@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{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{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{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{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} }