@article{JesusSchmidtFickeletal.2022, author = {Jesus, Sonia A. and Schmidt, Anke and Fickel, J{\"o}rns and Doherr, Marcus G. and Boonprasert, Khajohnpat and Thitaram, Chatchote and Sariya, Ladawan and Ratanakron, Parntep and Hildebrandt, Thomas Bernd}, title = {Assessing coagulation parameters in healthy Asian Elephants (Elephas maximus) from European and thai populations}, series = {Animals}, volume = {12}, journal = {Animals}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2076-2615}, doi = {10.3390/ani12030361}, pages = {16}, year = {2022}, abstract = {Simple Summary Asian elephants (Elephas maximus) are considered endangered and their population is in continuous decline. Understanding their social interactions, health, and welfare status has been a topic of intense research in recent decades. Coagulation assessments have been underutilized in wildlife but can give valuable information on individual health. This study aims to increase the knowledge of the coagulation status in healthy Asian elephants from different backgrounds and age groups, using a fast point-of-care analyzer. This tool can be further used in either routine health check-ups performed by caretakers or in a clinical emergency, such as in cases of elephant endotheliotropic herpesvirus hemorrhagic disease outbreaks. We have also investigated the presence of genomic mutations in one coagulation factor-factor VII-where a disorder was previously reported in an Asian elephant. Hereby, we report new reference values for coagulation parameters, such as coagulation times and fibrinogen concentration of Asian elephants assessed in Thailand and in Europe, as well as several single point mutations found in the exons of Elephas maximus coagulation F7 gene. We found the point-of-care analyzer used in this study to be very practical and user friendly for a zoo and field environment and hope that this project will incentivize further coagulation studies in Asian elephants and in other wildlife species. The Asian elephant population is continuously declining due to several extrinsic reasons in their range countries, but also due to diseases in captive populations worldwide. One of these diseases, the elephant endotheliotropic herpesvirus (EEHV) hemorrhagic disease, is very impactful because it particularly affects Asian elephant calves. It is commonly fatal and presents as an acute and generalized hemorrhagic syndrome. Therefore, having reference values of coagulation parameters, and obtaining such values for diseased animals in a very short time, is of great importance. We analyzed prothrombin time (PT), activated partial thromboplastin time (aPTT), and fibrinogen concentrations using a portable and fast point-of-care analyzer (VetScan Pro) in 127 Asian elephants from Thai camps and European captive herds. We found significantly different PT and aPTT coagulation times between elephants from the two regions, as well as clear differences in fibrinogen concentration. Nevertheless, these alterations were not expected to have biological or clinical implications. We have also sequenced the coagulation factor VII gene of 141 animals to assess the presence of a previously reported hereditary coagulation disorder in Asian elephants and to investigate the presence of other mutations. We did not find the previously reported mutation in our study population. Instead, we discovered the presence of several new single nucleotide polymorphisms, two of them being considered as deleterious by effect prediction software.}, language = {en} } @article{WendtKulanekVargaetal.2022, author = {Wendt, Martin and Kulanek, Dustin and Varga, Zoltan and Rakosy, Laszlo and Schmitt, Thomas}, title = {Pronounced mito-nuclear discordance and various Wolbachia infections in the water ringlet Erebia pronoe have resulted in a complex phylogeographic structure}, series = {Scientific reports}, volume = {12}, journal = {Scientific reports}, number = {1}, publisher = {Nature Portfolio}, address = {Berlin}, issn = {2045-2322}, doi = {10.1038/s41598-022-08885-8}, pages = {10}, year = {2022}, abstract = {Several morphological and mitochondrial lineages of the alpine ringlet butterfly species Erebia pronoe have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1 alpha, RPS5) gene sequences and compared them with sequences from the sister species Erebia melas. Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with Wolbachia strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the E. pronoe-melas complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in E. melas and E. pronoe glottis can be explained by different ages of Wolbachia infections with different Wolbachia strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of E. pronoe glottis in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.