language  = {en}
}
@article{AriasAndresKluemperRojasJimenezetal.2018,
  author    = {Arias-Andres, Maria and Kluemper, Uli and Rojas-Jimenez, Keilor and Grossart, Hans-Peter},
  title     = {Microplastic pollution increases gene exchange in aquatic ecosystems},
  series = {Environmental pollution},
  volume    = {237},
  journal   = {Environmental pollution},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0269-7491},
  doi       = {10.1016/j.envpol.2018.02.058},
  pages     = {253 -- 261},
  year      = {2018},
  abstract  = {Pollution by microplastics in aquatic ecosystems is accumulating at an unprecedented scale, emerging as a new surface for biofilm formation and gene exchange. In this study, we determined the permissiveness of aquatic bacteria towards a model antibiotic resistance plasmid, comparing communities that form biofilms on microplastics vs. those that are free-living. We used an exogenous and red-fluorescent E. coli donor strain to introduce the green-fluorescent broad-host-range plasmid pKJKS which encodes for trimethoprim resistance. We demonstrate an increased frequency of plasmid transfer in bacteria associated with microplastics compared to bacteria that are free-living or in natural aggregates. Moreover, comparison of communities grown on polycarbonate filters showed that increased gene exchange occurs in a broad range of phylogenetically-diverse bacteria. Our results indicate horizontal gene transfer in this habitat could distinctly affect the ecology of aquatic microbial communities on a global scale. The spread of antibiotic resistance through microplastics could also have profound consequences for the evolution of aquatic bacteria and poses a neglected hazard for human health.},
  language  = {en}
}
@article{FabianZlatanovicMutzetal.2018,
  author    = {Fabian, Jenny and Zlatanovic, Sanja and Mutz, Michael and Grossart, Hans-Peter and van Geldern, Robert and Ulrich, Andreas and Gleixner, Gerd and Premke, Katrin},
  title     = {Environmental control on microbial turnover of leaf carbon in streams},
  series = {Frontiers in microbiology},
  volume    = {9},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2018.01044},
  pages     = {16},
  year      = {2018},
  abstract  = {In aquatic ecosystems, light availability can significantly influence microbial turnover of terrestrial organic matter through associated metabolic interactions between phototrophic and heterotrophic communities. However, particularly in streams, microbial functions vary significantly with the structure of the streambed, that is the distribution and spatial arrangement of sediment grains in the streambed. It is therefore essential to elucidate how environmental factors synergistically define the microbial turnover of terrestrial organic matter in order to better understand the ecological role of photoheterotrophic interactions in stream ecosystem processes. In outdoor experimental streams, we examined how the structure of streambeds modifies the influence of light availability on microbial turnover of leaf carbon (C). Furthermore, we investigated whether the studied relationships of microbial leaf C turnover to environmental conditions are affected by flow intermittency commonly occurring in streams. We applied leaves enriched with a C-13-stable isotope tracer and combined quantitative and isotope analyses. We thereby elucidated whether treatment induced changes in C turnover were associated with altered use of leaf C within the microbial food web. Moreover, isotope analyses were combined with measurements of microbial community composition to determine whether changes in community function were associated with a change in community composition. In this study, we present evidence, that environmental factors interactively determine how phototrophs and heterotrophs contribute to leaf C turnover. Light availability promoted the utilization of leaf C within the microbial food web, which was likely associated with a promoted availability of highly bioavailable metabolites of phototrophic origin. However, our results additionally confirm that the structure of the streambed modifies light-related changes in microbial C turnover. From our observations, we conclude that the streambed structure influences the strength of photo-heterotrophic interactions by defining the spatial availability of algal metabolites in the streambed and the composition of microbial communities. Collectively, our multifactorial approach provides valuable insights into environmental controls on the functioning of stream ecosystems.},
