@article{RadosavljevicLantuitKnoblauchetal.2022, author = {Radosavljevic, Boris and Lantuit, Hugues and Knoblauch, Christian and Couture, Nicole and Herzschuh, Ulrike and Fritz, Michael}, title = {Arctic nearshore sediment dynamics - an example from Herschel Island - Qikiqtaruk, Canada}, series = {Journal of marine science and engineering}, volume = {10}, journal = {Journal of marine science and engineering}, number = {11}, publisher = {MDPI}, address = {Basel}, issn = {2077-1312}, doi = {10.3390/jmse10111589}, pages = {18}, year = {2022}, abstract = {Increasing arctic coastal erosion rates imply a greater release of sediments and organic matter into the coastal zone. With 213 sediment samples taken around Herschel Island-Qikiqtaruk, Canadian Beaufort Sea, we aimed to gain new insights on sediment dynamics and geochemical properties of a shallow arctic nearshore zone. Spatial characteristics of nearshore sediment texture (moderately to poorly sorted silt) are dictated by hydrodynamic processes, but ice-related processes also play a role. We determined organic matter (OM) distribution and inferred the origin and quality of organic carbon by C/N ratios and stable carbon isotopes delta C-13. The carbon content was higher offshore and in sheltered areas (mean: 1.0 wt.\%., S.D.: 0.9) and the C/N ratios also showed a similar spatial pattern (mean: 11.1, S.D.: 3.1), while the delta C-13 (mean: -26.4 parts per thousand VPDB, S.D.: 0.4) distribution was more complex. We compared the geochemical parameters of our study with terrestrial and marine samples from other studies using a bootstrap approach. Sediments of the current study contained 6.5 times and 1.8 times less total organic carbon than undisturbed and disturbed terrestrial sediments, respectively. Therefore, degradation of OM and separation of carbon pools take place on land and continue in the nearshore zone, where OM is leached, mineralized, or transported beyond the study area.}, language = {en} } @article{DommainAndamaMcDonoughetal.2020, author = {Dommain, Ren{\´e} and Andama, Morgan and McDonough, Molly M. and Prado, Natalia A. and Goldhammer, Tobias and Potts, Richard and Maldonado, Jes{\´u}s E. and Nkurunungi, John Bosco and Campana, Michael G.}, title = {The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA}, series = {Frontiers in Ecology and Evolution}, volume = {8}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-701X}, doi = {10.3389/fevo.2020.00218}, pages = {26}, year = {2020}, abstract = {Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth's biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3\% of our metagenomic data of a total 81.8 million unique, merged reads cannot be taxonomically identified due to the absence of genomic references in public databases. Of the remaining 7.7\%, most of the data (93.0\%) derive from Bacteria and Archaea, whereas only 0-5.8\% are from Metazoa and 0-6.9\% from Viridiplantae, in part due to unbalanced taxa representation in the reference data. The plant DNA record at ordinal level agrees well with local pollen data but resolves less diversity. Our animal DNA record reveals the presence of 41 native taxa (16 orders) including Afrotheria, Carnivora, and Ruminantia at Bwindi during the past 2200 years. Overall, we observe no decline in taxonomic richness with increasing age suggesting that several-thousand-year-old information on past biodiversity can be retrieved from tropical sediments. However, comprehensive genomic surveys of tropical biota need prioritization for sedimentary DNA to be a viable methodology for future tropical biodiversity studies.}, language = {en} } @article{KocSimovichSchoenemannetal.2019, author = {Koc, Julian and Simovich, Tomer and Sch{\"o}nemann, Eric and Chilkoti, Ashutosh and Gardner, Harrison and Swain, Geoffrey W. and Hunsucker, Kelli and Laschewsky, Andr{\´e} and Rosenhahn, Axel}, title = {Sediment challenge to promising ultra-low fouling hydrophilic surfaces in the marine environment}, series = {Biofouling : the journal of bioadhesion and biofilm research}, volume = {35}, journal = {Biofouling : the journal of bioadhesion and biofilm research}, number = {4}, publisher = {Taylor \& Francis}, address = {London}, issn = {0892-7014}, doi = {10.1080/08927014.2019.1611790}, pages = {454 -- 462}, year = {2019}, abstract = {Hydrophilic coatings exhibit ultra-low fouling properties in numerous laboratory experiments. In stark contrast, the antifouling effect of such coatings in vitro failed when performing field tests in the marine environment. The fouling release performance of nonionic and zwitterionic hydrophilic polymers was substantially reduced compared to the controlled laboratory environment. Microscopy and spectroscopy revealed that a large proportion of the accumulated material in field tests contains inorganic compounds and diatomaceous soil. Diatoms adhered to the accumulated material on the coating, but not to the pristine polymer. Simulating field tests in the laboratory using sediment samples collected from the test sites showed that incorporated sand and diatomaceous earth impairs the fouling release characteristics of the coatings. When exposed to marine sediment from multiple locations, particulate matter accumulated on these coatings and served as attachment points for diatom adhesion and enhanced fouling. Future developments of hydrophilic coatings should consider accumulated sediment and its potential impact on the antifouling performance.}, language = {en} } @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{FranckeBaroniBrosinskyetal.2018, author = {Francke, Till and Baroni, Gabriele and Brosinsky, Arlena and Foerster, Saskia and Lopez-Tarazon, Jos{\´e} Andr{\´e}s and Sommerer, Erik and Bronstert, Axel}, title = {What Did Really Improve Our Mesoscale Hydrological Model?}, series = {Water resources research}, volume = {54}, journal = {Water resources research}, number = {11}, publisher = {American Geophysical Union}, address = {Washington}, issn = {0043-1397}, doi = {10.1029/2018WR022813}, pages = {8594 -- 8612}, year = {2018}, abstract = {Modelers can improve a model by addressing the causes for the model errors (data errors and structural errors). This leads to implementing model enhancements (MEs), for example, meteorological data based on more monitoring stations, improved calibration data, and/or modifications in process formulations. However, deciding on which MEs to implement remains a matter of expert knowledge. After implementing multiple MEs, any improvement in model performance is not easily attributed, especially when considering different objectives or aspects of this improvement (e.g., better dynamics vs. reduced bias). We present an approach for comparing the effect of multiple MEs based on real observations and considering multiple objectives (MMEMO). A stepwise selection approach and structured plots help to address the multidimensionality of the problem. Tailored analyses allow a differentiated view on the effect of MEs and their interactions. MMEMO is applied to a case study employing the mesoscale hydro-sedimentological model WASA-SED for the Mediterranean-mountainous Isabena catchment, northeast Spain. The investigated seven MEs show diverse effects: some MEs (e.g., rainfall data) cause improvements for most objectives, while other MEs (e.g., land use data) only affect a few objectives or even decrease model performance. Interaction of MEs was observed for roughly half of the MEs, confirming the need to address them in the analysis. Calibration and increasing the temporal resolution showed by far stronger impact than any of the other MEs. The proposed framework can be adopted in other studies to analyze the effect of MEs and, thus, facilitate the identification and implementation of the most promising MEs for comparable cases.}, language = {en} } @article{WurzbacherWarthmannBourneetal.2016, author = {Wurzbacher, Christian and Warthmann, Norman and Bourne, Elizabeth Charlotte and Attermeyer, Katrin and Allgaier, Martin and Powell, Jeff R. and Detering, Harald and Mbedi, Susan and Großart, Hans-Peter and Monaghan, Michael T.}, title = {High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)}, series = {MycoKeys}, volume = {41}, journal = {MycoKeys}, publisher = {Pensoft Publ.}, address = {Sofia}, issn = {1314-4057}, doi = {10.3897/mycokeys.16.9646}, pages = {17 -- 44}, year = {2016}, abstract = {Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97\% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75\%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body.}, language = {en} }