}, language = {en} } @article{GhoddousiVanCayzeeleNegahdaretal.2022, author = {Ghoddousi, Arash and Van Cayzeele, Corinna and Negahdar, Pegah and Soofi, Mahmood and Kh. Hamidi, Amirhossein and Bleyhl, Benjamin and Fandos, Guillermo and Khorozyan, Igor and Waltert, Matthias and Kuemmerle, Tobias}, title = {Understanding spatial patterns of poaching pressure using ranger logbook data to optimize future patrolling strategies}, series = {Ecological applications : a publication of the Ecological Society of America}, volume = {32}, journal = {Ecological applications : a publication of the Ecological Society of America}, number = {5}, publisher = {Wiley}, address = {Hoboken}, issn = {1051-0761}, doi = {10.1002/eap.2601}, pages = {13}, year = {2022}, abstract = {Poaching is driving many species toward extinction, and as a result, lowering poaching pressure is a conservation priority. This requires understanding where poaching pressure is high and which factors determine these spatial patterns. However, the cryptic and illegal nature of poaching makes this difficult. Ranger patrol data, typically recorded in protected area logbooks, contain information on patrolling efforts and poaching detection and should thus provide opportunities for a better understanding of poaching pressure. However, these data are seldom analyzed and rarely used to inform adaptive management strategies. We developed a novel approach to making use of analog logbook records to map poaching pressure and to test environmental criminology and predator-prey relationship hypotheses explaining poaching patterns. We showcase this approach for Golestan National Park in Iran, where poaching has substantially depleted ungulate populations. We digitized data from >4800 ranger patrols from 2014 to 2016 and used an occupancy modeling framework to relate poaching to (1) accessibility, (2) law enforcement, and (3) prey availability factors. Based on predicted poaching pressure and patrolling intensity, we provide suggestions for future patrol allocation strategies. Our results revealed a low probability (12\%) of poacher detection during patrols. Poaching distribution was best explained by prey availability, indicating that poachers target areas with high concentrations of ungulates. Poaching pressure was estimated to be high (>0.49) in 39\% of our study area. To alleviate poaching pressure, we recommend ramping up patrolling intensity in 12\% of the national park, which could be achievable by reducing excess patrols in about 20\% of the park. However, our results suggest that for 27\% of the park, it is necessary to improve patrolling quality to increase detection probability of poaching, for example, by closing temporal patrolling gaps or expanding informant networks. Our approach illustrates that analog ranger logbooks are an untapped resource for evidence-based and adaptive planning of protected area management. Using this wealth of data can open up new avenues to better understand poaching and its determinants, to expand effectiveness assessments to the past, and, more generally, to allow for strategic conservation planning in protected areas.}, language = {en} } @article{ZoccaratoSherMikietal.2022, author = {Zoccarato, Luca and Sher, Daniel and Miki, Takeshi and Segre, Daniel and Grossart, Hans-Peter}, title = {A comparative whole-genome approach identifies bacterial traits for marine microbial interactions}, series = {Communications biology}, volume = {5}, journal = {Communications biology}, number = {1}, publisher = {Springer Nature}, address = {Berlin}, issn = {2399-3642}, doi = {10.1038/s42003-022-03184-4}, pages = {13}, year = {2022}, abstract = {Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions. Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics. Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10\% of genomes), phytohormones (3-8\%) and different B vitamins (57-70\%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.}, language = {en} } @article{OmranianAngeleskaNikoloski2021, author = {Omranian, Sara and Angeleska, Angela and Nikoloski, Zoran}, title = {PC2P}, series = {Bioinformatics}, volume = {37}, journal = {Bioinformatics}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btaa1089}, pages = {73 -- 81}, year = {2021}, abstract = {Motivation: Prediction of protein complexes from protein-protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ algorithms for network community detection that identify dense subgraphs in PPI networks. However, gold standards in yeast and human indicate that protein complexes can also induce sparse subgraphs, introducing further challenges in protein complex prediction. Results: To address this issue, we formalize protein complexes as biclique spanned subgraphs, which include both sparse and dense subgraphs. We then cast the problem of protein complex prediction as a network partitioning into biclique spanned subgraphs with removal of minimum number of edges, called coherent partition. Since finding a coherent partition is a computationally intractable problem, we devise a parameter-free greedy approximation algorithm, termed Protein Complexes from Coherent Partition (PC2P), based on key properties of biclique spanned subgraphs. Through comparison with nine contenders, we demonstrate that PC2P: (i) successfully identifies modular structure in networks, as a prerequisite for protein complex prediction, (ii) outperforms the existing solutions with respect to a composite score of five performance measures on 75\% and 100\% of the analyzed PPI networks and gold standards in yeast and human, respectively, and (iii,iv) does not compromise GO semantic similarity and enrichment score of the predicted protein complexes. Therefore, our study demonstrates that clustering of networks in terms of biclique spanned subgraphs is a promising framework for detection of complexes in PPI networks.