  language  = {en}
}
@article{RevereyGanzertLischeidetal.2018,
  author    = {Reverey, Florian and Ganzert, Lars and Lischeid, Gunnar and Ulrich, Andreas and Premke, Katrin and Grossart, Hans-Peter},
  title     = {Dry-wet cycles of kettle hole sediments leave a microbial and biogeochemical legacy},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {627},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2018.01.220},
  pages     = {985 -- 996},
  year      = {2018},
  abstract  = {Understanding interrelations between an environment's hydrological past and its current biogeochemistry is necessary for the assessment of biogeochemical and microbial responses to changing hydrological conditions. The question how previous dry-wet events determine the contemporary microbial and biogeochemical state is addressed in this study. Therefore, sediments exposed to the atmosphere of areas with a different hydrological past within one kettle hole, i.e. (1) the predominantly inundated pond center, (2) the pond margin frequently desiccated for longer periods and (3) an intermediate zone, were incubated with the same rewetting treatment. Physicochemical and textural characteristics were related to structural microbial parameters regarding carbon and nitrogen turnover, i.e. abundance of bacteria and fungi, denitrifiers (targeted by the nirK und nirS functional genes) and nitrate ammonifiers (targeted by the nrfA functional gene). Our study reveals that, in combination with varying sediment texture, the hydrological history creates distinct microbial habitats with defined boundary conditions within the kettle hole, mainly driven by redox conditions, pH and organic matter (OM) composition. OM mineralization, as indicated by CO2-outgassing, was most efficient in exposed sediments with a less stable hydrological past. The potential for nitrogen retention via nitrate ammonification was highest in the hydrologically rather stable pond center, counteracting nitrogen loss due to denitrification. Therefore, the degree of hydrological stability is an important factor leaving a microbial and biogeochemical legacy, which determines carbon and nitrogen losses from small lentic freshwater systems in the long term run.},
  language  = {en}
}
@misc{MuehlenbruchGrossartEigemannetal.2018,
  author    = {M{\"u}hlenbruch, Marco and Grossart, Hans-Peter and Eigemann, Falk and Voss, Maren},
  title     = {Mini-review: Phytoplankton-derived polysaccharides in the marine environment and their interactions with heterotrophic bacteria},
  series = {Environmental microbiology},
  volume    = {20},
  journal   = {Environmental microbiology},
  number    = {8},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1462-2912},
  doi       = {10.1111/1462-2920.14302},
  pages     = {2671 -- 2685},
  year      = {2018},
  abstract  = {Within the wealth of molecules constituting marine dissolved organic matter, carbohydrates make up the largest coherent and quantifiable fraction. Their main sources are from primary producers, which release large amounts of photosynthetic products - mainly polysaccharides - directly into the surrounding water via passive and active exudation. The organic carbon and other nutrients derived from these photosynthates enrich the 'phycosphere' and attract heterotrophic bacteria. The rapid uptake and remineralization of dissolved free monosaccharides by heterotrophic bacteria account for the barely detectable levels of these compounds. By contrast, dissolved combined polysaccharides can reach high concentrations, especially during phytoplankton blooms. Polysaccharides are too large to be taken up directly by heterotrophic bacteria, instead requiring hydrolytic cleavage to smaller oligo- or monomers by bacteria with a suitable set of exoenzymes. The release of diverse polysaccharides by various phytoplankton taxa is generally interpreted as the deposition of excess organic material. However, these molecules likely also fulfil distinct, yet not fully understood functions, as inferred from their active modulation in terms of quality and quantity when phytoplankton becomes nutrient limited or is exposed to heterotrophic bacteria. This minireview summarizes current knowledge regarding the exudation and composition of phytoplankton-derived exopolysaccharides and acquisition of these compounds by heterotrophic bacteria.},
  language  = {en}
}
@article{DarwallBremerichDeWeveretal.2018,
