@article{MinutilloRuanoRosaAbdelfattahetal.2022, author = {Minutillo, Serena A. and Ruano-Rosa, David and Abdelfattah, Ahmed and Schena, Leonardo and Malacrino, Antonino}, title = {The fungal microbiome of wheat flour includes potential mycotoxin producers}, series = {Foods}, volume = {11}, journal = {Foods}, number = {5}, publisher = {MDPI}, address = {Basel}, issn = {2304-8158}, doi = {10.3390/foods11050676}, pages = {9}, year = {2022}, abstract = {Consumers are increasingly demanding higher quality and safety standards for the products they consume, and one of this is wheat flour, the basis of a wide variety of processed products. This major component in the diet of many communities can be contaminated by microorganisms before the grain harvest, or during the grain storage right before processing. These microorganisms include several fungal species, many of which produce mycotoxins, secondary metabolites that can cause severe acute and chronic disorders. Yet, we still know little about the overall composition of fungal communities associated with wheat flour. In this study, we contribute to fill this gap by characterizing the fungal microbiome of different types of wheat flour using culture-dependent and -independent techniques. Qualitatively, these approaches suggested similar results, highlighting the presence of several fungal taxa able to produce mycotoxins. In-vitro isolation of fungal species suggest a higher frequency of Penicillium, while metabarcoding suggest a higher abundance of Alternaria. This discrepancy might reside on the targeted portion of the community (alive vs. overall) or in the specific features of each technique. Thus, this study shows that commercial wheat flour hosts a wide fungal diversity with several taxa potentially representing concerns for consumers, aspects that need more attention throughout the food production chain.}, language = {en} } @article{CourtinAndreevRaschkeetal.2021, author = {Courtin, J{\´e}r{\´e}my and Andreev, Andrei and Raschke, Elena and Bala, Sarah and Biskaborn, Boris and Liu, Sisi and Zimmermann, Heike and Diekmann, Bernhard and Stoof-Leichsenring, Kathleen R. and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike}, title = {Vegetation changes in Southeastern Siberia during the late pleistocene and the holocene}, series = {Frontiers in Ecology and Evolution}, volume = {9}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-701X}, doi = {10.3389/fevo.2021.625096}, pages = {18}, year = {2021}, abstract = {Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last similar to 35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake's vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the "keystone herbivore" hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene.}, language = {en} } @article{LiuStoofLeichsenringKruseetal.2020, author = {Liu, Sisi and Stoof-Leichsenring, Kathleen Rosemarie and Kruse, Stefan and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike}, title = {Holocene vegetation and plant diversity changes in the north-eastern Siberian treeline region from pollen and 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.2020.560243}, pages = {17}, year = {2020}, abstract = {Although sedimentary ancient DNA (sedaDNA) has been increasingly used to study paleoecological dynamics (Schulte et al., 2020), the approach has rarely been compared with the traditional method of pollen analysis for investigating past changes in the vegetation composition and diversity of Arctic treeline areas. Here, we provide a history of latitudinal floristic composition and species diversity based on a comparison ofsedaDNA and pollen data archived in three Siberian lake sediment cores spanning the mid-Holocene to the present (7.6-0 cal ka BP), from northern typical tundra to southern open larch forest in the Omoloy region. Our results show that thesedaDNA approach identifies more plant taxa found in the local vegetation communities, while the corresponding pollen analysis mainly captures the regional vegetation development and has its limitations for plant diversity reconstruction. Measures of alpha diversity were calculated based onsedaDNA data recovered from along a tundra to forest tundra to open larch forest gradient. Across all sites,sedaDNA archives provide a complementary record of the vegetation transition within each lake's catchment, tracking a distinct latitudinal vegetation type range from larch tree/alder shrub (open larch forest site) to dwarf shrub-steppe (forest tundra) to wet sedge tundra (typical tundra site). By contrast, the pollen data reveal an open landscape, which cannot distinguish the temporal changes in compositional vegetation for the open larch forest site and forest-tundra site. IncreasingLarixpollen percentages were recorded in the forest-tundra site in the last millenium although noLarixDNA was detected, suggesting that thesedaDNA approach performs better for tracking the local establishment ofLarix. Highest species richness and diversity are found in the mid-Holocene (before 4.4 ka) at the typical tundra site with a diverse range of vegetational habitats, while lowest species richness is recorded for the forest tundra where dwarf-willow habitats dominated the lake's catchment. During the late Holocene, strong declines in species richness and diversity are found at the typical tundra site with the vegetation changing to relatively simple communities. Nevertheless, plant species richness is mostly higher than at the forest-tundra site, which shows a slightly decreasing trend. Plant species richness at the open larch forest site fluctuates through time and is higher than the other sites since around 2.5 ka. Taken together, there is no evidence to suggest that the latitudinal gradients in species diversity changes are present at a millennial scale. Additionally, a weak correlation between the principal component analysis (PCA) site scores ofsedaDNA and species richness suggests that climate may not be a direct driver of species turnover within a lake's catchment. Our data suggest thatsedaDNA and pollen have different but complementary abilities for reconstructing past vegetation and species diversity along a latitude.}, language = {en} } @article{SallehRamosMadrigalPenalozaetal.2017, author = {Salleh, Faezah Mohd and Ramos-Madrigal, Jazmin and Penaloza, Fernando and Liu, Shanlin and Sinding, Mikkel-Holger S. and Patel, Riddhi P. and Martins, Renata and Lenz, Dorina and Fickel, J{\"o}rns and Roos, Christian and Shamsir, Mohd Shahir and Azman, Mohammad Shahfiz and Lim, Burton K. and Rossiter, Stephen J. and Wilting, Andreas and Gilbert, M. Thomas P.}, title = {An expanded mammal mitogenome dataset from Southeast Asia}, series = {Gigascience}, volume = {6}, journal = {Gigascience}, number = {8}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2047-217X}, pages = {1 -- 19}, year = {2017}, abstract = {Background: Findings: Approximately 55 gigabases of raw sequence were generated. From this data we assembled 72 complete mitogenome sequences, with an average depth of coverage of 102.9x and 55.2x for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Conclusion:}, 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{ZimmermannRaschkeEppetal.2017, author = {Zimmermann, Heike Hildegard and Raschke, Elena and Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Schirrmeister, Lutz and Schwamborn, Georg and Herzschuh, Ulrike}, title = {The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data}, series = {Genes}, volume = {8}, journal = {Genes}, number = {10}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes8100273}, pages = {273}, year = {2017}, abstract = {Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.}, language = {en} } @article{NiemeyerEppStoofLeichsenringetal.2017, author = {Niemeyer, Bastian and Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike}, title = {A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline}, series = {Molecular ecology resources}, volume = {17}, journal = {Molecular ecology resources}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12689}, pages = {e46 -- e62}, year = {2017}, abstract = {Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition.}, 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} }