}, language = {en} } @article{NwosuRoeserYangetal.2021, author = {Nwosu, Ebuka Canisius and Roeser, Patricia Angelika and Yang, Sizhong and Ganzert, Lars and Dellwig, Olaf and Pinkerneil, Sylvia and Brauer, Achim and Dittmann, Elke and Wagner, Dirk and Liebner, Susanne}, title = {From water into sediment-tracing freshwater cyanobacteria via DNA analyses}, series = {Microorganisms : open access journal}, volume = {9}, journal = {Microorganisms : open access journal}, number = {8}, publisher = {MDPI}, address = {Basel}, issn = {2076-2607}, doi = {10.3390/microorganisms9081778}, pages = {20}, year = {2021}, abstract = {Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May-October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.}, language = {en} } @article{StoofLeichsenringHuangLiuetal.2022, author = {Stoof-Leichsenring, Kathleen R. and Huang, Sichao and Liu, Sisi and Jia, Weihan and Li, Kai and Liu, Xingqi and Pestryakova, Luidmila A. and Herzschuh, Ulrike}, title = {Sedimentary DNA identifies modern and past macrophyte diversity and its environmental drivers in high-latitude and high-elevation lakes in Siberia and China}, series = {Limnology and oceanography}, volume = {67}, journal = {Limnology and oceanography}, number = {5}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {0024-3590}, doi = {10.1002/lno.12061}, pages = {1126 -- 1141}, year = {2022}, abstract = {Arctic and alpine aquatic ecosystems are changing rapidly under recent global warming, threatening water resources by diminishing trophic status and changing biotic composition. Macrophytes play a key role in the ecology of freshwaters and we need to improve our understanding of long-term macrophytes diversity and environmental change so far limited by the sporadic presence of macrofossils in sediments. In our study, we applied metabarcoding using the trnL P6 loop marker to retrieve macrophyte richness and composition from 179 surface-sediment samples from arctic Siberian and alpine Chinese lakes and three representative lake cores. The surface-sediment dataset suggests that macrophyte richness and composition are mostly affected by temperature and conductivity, with highest richness when mean July temperatures are higher than 12 degrees C and conductivity ranges between 40 and 400 mu S cm(-1). Compositional turnover during the Late Pleistocene/Holocene is minor in Siberian cores and characterized by a less rich, but stable emergent macrophyte community. Richness decreases during the Last Glacial Maximum and rises during wetter and warmer climate in the Late-glacial and Mid-Holocene. In contrast, we detect a pronounced change from emergent to submerged taxa at 14 ka in the Tibetan alpine core, which can be explained by increasing temperature and conductivity due to glacial runoff and evaporation. Our study provides evidence for the suitability of the trnL marker to recover modern and past macrophyte diversity and its applicability for the response of macrophyte diversity to lake-hydrochemical and climate variability predicting contrasting macrophyte changes in arctic and alpine lakes under intensified warming and human impact.}, language = {en} } @article{BizicIonescuKarnataketal.2022, author = {Bizic, Mina and Ionescu, Danny and Karnatak, Rajat and Musseau, Camille L. and Onandia, Gabriela and Berger, Stella A. and Nejstgaard, Jens C. and Lischeid, Gunnar and Gessner, Mark O. and Wollrab, Sabine and Grossart, Hans-Peter}, title = {Land-use type temporarily affects active pond community structure but not gene expression patterns}, series = {Molecular ecology}, volume = {31}, journal = {Molecular ecology}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.16348}, pages = {1716 -- 1734}, year = {2022}, abstract = {Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics to understand the responses of active bacterial, archaeal and eukaryotic communities to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel environmental DNA study that suggests the homogenization of biodiversity across KH, conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced for eukaryotes than for bacteria. In contrast, gene expression patterns did not differ between months or across land-use types, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results indicate that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This potential needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.