  author    = {Darwall, William and Bremerich, Vanessa and De Wever, Aaike and Dell, Anthony I. and Freyhof, Joerg and Gessner, Mark O. and Grossart, Hans-Peter and Harrison, Ian and Irvine, Ken and J{\"a}hnig, Sonja C. and Jeschke, Jonathan M. and Lee, Jessica J. and Lu, Cai and Lewandowska, Aleksandra M. and Monaghan, Michael T. and Nejstgaard, Jens C. and Patricio, Harmony and Schmidt-Kloiber, Astrid and Stuart, Simon N. and Thieme, Michele and Tockner, Klement and Turak, Eren and Weyl, Olaf},
  title     = {The alliance for freshwater life},
  series = {Aquatic Conservation: Marine and Freshwater Ecosystems},
  volume    = {28},
  journal   = {Aquatic Conservation: Marine and Freshwater Ecosystems},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1052-7613},
  doi       = {10.1002/aqc.2958},
  pages     = {1015 -- 1022},
  year      = {2018},
  abstract  = {1. Global pressures on freshwater ecosystems are high and rising. Viewed primarily as a resource for humans, current practices of water use have led to catastrophic declines in freshwater species and the degradation of freshwater ecosystems, including their genetic and functional diversity. Approximately three-quarters of the world's inland wetlands have been lost, one-third of the 28 000 freshwater species assessed for the International Union for Conservation of Nature (IUCN) Red List are threatened with extinction, and freshwater vertebrate populations are undergoing declines that are more rapid than those of terrestrial and marine species. This global loss continues unchecked, despite the importance of freshwater ecosystems as a source of clean water, food, livelihoods, recreation, and inspiration. 2. The causes of these declines include hydrological alterations, habitat degradation and loss, overexploitation, invasive species, pollution, and the multiple impacts of climate change. Although there are policy initiatives that aim to protect freshwater life, these are rarely implemented with sufficient conviction and enforcement. Policies that focus on the development and management of fresh waters as a resource for people almost universally neglect the biodiversity that they contain. 3. Here we introduce the Alliance for Freshwater Life, a global initiative, uniting specialists in research, data synthesis, conservation, education and outreach, and policymaking. This expert network aims to provide the critical mass required for the effective representation of freshwater biodiversity at policy meetings, to develop solutions balancing the needs of development and conservation, and to better convey the important role freshwater ecosystems play in human well-being. Through this united effort we hope to reverse this tide of loss and decline in freshwater biodiversity. We introduce several short- and medium-term actions as examples for making positive change, and invite individuals, organizations, authorities, and governments to join the Alliance for Freshwater Life.},
  language  = {en}
}
@article{AriasAndresKettnerMikietal.2018,
  author    = {Arias Andr{\´e}s, Mar{\´i}a de Jes{\´u}s and Kettner, Marie Therese and Miki, Takeshi and Grossart, Hans-Peter},
  title     = {Microplastics: New substrates for heterotrophic activity contribute to altering organic matter cycles in aquatic ecosystems},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {635},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2018.04.199},
  pages     = {1152 -- 1159},
  year      = {2018},
  abstract  = {Heterotrophic microbes with the capability to process considerable amounts of organic matter can colonize microplastic particles (MP) in aquatic ecosystems. Weather colonization of microorganisms on MP will alter ecological niche and functioning of microbial communities remains still unanswered. Therefore, we compared the functional diversity of biofilms on microplastics when incubated in three lakes in northeastern Germany differing in trophy and limnological features. For all lakes, we compared heterotrophic activities of MP biofilms with those of microorganisms in the surrounding water by using Biolog (R) EcoPlates and assessed their oxygen consumption in microcosm assays with and without MP. The present study found that the total biofilm biomass was higher in the oligo-mesotrophic and dystrophic lakes than in the eutrophic lake. In all lakes, functional diversity profiles of MP biofilms consistently differed from those in the surrounding water. However, solely in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. These results demonstrate that the functionality and hence the ecological role of MP-associated microbial communities are context-dependent, i.e. different environments lead to substantial changes in biomass build up and heterotrophic activities of MP biofilms. We propose that MP surfaces act as new niches for aquatic microorganisms and that the constantly increasing MP pollution has the potential to globally impact carbon dynamics of pelagic environments by altering heterotrophic activities. (C) 2018 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{MantzoukiCampbellvanLoonetal.2018,
  author    = {Mantzouki, Evanthia and Campbell, James and van Loon, Emiel and Visser, Petra and Konstantinou, Iosif and Antoniou, Maria and Giuliani, Gregory and Machado-Vieira, Danielle and de Oliveira, Alinne Gurjao and Maronic, Dubravka Spoljaric and Stevic, Filip and Pfeiffer, Tanja Zuna and Vucelic, Itana Bokan and Zutinic, Petar and Udovic, Marija Gligora and Plenkovic-Moraj, Andelka and Tsiarta, Nikoletta and Blaha, Ludek and Geris, Rodan and Frankova, Marketa and Christoffersen, Kirsten Seestern and Warming, Trine Perlt and Feldmann, Tonu and Laas, Alo and Panksep, Kristel and Tuvikene, Lea and Kangro, Kersti and Haggqvist, Kerstin and Salmi, Pauliina and Arvola, Lauri and Fastner, Jutta and Straile, Dietmar and Rothhaupt, Karl-Otto and Fonvielle, Jeremy Andre and Grossart, Hans-Peter and Avagianos, Christos and Kaloudis, Triantafyllos and Triantis, Theodoros and Zervou, Sevasti-Kiriaki and Hiskia, Anastasia and Gkelis, Spyros and Panou, Manthos and McCarthy, Valerie and Perello, Victor C. and Obertegger, Ulrike and Boscaini, Adriano and Flaim, Giovanna and Salmaso, Nico and Cerasino, Leonardo and Koreiviene, Judita and Karosiene, Jurate and Kasperoviciene, Jurate and Savadova, Ksenija and Vitonyte, Irma and Haande, Sigrid and Skjelbred, Birger and Grabowska, Magdalena and Karpowicz, Maciej and Chmura, Damian and Nawrocka, Lidia and Kobos, Justyna and Mazur-Marzec, Hanna and Alcaraz-Parraga, Pablo and Wilk-Wozniak, Elzbieta and Krzton, Wojciech and Walusiak, Edward and Gagala, Ilona and Mankiewicz-Boczek, Joana and Toporowska, Magdalena and Pawlik-Skowronska, Barbara and Niedzwiecki, Michal and Peczula, Wojciech and Napiorkowska-Krzebietke, Agnieszka and Dunalska, Julita and Sienska, Justyna and Szymanski, Daniel and Kruk, Marek and Budzynska, Agnieszka and Goldyn, Ryszard and Kozak, Anna and Rosinska, Joanna and Szelag-Wasielewska, Elzbieta and Domek, Piotr and Jakubowska-Krepska, Natalia and Kwasizur, Kinga and Messyasz, Beata and Pelechata, Aleksandra and Pelechaty, Mariusz and Kokocinski, Mikolaj and Madrecka, Beata and Kostrzewska-Szlakowska, Iwona and Frak, Magdalena and Bankowska-Sobczak, Agnieszka and Wasilewicz, Michal and Ochocka, Agnieszka and Pasztaleniec, Agnieszka and Jasser, Iwona and Antao-Geraldes, Ana M. and Leira, Manel and Hernandez, Armand and Vasconcelos, Vitor and Morais, Joao and Vale, Micaela and Raposeiro, Pedro M. and Goncalves, Vitor and Aleksovski, Boris and Krstic, Svetislav and Nemova, Hana and Drastichova, Iveta and Chomova, Lucia and Remec-Rekar, Spela and Elersek, Tina and Delgado-Martin, Jordi and Garcia, David and Luis Cereijo, Jose and Goma, Joan and Carmen Trapote, Mari and Vegas-Vilarrubia, Teresa and Obrador, Biel and Garcia-Murcia, Ana and Real, Monserrat and Romans, Elvira and Noguero-Ribes, Jordi and Parreno Duque, David and Fernandez-Moran, Elisabeth and Ubeda, Barbara and Angel Galvez, Jose and Marce, Rafael and Catalan, Nuria and Perez-Martinez, Carmen and Ramos-Rodriguez, Eloisa and Cillero-Castro, Carmen and Moreno-Ostos, Enrique and Maria Blanco, Jose and Rodriguez, Valeriano and Juan Montes-Perez, Jorge and Palomino, Roberto L. and Rodriguez-Perez, Estela and Carballeira, Rafael and Camacho, Antonio and Picazo, Antonio and Rochera, Carlos and Santamans, Anna C. and Ferriol, Carmen and Romo, Susana and Soria, Juan Miguel and Hansson, Lars-Anders and Urrutia-Cordero, Pablo and Ozen, Arda and Bravo, Andrea G. and Buck, Moritz and Colom-Montero, William and Mustonen, Kristiina and Pierson, Don and Yang, Yang and Verspagen, Jolanda M. H. and Domis, Lisette N. de Senerpont and Seelen, Laura and Teurlincx, Sven and Verstijnen, Yvon and Lurling, Miquel and Maliaka, Valentini and Faassen, Elisabeth J. and Latour, Delphine and Carey, Cayelan C. and Paerl, Hans W. and Torokne, Andrea and Karan, Tunay and Demir, Nilsun and Beklioglu, Meryem and Filiz, Nur and Levi, Eti E. and Iskin, Ugur and Bezirci, Gizem and Tavsanoglu, Ulku Nihan and Celik, Kemal and Ozhan, Koray and Karakaya, Nusret and Kocer, Mehmet Ali Turan and Yilmaz, Mete and Maraslioglu, Faruk and Fakioglu, Ozden and Soylu, Elif Neyran and Yagci, Meral Apaydin and Cinar, Sakir and Capkin, Kadir and Yagci, Abdulkadir and Cesur, Mehmet and Bilgin, Fuat and Bulut, Cafer and Uysal, Rahmi and Koker, Latife and Akcaalan, Reyhan and Albay, Meric and Alp, Mehmet Tahir and Ozkan, Korhan and Sevindik, Tugba Ongun and Tunca, Hatice and Onem, Burcin and Richardson, Jessica and Edwards, Christine and Bergkemper, Victoria and Beirne, Eilish and Cromie, Hannah and Ibelings, Bastiaan W.},