}, language = {en} } @article{HerzschuhLiBoehmeretal.2022, author = {Herzschuh, Ulrike and Li, Chenzhi and Boehmer, Thomas and Postl, Alexander K. and Heim, Birgit and Andreev, Andrei A. and Cao, Xianyong and Wieczorek, Mareike and Ni, Jian}, title = {LegacyPollen 1.0}, series = {Earth system science data : ESSD}, volume = {14}, journal = {Earth system science data : ESSD}, number = {7}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1866-3508}, doi = {10.5194/essd-14-3213-2022}, pages = {3213 -- 3227}, year = {2022}, abstract = {Here we describe the LegacyPollen 1.0, a dataset of 2831 fossil pollen records with metadata, a harmonized taxonomy, and standardized chronologies. A total of 1032 records originate from North America, 1075 from Europe, 488 from Asia, 150 from Latin America, 54 from Africa, and 32 from the Indo-Pacific. The pollen data cover the late Quaternary (mostly the Holocene). The original 10 110 pollen taxa names (including variations in the notations) were harmonized to 1002 terrestrial taxa (including Cyperaceae), with woody taxa and major herbaceous taxa harmonized to genus level and other herbaceous taxa to family level. The dataset is valuable for synthesis studies of, for example, taxa areal changes, vegetation dynamics, human impacts (e.g., deforestation), and climate change at global or continental scales. The harmonized pollen and metadata as well as the harmonization table are available from PANGAEA (https://doi.org/10.1594/PANGAEA.929773; Herzschuh et al., 2021). R code for the harmonization is provided at Zenodo (https://doi.org/10.5281/zenodo.5910972; Herzschuh et al., 2022) so that datasets at a customized harmonization level can be easily established.}, language = {en} } @article{StuenziKruseBoikeetal.2022, author = {Stuenzi, Simone Maria and Kruse, Stefan and Boike, Julia and Herzschuh, Ulrike and Oehme, Alexander and Pestryakova, Luidmila A. and Westermann, Sebastian and Langer, Moritz}, title = {Thermohydrological impact of forest disturbances on ecosystem-protected permafrost}, series = {Journal of geophysical research : Biogeosciences}, volume = {127}, journal = {Journal of geophysical research : Biogeosciences}, number = {5}, publisher = {American Geophysical Union}, address = {Washington}, issn = {2169-8953}, doi = {10.1029/2021JG006630}, pages = {24}, year = {2022}, abstract = {Boreal forests cover over half of the global permafrost area and protect underlying permafrost. Boreal forest development, therefore, has an impact on permafrost evolution, especially under a warming climate. Forest disturbances and changing climate conditions cause vegetation shifts and potentially destabilize the carbon stored within the vegetation and permafrost. Disturbed permafrost-forest ecosystems can develop into a dry or swampy bush- or grasslands, shift toward broadleaf- or evergreen needleleaf-dominated forests, or recover to the pre-disturbance state. An increase in the number and intensity of fires, as well as intensified logging activities, could lead to a partial or complete ecosystem and permafrost degradation. We study the impact of forest disturbances (logging, surface, and canopy fires) on the thermal and hydrological permafrost conditions and ecosystem resilience. We use a dynamic multilayer canopy-permafrost model to simulate different scenarios at a study site in eastern Siberia. We implement expected mortality, defoliation, and ground surface changes and analyze the interplay between forest recovery and permafrost. We find that forest loss induces soil drying of up to 44\%, leading to lower active layer thicknesses and abrupt or steady decline of a larch forest, depending on disturbance intensity. Only after surface fires, the most common disturbances, inducing low mortality rates, forests can recover and overpass pre-disturbance leaf area index values. We find that the trajectory of larch forests after surface fires is dependent on the precipitation conditions in the years after the disturbance. Dryer years can drastically change the direction of the larch forest development within the studied period.}, language = {en} } @article{ReeveNicholsonAltafetal.2022, author = {Reeve, Holly A. and Nicholson, Jake and Altaf, Farieha and Lonsdale, Thomas H. and Preissler, Janina and Lauterbach, Lars and Lenz, Oliver and Leimk{\"u}hler, Silke and Hollmann, Frank and Paul, Caroline E. and Vincent, Kylie A.}, title = {A hydrogen-driven biocatalytic approach to recycling synthetic analogues of NAD(P)H}, series = {Chemical communications : ChemComm}, volume = {58}, journal = {Chemical communications : ChemComm}, number = {75}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-7345}, doi = {10.1039/d2cc02411j}, pages = {10540 -- 10543}, year = {2022}, abstract = {We demonstrate a recycling system for synthetic nicotinamide cofactor analogues using a soluble hydrogenase with turnover number of >1000 for reduction of the cofactor analogues by H-2. Coupling this system to an ene reductase, we show quantitative conversion of N-ethylmaleimide to N-ethylsuccinimide. The biocatalyst system retained >50\% activity after 7 h.