  title     = {Data Descriptor: A European Multi Lake Survey dataset of environmental variables, phytoplankton pigments and cyanotoxins},
  series = {Scientific Data},
  volume    = {5},
  journal   = {Scientific Data},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2052-4463},
  doi       = {10.1038/sdata.2018.226},
  pages     = {13},
  year      = {2018},
  abstract  = {Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment.},
  language  = {en}
}
@article{BizicIonescuIonescuGrossart2018,
  author    = {Bizic-Ionescu, Mina and Ionescu, Danny and Grossart, Hans-Peter},
  title     = {Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems},
  series = {Frontiers in microbiology},
  volume    = {9},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2018.02569},
  pages     = {15},
  year      = {2018},
  abstract  = {The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3-4 particles of identical source and age and further evaluated the consequences of averaging 10-1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as "the bottle-effect." In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn't change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.},
  language  = {en}
}
@article{VandenWyngaertRojasJimenezSetoetal.2018,
  author    = {Van den Wyngaert, Silke and Rojas-Jimenez, Keilor and Seto, Kensuke and Kagami, Maiko and Grossart, Hans-Peter},
  title     = {Diversity and Hidden Host Specificity of Chytrids Infecting Colonial Volvocacean Algae},
  series = {Journal of Eukaryotic Microbiology},
  volume    = {65},
  journal   = {Journal of Eukaryotic Microbiology},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1066-5234},
  doi       = {10.1111/jeu.12632},
  pages     = {870 -- 881},
  year      = {2018},
  abstract  = {Chytrids are zoosporic fungi that play an important, but yet understudied, ecological role in aquatic ecosystems. Many chytrid species have been morphologically described as parasites on phytoplankton. However, the majority of them have rarely been isolated and lack DNA sequence data. In this study we isolated and cultivated three parasitic chytrids, infecting a common volvocacean host species, Yamagishiella unicocca. To identify the chytrids, we characterized morphology and life cycle, and analyzed phylogenetic relationships based on 18S and 28S rDNA genes. Host range and specificity of the chytrids was determined by cross-infection assays with host strains, characterized by rbcL and ITS markers. We were able to confirm the identity of two chytrid strains as Endocoenobium eudorinae Ingold and Dangeardia mamillata Schroder and described the third chytrid strain as Algomyces stechlinensis gen. et sp. nov. The three chytrids were assigned to novel and phylogenetically distant clades within the phylum Chytridiomycota, each exhibiting different host specificities. By integrating morphological and molecular data of both the parasitic chytrids and their respective host species, we unveiled cryptic host-parasite associations. This study highlights that a high prevalence of (pseudo)cryptic diversity requires molecular characterization of both phytoplankton host and parasitic chytrid to accurately identify and compare host range and specificity, and to study phytoplankton-chytrid interactions in general.},
  language  = {en}
}
@article{BachmannHeimbachHassenruecketal.2018,
  author    = {Bachmann, Jennifer and Heimbach, Tabea and Hassenr{\"u}ck, Christiane and Kopprio, German A. and Iversen, Morten Hvitfeldt and Grossart, Hans-Peter and G{\"a}rdes, Astrid},
  title     = {Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System},
  series = {Frontiers in microbiology},
  volume    = {9},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2018.02836},
  pages     = {13},
  year      = {2018},
  abstract  = {Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; > 3.0 mu m) and free-living (FL; 0.2-3.0 mu m) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.},
  language  = {en}
}
@article{MantzoukiBekliogluBrookesetal.2018,
  author    = {Mantzouki, Evanthia and Beklioglu, Meryem and Brookes, Justin D. and Domis, Lisette Nicole de Senerpont and Dugan, Hilary A. and Doubek, Jonathan P. and Grossart, Hans-Peter and Nejstgaard, Jens C. and Pollard, Amina I. and Ptacnik, Robert and Rose, Kevin C. and Sadro, Steven and Seelen, Laura and Skaff, Nicholas K. and Teubner, Katrin and Weyhenmeyer, Gesa A. and Ibelings, Bastiaan W.},
  title     = {Snapshot surveys for lake monitoring, more than a shot in the dark},
  series = {Frontiers in Ecology and Evolution},
  volume    = {6},
  journal   = {Frontiers in Ecology and Evolution},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {2296-701X},
  doi       = {10.3389/fevo.2018.00201},
  pages     = {5},
  year      = {2018},
  language  = {en}
}
@misc{BalintPfenningerGrossartetal.2018,
  author    = {B{\´a}lint, Mikl{\´o}s and Pfenninger, Markus and Grossart, Hans-Peter and Taberlet, Pierre and Vellend, Mark and Leibold, Mathew A. and Englund, Goran and Bowler, Diana},
  title     = {Environmental DNA time series in ecology},
  series = {Trends in ecology \& evolution},
  volume    = {33},
  journal   = {Trends in ecology \& evolution},
  number    = {12},
  publisher = {Elsevier},
  address   = {London},
  issn      = {0169-5347},
  doi       = {10.1016/j.tree.2018.09.003},
  pages     = {945 -- 957},
  year      = {2018},
  abstract  = {Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.},
  language  = {en}
}
@article{BatistaWoodhouseGrossartetal.2018,
  author    = {Batista, A. M. M. and Woodhouse, Jason Nicholas and Grossart, Hans-Peter and Giani, A.},
  title     = {Methanogenic archaea associated to Microcystis sp. in field samples and in culture},
  series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  volume    = {831},
  journal   = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0018-8158},
  doi       = {10.1007/s10750-018-3655-3},
  pages     = {163 -- 172},
  year      = {2018},
  abstract  = {Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities.},
  language  = {en}
}
@misc{AriasAndresRojasJimenezGrossart2018,
  author    = {Arias-Andres, Maria and Rojas-Jimenez, Keilor and Grossart, Hans-Peter},
  title     = {Collateral effects of microplastic pollution on aquatic microorganisms},
  series = {Trends in Analytical Chemistry},
  volume    = {112},
  journal   = {Trends in Analytical Chemistry},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0165-9936},
  doi       = {10.1016/j.trac.2018.11.041},
  pages     = {234 -- 240},
  year      = {2018},
  abstract  = {Microplastics (MP) provide a unique and extensive surface for microbial colonization in aquatic ecosystems. The formation of microorganism-microplastic complexes, such as biofilms, maximizes the degradation of organic matter and horizontal gene transfer. In this context, MP affect the structure and function of microbial communities, which in turn render the physical and chemical fate of MP. This new paradigm generates challenges for microbiology, ecology, and ecotoxicology. Dispersal of MP is concomitant with that of their associated microorganisms and their mobile genetic elements, including antibiotic resistance genes, islands of pathogenicity, and diverse metabolic pathways. Functional changes in aquatic microbiomes can alter carbon metabolism and food webs, with unknown consequences on higher organisms or human microbiomes and hence health. Here, we examine a variety of effects of MP pollution from the microbial ecology perspective, whose repercussions on aquatic ecosystems begin to be unraveled. (C) 2018 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@misc{MantzoukiLuerlingFastneretal.2018,
  author    = {Mantzouki, Evanthia and L{\"u}rling, Miquel and Fastner, Jutta and Domis, Lisette Nicole de Senerpont and Wilk-Wo{\'{z}}niak, Elżbieta and Koreiviene, Judita and Seelen, Laura and Teurlincx, Sven and Verstijnen, Yvon and Krztoń, Wojciech and Walusiak, Edward and Karosienė, Jūratė and Kasperovičienė, Jūratė and Savadova, Ksenija and Vitonytė, Irma and Cillero-Castro, Carmen and Budzyńska, Agnieszka and Goldyn, Ryszard and Kozak, Anna and Rosińska, Joanna and Szeląg-Wasielewska, Elżbieta and Domek, Piotr and Jakubowska-Krepska, Natalia and Kwasizur, Kinga and Messyasz, Beata and Pełechata, Aleksandra and Pełechaty, Mariusz and Kokocinski, Mikolaj and Garc{\´i}a-Murcia, Ana and Real, Monserrat and Romans, Elvira and Noguero-Ribes, Jordi and Duque, David Parre{\~n}o and Fern{\´a}ndez-Mor{\´a}n, El{\´i}sabeth and Karakaya, Nusret and H{\"a}ggqvist, Kerstin and Beklioğlu, Meryem and Filiz, Nur and Levi, Eti E. and Iskin, Uğur and Bezirci, Gizem and Tav{\c{s}}anoğlu, {\"U}lk{\"u} Nihan