}, language = {en} } @phdthesis{Hippel2024, author = {Hippel, Barbara von}, title = {Long-term bacteria-fungi-plant associations in permafrost soils inferred from palaeometagenomics}, doi = {10.25932/publishup-63600}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-636009}, school = {Universit{\"a}t Potsdam}, pages = {xii, 198}, year = {2024}, abstract = {The arctic is warming 2 - 4 times faster than the global average, resulting in a strong feedback on northern ecosystems such as boreal forests, which cover a vast area of the high northern latitudes. With ongoing global warming, the treeline subsequently migrates northwards into tundra areas. The consequences of turning ecosystems are complex: on the one hand, boreal forests are storing large amounts of global terrestrial carbon and act as a carbon sink, dragging carbon dioxide out of the global carbon cycle, suggesting an enhanced carbon uptake with increased tree cover. On the other hand, with the establishment of trees, the albedo effect of tundra decreases, leading to enhanced soil warming. Meanwhile, permafrost thaws, releasing large amounts of previously stored carbon into the atmosphere. So far, mainly vegetation dynamics have been assessed when studying the impact of warming onto ecosystems. Most land plants are living in close symbiosis with bacterial and fungal communities, sustaining their growth in nutrient poor habitats. However, the impact of climate change on these subsoil communities alongside changing vegetation cover remains poorly understood. Therefore, a better understanding of soil community dynamics on multi millennial timescales is inevitable when addressing the development of entire ecosystems. Unravelling long-term cross-kingdom dependencies between plant, fungi, and bacteria is not only a milestone for the assessment of warming on boreal ecosystems. On top, it also is the basis for agriculture strategies to sustain society with sufficient food in a future warming world. The first objective of this thesis was to assess ancient DNA as a proxy for reconstructing the soil microbiome (Manuscripts I, II, III, IV). Research findings across these projects enable a comprehensive new insight into the relationships of soil microorganisms to the surrounding vegetation. First, this was achieved by establishing (Manuscript I) and applying (Manuscript II) a primer pair for the selective amplification of ancient fungal DNA from lake sediment samples with the metabarcoding approach. To assess fungal and plant co-variation, the selected primer combination (ITS67, 5.8S) amplifying the ITS1 region was applied on samples from five boreal and arctic lakes. The obtained data showed that the establishment of fungal communities is impacted by warming as the functional ecological groups are shifting. Yeast and saprotroph dominance during the Late Glacial declined with warming, while the abundance of mycorrhizae and parasites increased with warming. The overall species richness was also alternating. The results were compared to shotgun sequencing data reconstructing fungi and bacteria (Manuscripts III, IV), yielding overall comparable results to the metabarcoding approach. Nonetheless, the comparison also pointed out a bias in the metabarcoding, potentially due to varying ITS lengths or copy numbers per genome. The second objective was to trace fungus-plant interaction changes over time (Manuscripts II, III). To address this, metabarcoding targeting the ITS1 region for fungi and the chloroplast P6 loop for plants for the selective DNA amplification was applied (Manuscript II). Further, shotgun sequencing data was compared to the metabarcoding results (Manuscript III). Overall, the results between the metabarcoding and the shotgun approaches were comparable, though a bias in the metabarcoding was assumed. We demonstrated that fungal shifts were coinciding with changes in the vegetation. Yeast and lichen were mainly dominant during the Late Glacial with tundra vegetation, while warming in the Holocene lead to the expansion of boreal forests with increasing mycorrhizae and parasite abundance. Aside, we highlighted that Pinaceae establishment is dependent on mycorrhizal fungi such as Suillineae, Inocybaceae, or Hyaloscypha species also on long-term scales. The third objective of the thesis was to assess soil community development on a temporal gradient (Manuscripts III, IV). Shotgun sequencing was applied on sediment samples from the northern Siberian lake Lama and the soil microbial community dynamics compared to ecosystem turnover. Alongside, podzolization processes from basaltic bedrock were recovered (Manuscript III). Additionally, the recovered soil microbiome was compared to shotgun data from granite and sandstone catchments (Manuscript IV, Appendix). We assessed if the establishment of the soil microbiome is dependent on the plant taxon and as such comparable between multiple geographic locations or if the community establishment is driven by abiotic soil properties and as such the bedrock area. We showed that the development of soil communities is to a great extent driven by the vegetation changes and temperature variation, while time only plays a minor role. The analyses showed general ecological similarities especially between the granite and basalt locations, while the microbiome on species-level was rather site-specific. A greater number of correlated soil taxa was detected for deep-rooting boreal taxa in comparison to grasses with shallower roots. Additionally, differences between herbaceous taxa of the late Glacial compared to taxa of the Holocene were revealed. With this thesis, I demonstrate the necessity to investigate subsoil community dynamics on millennial time scales as it enables further understanding of long-term ecosystem as well as soil development processes and such plant establishment. Further, I trace long-term processes leading to podzolization which supports the development of applied carbon capture strategies under future global warming.}, language = {en} } @article{KrebsRakotoarinoroStechetal.2022, author = {Krebs, Simon K. and Rakotoarinoro, Nathanael and Stech, Marlitt and Zemella, Anne and Kubick, Stefan}, title = {A CHO-based cell-free dual fluorescence reporter system for the straightforward assessment of amber suppression and scFv functionality}, series = {Frontiers in Bioengineering and Biotechnology}, volume = {10}, journal = {Frontiers in Bioengineering and Biotechnology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-4185}, doi = {10.3389/fbioe.2022.873906}, pages = {15}, year = {2022}, abstract = {Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).}, language = {en} } @article{KuehnBeckerHarpkeetal.2022, author = {K{\"u}hn, Elisabeth and Becker, Marc and Harpke, Alexander and K{\"u}hn, Ingolf and Kuhlicke, Christian and Schmitt, Thomas and Settele, Josef and Musche, Martin}, title = {The benefits of counting butterflies: recommendations for a successful citizen science project}, series = {Ecology and Society}, volume = {27}, journal = {Ecology and Society}, number = {2}, publisher = {Resilience Alliance}, address = {Wolfville}, issn = {1708-3087}, doi = {10.5751/ES-12861-270238}, pages = {39}, year = {2022}, abstract = {Citizen science (CS) projects, being popular across many fields of science, have recently also become a popular tool to collect biodiversity data. Although the benefits of such projects for science and policy making are well understood, relatively little is known about the benefits participants get from these projects as well as their personal backgrounds and motivations. Furthermore, very little is known about their expectations. We here examine these aspects, with the citizen science project "German Butterfly Monitoring" as an example. A questionnaire was sent to all participants of the project and the responses to the questionnaire indicated the following: center dot Most transect walkers do not have a professional background in this field, though they do have a high educational level, and are close to retirement, with a high number of females; center dot An important motivation to join the project is to preserve the natural environment and to contribute to scientific knowledge; center dot Participants benefit by enhancing their knowledge about butterflies and especially their ability to identify different species (taxonomic knowledge); center dot Participants do not have specific expectations regarding the project beyond proper management and coordination, but have an intrinsic sense of working for a greater good. The willingness to join a project is higher if the project contributes to the solution of a problem discussed in the media (here, insect decline). Based on our findings from the analysis of the questionnaire we can derive a set of recommendations for establishing a successful CS project. These include the importance of good communication, e.g., by explaining what the (scientific) purpose of the project is and what problems are to be solved with the help of the data collected in the project. The motivation to join a CS project is mostly intrinsic and CS is a good tool to engage people during difficult times such as the COVID-19 pandemic, giving participants the feeling of doing something useful.}, language = {en} } @article{NieWangXuetal.2021, author = {Nie, Yan and Wang, Weiwei and Xu, Xun and Ma, Nan and Lendlein, Andreas}, title = {The response of human induced pluripotent stem cells to cyclic temperature changes explored by BIO-AFM}, series = {MRS advances : a journal of the Materials Research Society (MRS)}, volume = {6}, journal = {MRS advances : a journal of the Materials Research Society (MRS)}, number = {31}, publisher = {Springer}, address = {Cham}, issn = {2059-8521}, doi = {10.1557/s43580-021-00110-4}, pages = {745 -- 749}, year = {2021}, abstract = {Human induced pluripotent stem cells (hiPSCs) are highly sensitive to extrinsic physical and biochemical signals from their extracellular microenvironments. In this study, we analyzed the effect of cyclic temperature changes on hiPSCs behaviors, especially by means of scanning force microscopy (BIO-AFM). The alternation in cellular mechanics, as well as the secretion and pattern of deposition of extracellular matrix (ECM) protein in hiPSCs were evaluated. The arrangement of the actin cytoskeleton changed with the variation of the temperature. The rearranged cytoskeleton architecture led to the subsequent changes in cell mechanics (Young's modulus of hiPSCs). With the exposure to the cyclic cold stimuli, an increase in the average surface roughness (Ra) and roughness mean square (RMS) was detected. This observation might be at least in part due to the upregulated secretion of Laminin alpha 5 during repeated temporary cooling. The expression of pluripotent markers, NANOG and SOX2, was not impaired in hiPSCs, when exposed to the cyclic cold stimuli for 24 h. Our findings provide an insight into the effect of temperature on the hiPSC behaviors, which may contribute to a better understanding of the application of locally controlled therapeutic hypothermia.