and {\"O}zhan, Koray and Gkelis, Spyros and Panou, Manthos and Fakioglu, {\"O}zden and Avagianos, Christos and Kaloudis, Triantafyllos and {\c{C}}elik, Kemal and Yilmaz, Mete and Marc{\´e}, Rafael and Catal{\´a}n, Nuria and Bravo, Andrea G. and Buck, Moritz and Colom-Montero, William and Mustonen, Kristiina and Pierson, Don and Yang, Yang and Raposeiro, Pedro M. and Gon{\c{c}}alves, V{\´i}tor and Antoniou, Maria G. and Tsiarta, Nikoletta and McCarthy, Valerie and Perello, Victor C. and Feldmann, T{\~o}nu and Laas, Alo and Panksep, Kristel and Tuvikene, Lea and Gagala, Ilona and Mankiewicz-Boczek, Joana and Yağc{\i}, Meral Apayd{\i}n and {\c{C}}{\i}nar, Şakir and {\c{C}}apk{\i}n, Kadir and Yağc{\i}, Abdulkadir and Cesur, Mehmet and Bilgin, Fuat and Bulut, Cafer and Uysal, Rahmi and Obertegger, Ulrike and Boscaini, Adriano and Flaim, Giovanna and Salmaso, Nico and Cerasino, Leonardo and Richardson, Jessica and Visser, Petra M. and Verspagen, Jolanda M. H. and Karan, T{\"u}nay and Soylu, Elif Neyran and Mara{\c{s}}l{\i}oğlu, Faruk and Napi{\´o}rkowska-Krzebietke, Agnieszka and Ochocka, Agnieszka and Pasztaleniec, Agnieszka and Ant{\~a}o-Geraldes, Ana M. and Vasconcelos, Vitor and Morais, Jo{\~a}o and Vale, Micaela and K{\"o}ker, Latife and Ak{\c{c}}aalan, Reyhan and Albay, Meri{\c{c}} and Maronić, Dubravka Špoljarić and Stević, Filip and Pfeiffer, Tanja Žuna and Fonvielle, Jeremy Andre and Straile, Dietmar and Rothhaupt, Karl-Otto and Hansson, Lars-Anders and Urrutia-Cordero, Pablo and Bl{\´a}ha, Luděk and Geriš, Rodan and Fr{\´a}nkov{\´a}, Mark{\´e}ta and Ko{\c{c}}er, Mehmet Ali Turan and Alp, Mehmet Tahir and Remec-Rekar, Spela and Elersek, Tina and Triantis, Theodoros and Zervou, Sevasti-Kiriaki and Hiskia, Anastasia and Haande, Sigrid and Skjelbred, Birger and Madrecka, Beata and Nemova, Hana and Drastichova, Iveta and Chomova, Lucia and Edwards, Christine and Sevindik, Tuğba Ongun and Tunca, Hatice and {\"O}nem, Bur{\c{c}}in and Aleksovski, Boris and Krstić, Svetislav and Vucelić, Itana Bokan and Nawrocka, Lidia and Salmi, Pauliina and Machado-Vieira, Danielle and Oliveira, Alinne Gurj{\~a}o De and Delgado-Mart{\´i}n, Jordi and Garc{\´i}a, David and Cereijo, Jose Lu{\´i}s and Gom{\`a}, Joan and Trapote, Mari Carmen and Vegas-Vilarr{\´u}bia, Teresa and Obrador, Biel and Grabowska, Magdalena and Karpowicz, Maciej and Chmura, Damian and {\´U}beda, B{\´a}rbara and G{\´a}lvez, Jos{\´e} {\´A}ngel and {\"O}zen, Arda and Christoffersen, Kirsten Seestern and Warming, Trine Perlt and Kobos, Justyna and Mazur-Marzec, Hanna and P{\´e}rez-Mart{\´i}nez, Carmen and Ramos-Rodr{\´i}guez, Elo{\´i}sa and Arvola, Lauri and Alcaraz-P{\´a}rraga, Pablo and Toporowska, Magdalena and Pawlik-Skowronska, Barbara and Nied{\'{z}}wiecki, Michał and Pęczuła, Wojciech and Leira, Manel and Hern{\´a}ndez, Armand and Moreno-Ostos, Enrique and Blanco, Jos{\´e} Mar{\´i}a and Rodr{\´i}guez, Valeriano and Montes-P{\´e}rez, Jorge Juan and Palomino, Roberto L. and Rodr{\´i}guez-P{\´e}rez, Estela and Carballeira, Rafael and Camacho, Antonio and Picazo, Antonio and Rochera, Carlos and Santamans, Anna C. and Ferriol, Carmen and Romo, Susana and Soria, Juan Miguel and Dunalska, Julita and Sieńska, Justyna and Szymański, Daniel and Kruk, Marek and Kostrzewska-Szlakowska, Iwona and Jasser, Iwona and Žutinić, Petar and Udovič, Marija Gligora and Plenković-Moraj, Anđelka and Frąk, Magdalena and Bańkowska-Sobczak, Agnieszka and Wasilewicz, Michał and {\"O}zkan, Korhan and Maliaka, Valentini and Kangro, Kersti and Grossart, Hans-Peter and Paerl, Hans W. and Carey, Cayelan C. and Ibelings, Bas W.},
  title     = {Temperature effects explain continental scale distribution of cyanobacterial toxins},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1105},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42790},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427902},
  pages     = {26},
  year      = {2018},
  abstract  = {Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.},
  language  = {en}
}
@misc{GoeritzBergerGegeetal.2018,
  author    = {G{\"o}ritz, Anna and Berger, Stella A. and Gege, Peter and Grossart, Hans-Peter and Nejstgaard, Jens C. and Riedel, Sebastian and R{\"o}ttgers, R{\"u}diger and Utschig, Christian},
  title     = {Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {941},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-45983},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459837},
  pages     = {21},
  year      = {2018},
  abstract  = {Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring.},