}, language = {en} } @article{LozanoAguilarTriguerosOnandiaetal.2021, author = {Lozano, Yudi M. and Aguilar-Trigueros, Carlos A. and Onandia, Gabriela and Maaß, Stefanie and Zhao, Tingting and Rillig, Matthias C.}, title = {Effects of microplastics and drought on soil ecosystem functions and multifunctionality}, series = {Journal of applied ecology : an official journal of the British Ecological Society}, volume = {58}, journal = {Journal of applied ecology : an official journal of the British Ecological Society}, number = {5}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {1365-2664}, doi = {10.1111/1365-2664.13839}, pages = {988 -- 996}, year = {2021}, abstract = {1. Microplastics in soils have become an important threat for terrestrial systems as they may potentially alter the geochemical/biophysical soil environment and can interact with drought. As microplastics may affect soil water content, this could exacerbate the well-known negative effects of drought on ecosystem functionality. Thus, functions including litter decomposition, soil aggregation or those related with nutrient cycling can be altered. Despite this potential interaction, we know relatively little about how microplastics, under different soil water conditions, affect ecosystem functions and multifunctionality. 2. To address this gap, we performed an experiment using grassland plant communities growing in microcosms. Microplastic fibres (absent, present) and soil water conditions (well-watered, drought) were applied in a fully factorial design. At harvest, we measured soil ecosystem functions related to nutrient cycling (beta-glucosaminidase, beta-D-cellobiosidase, phosphatase, beta-glucosidase enzymes), respiration, nutrient retention, pH, litter decomposition and soil aggregation (water stable aggregates). As terrestrial systems provide these functions simultaneously, we also assessed ecosystem multifunctionality, an index that encompasses the array of ecosystem functions measured here. 3. We found that the interaction between microplastic fibres and drought affected ecosystem functions and multifunctionality. Drought had negatively affected nutrient cycling by decreasing enzymatic activities by up to similar to 39\%, while microplastics increased soil aggregation by similar to 18\%, soil pH by similar to 4\% and nutrient retention by up to similar to 70\% by diminishing nutrient leaching. Microplastic fibres also impacted soil enzymes, respiration and ecosystem multifunctionality, but importantly, the direction of these effects depended on soil water status. That is, under well-watered conditions, these functions decreased with microplastic fibres by up to similar to 34\% while under drought they had similar values irrespective of the microplastic presence, or tended to increase with microplastics. Litter decomposition had a contrary pattern increasing with microplastics by similar to 6\% under well-watered conditions while decreasing to a similar percentage under drought. 4. Synthesis and applications. Single ecosystem functions can be positively or negatively affected by microplastics fibres depending on soil water status. However, our results suggest that microplastic fibres may cause negative effects on ecosystem soil multifunctionality of a similar magnitude as drought. Thus, strategies to counteract this new global change factor are necessary.}, language = {en} } @article{HuangQiaoXuetal.2021, author = {Huang, Lixing and Qiao, Ying and Xu, Wei and Gong, Linfeng and He, Rongchao and Qi, Weilu and Gao, Qiancheng and Cai, Hongyan and Grossart, Hans-Peter and Yan, Qingpi}, title = {Full-length transcriptome}, series = {Frontiers in immunology}, volume = {12}, journal = {Frontiers in immunology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-3224}, doi = {10.3389/fimmu.2021.737332}, pages = {18}, year = {2021}, abstract = {Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/M phi) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/M phi including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.}, language = {en} } @article{HabelUlrichEberleetal.2022, author = {Habel, Jan Christian and Ulrich, Werner and Eberle, Jonas and Schmitt, Thomas}, title = {Species community structures of Afrotropical butterflies differ depending on the monitoring method}, series = {Biodiversity and conservation}, volume = {31}, journal = {Biodiversity and conservation}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0960-3115}, doi = {10.1007/s10531-021-02332-2}, pages = {245 -- 259}, year = {2022}, abstract = {Standardised biodiversity assessment is crucial to understand community structures and population dynamics of animals. There exist various methods to monitor biodiversity. Approaches differ depending on the target species group and the aim of study, and show advantages and disadvantages. The obtained data and results are influenced by local environmental conditions and seasonal variability. In a comparative approach, we studied butterfly diversity and community structure in the dryland savannah biome of south-eastern Kenya with two different methods, transect counts and bait trapping. We repeatedly collected data throughout the dry and rainy seasons, in both near natural and anthropogenically influenced landscapes. Significantly more species and individuals were recorded by transect counts than by bait trapping, though the larger and more mobile Nymphalid species (and in particular representatives of the genus Charaxes) were comparatively overrepresented in traps. The transect data revealed much more pronounced effects of land-use and seasonality than the trap data. These results show that the choice of data collection methods must depend on the general research question, habitat conditions and season. To study the relative variation of species diversity and abundance, the collection of a fraction of the total species diversity might be sufficient. However, if the focus is on a largely complete recording of species diversity, the use of various collection methods is essential. More specifically, our data clearly demonstrate that transect counts represent a reasonable method for assessing butterfly diversity for the African dryland savannah region, but fails to fully capture occurrences of all species. Bait trapping can be used only as a supplementary method for assessing some few highly mobile low-density species.}, language = {en} } @article{MbebiBreitlerBordeauxetal.2022, author = {Mbebi, Alain J. and Breitler, Jean-Christophe and Bordeaux, M'elanie and Sulpice, Ronan and McHale, Marcus and Tong, Hao and Toniutti, Lucile and Castillo, Jonny Alonso and Bertrand, Benoit and Nikoloski, Zoran}, title = {A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids}, series = {G3: Genes, genomes, genetics}, volume = {12}, journal = {G3: Genes, genomes, genetics}, number = {9}, publisher = {Genetics Soc. of America}, address = {Pittsburgh, PA}, issn = {2160-1836}, doi = {10.1093/g3journal/jkac170}, pages = {11}, year = {2022}, abstract = {Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.}, language = {en} } @article{HeimLisovskiWieczoreketal.2022, author = {Heim, Birgit and Lisovski, Simeon and Wieczorek, Mareike and Morgenstern, Anne and Juhls, Bennet and Shevtsova, Iuliia and Kruse, Stefan and Boike, Julia and Fedorova, Irina and Herzschuh, Ulrike}, title = {Spring snow cover duration and tundra greenness in the Lena Delta, Siberia}, series = {Environmental research letters}, volume = {17}, journal = {Environmental research letters}, number = {8}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1748-9326}, doi = {10.1088/1748-9326/ac8066}, pages = {18}, year = {2022}, abstract = {The Lena Delta in Siberia is the largest delta in the Arctic and as a snow-dominated ecosystem particularly vulnerable to climate change. Using the two decades of MODerate resolution Imaging Spectroradiometer satellite acquisitions, this study investigates interannual and spatial variability of snow-cover duration and summer vegetation vitality in the Lena Delta. We approximated snow by the application of the normalized difference snow index and vegetation greenness by the normalized difference vegetation index (NDVI). We consolidated the analyses by integrating reanalysis products on air temperature from 2001 to 2021, and air temperature, ground temperature, and the date of snow-melt from time-lapse camera (TLC) observations from the Samoylov observatory located in the central delta. We extracted spring snow-cover duration determined by a latitudinal gradient. The 'regular year' snow-melt is transgressing from mid-May to late May within a time window of 10 days across the delta. We calculated yearly deviations per grid cell for two defined regions, one for the delta, and one focusing on the central delta. We identified an ensemble of early snow-melt years from 2012 to 2014, with snow-melt already starting in early May, and two late snow-melt years in 2004 and 2017, with snow-melt starting in June. In the times of TLC recording, the years of early and late snow-melt were confirmed. In the three summers after early snow-melt, summer vegetation greenness showed neither positive nor negative deviations. Whereas, vegetation greenness was reduced in 2004 after late snow-melt together with the lowest June monthly air temperature of the time series record. Since 2005, vegetation greenness is rising, with maxima in 2018 and 2021. The NDVI rise since 2018 is preceded by up to 4 degrees C warmer than average June air temperature. The ongoing operation of satellite missions allows to monitor a wide range of land surface properties and processes that will provide urgently needed data in times when logistical challenges lead to data gaps in land-based observations in the rapidly changing Arctic.}, language = {en} }