  language  = {en}
}
@misc{CuadratIonescuDavilaetal.2018,
  author    = {Cuadrat, Rafael R. C. and Ionescu, Danny and D{\´a}vila, Alberto M. R. and Grossart, Hans-Peter},
  title     = {Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {924},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44565},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445656},
  pages     = {15},
  year      = {2018},
  abstract  = {Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.},
  language  = {en}
}
@misc{GarciaBuckHamiltonetal.2018,
  author    = {Garcia, Sarahi L. and Buck, Moritz and Hamilton, Joshua J. and Wurzbacher, Christian and Grossart, Hans-Peter and McMahon, Katherine D. and Eiler, Alexander},
  title     = {Model communities hint at promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {714},
  doi       = {10.25932/publishup-42729},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427299},
  pages     = {8},
  year      = {2018},
  abstract  = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.},
  language  = {en}
}
@misc{FabianZlatanovićMutzetal.2018,
  author    = {Fabian, Jenny and Zlatanović, Sanja and Mutz, Michael and Grossart, Hans-Peter and Geldern, Robert van and Ulrich, Andreas and Gleixner, Gerd and Premke, Katrin},
  title     = {Environmental control on microbial turnover of leaf carbon in streams},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {693},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42633},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-426336},
  pages     = {16},
  year      = {2018},
  abstract  = {In aquatic ecosystems, light availability can significantly influence microbial turnover of terrestrial organic matter through associated metabolic interactions between phototrophic and heterotrophic communities. However, particularly in streams, microbial functions vary significantly with the structure of the streambed, that is the distribution and spatial arrangement of sediment grains in the streambed. It is therefore essential to elucidate how environmental factors synergistically define the microbial turnover of terrestrial organic matter in order to better understand the ecological role of photo-heterotrophic interactions in stream ecosystem processes. In outdoor experimental streams, we examined how the structure of streambeds modifies the influence of light availability on microbial turnover of leaf carbon (C). Furthermore, we investigated whether the studied relationships of microbial leaf C turnover to environmental conditions are affected by flow intermittency commonly occurring in streams. We applied leaves enriched with a 13C-stable isotope tracer and combined quantitative and isotope analyses. We thereby elucidated whether treatment induced changes in C turnover were associated with altered use of leaf C within the microbial food web. Moreover, isotope analyses were combined with measurements of microbial community composition to determine whether changes in community function were associated with a change in community composition. In this study, we present evidence, that environmental factors interactively determine how phototrophs and heterotrophs contribute to leaf C turnover. Light availability promoted the utilization of leaf C within the microbial food web, which was likely associated with a promoted availability of highly bioavailable metabolites of phototrophic origin. However, our results additionally confirm that the structure of the streambed modifies light-related changes in microbial C turnover. From our observations, we conclude that the streambed structure influences the strength of photo-heterotrophic interactions by defining the spatial availability of algal metabolites in the streambed and the composition of microbial communities. Collectively, our multifactorial approach provides valuable insights into environmental controls on the functioning of stream ecosystems.},
  language  = {en}
}
@misc{BalintMartonSchatzetal.2018,
  author    = {B{\´a}lint, Mikl{\´o}s and M{\´a}rton, Orsolya and Schatz, Marlene and D{\"u}ring, Rolf-Alexander and Grossart, Hans-Peter},
  title     = {Proper experimental design requires randomization/balancing of molecular ecology experiments},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {616},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42387},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-423878},
  pages     = {8},
  year      = {2018},
  abstract  = {Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.},
  language  = {en}
}