bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying genome level variation in generalist and specialist bacteria and their relationship to abiotic conditions in European freshwater ecosystems
Authors: Shah Manan , Bornemann Till , Nuy Julia , Probst Alexander , Beisser Daniela , Boenigk Jens 
Published: March 2021

Microbial biodiversity is one of the increasingly studied fields, yet we are unable to accurately pinpoint the intricacies of how the biotic landscape changes with its abiotic counterpart. Every organism reacts differently to physical changes in its surrounding(Zeglin (2015)). While there are some generalist microbes that can grow in limited capacity in many different types of environment, there are also some specialists that can flourish in very specific environments(Monard et al. (2016)).
We hypothesize that both generalists and specialists have developed advanced strategies that allow them thrive under diverse conditions or in very specific niches, and that these changes should be traceable on the genomic level. We expect to see variations in factors like genome sizes, number of genes, GC content, metabolic pathways that yield growth and replication advantages in nutrient deficient niches and defense mechanisms. We also expect to identify genomic streamlining in organisms that survive in nutrient deficient environments.
We are currently studying the genetic basis of why these generalists are so universally present though in smaller numbers, and what allows the specialists to efficiently exploit the abiotic factors of their specific environment in order to flourish. To pursue this, we have sampled and sequenced metagenomes from 47 lakes spread across Europe with strongly diverging environmental conditions such as pH, temperature, organic and nutrient content, elevation, and conductivity.
We’ve identified reads from more than 9000 taxonomically unique organisms, of which 700 were identified as generalists and 1200 as specialists, based on niche width permutations. In total we have assembled 313 high quality Metagenome Assembled Genomes (MAGs). Which now allow us to get a more detailed insight into the genetic basis and specific adaptations of these organisms.
PEMA v2: addressing metabarcoding bioinformatics analysis challenges
Authors: Zafeiropoulos Haris , Pavloudi Christina , Pafilis Evangelos 
Published: March 2021

Environmental DNA (eDNA) and metabarcoding have launched a new era in bio- and eco-assessment over the last years (Ruppert et al. 2019). The simultaneous identification, at the lowest taxonomic level possible, of a mixture of taxa from a great range of samples is now feasible; thus, the number of eDNA metabarcoding studies has increased radically (Deiner and 2017). While the experimental part of eDNA metabarcoding can be rather challenging depending on the special characteristics of the different studies, computational issues are considered to be its major bottlenecks. Among the latter, the bioinformatics analysis of metabarcoding data and especially the taxonomy assignment of the sequences are fundamental challenges.
Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available. However, each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy; thus, tuning bioinformatics analysis has proved itself fundamental (Kamenova 2020). The computation capacity of high-performance computing systems (HPC) is frequently required for such analyses. On top of that, the non perfect completeness and correctness of the reference taxonomy databases is another important issue (Loos et al. 2020).
Based on third-party tools, we have developed the Pipeline for Environmental Metabarcoding Analysis (PEMA), a HPC-centered, containerized assembly of key metabarcoding analysis tools. PEMA combines state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune thoroughly each study thanks to roll-back checkpoints and on-demand partial pipeline execution features (Zafeiropoulos 2020).
Once PEMA was released, there were two main pitfalls soon to be highlighted by users. PEMA supported 4 marker genes and was bounded by specific reference databases. In this new version of PEMA the analysis of any marker gene is now available since a new feature was added, allowing classifiers to train a user-provided reference database and use it for taxonomic assignment. Fig. 1 shows the taxonomy assignment related PEMA modules; all those out of the dashed box have been developed for this new PEMA release. As shown, the RDPClassifier has been trained with Midori reference 2 and has been added as an option, classifying not only metazoans but sequences from all taxonomic groups of Eukaryotes for the case of the COI marker gene. A PEMA documentation site is now also available. PEMA.v2 containers are available via the DockerHub and SingularityHub as well as through the Elixir Greece AAI Service. It has also been selected to be part of the LifeWatch ERIC Internal Joint Initiative for the analysis of ARMS data and soon will be available through the Tesseract VRE.
Applications of environmental DNA methods for charophyte biodiversity
Authors: Nowak Petra , Wiebe Christina , Karez Rolf , Schubert Hendrik 
Published: March 2021

The use of environmental DNA (eDNA) for qualitative species inventories offers great potential as a cost-effective tool for species identification. This requires that the target species release DNA, reference information is available and detection methods exist. Environmental DNA analyses are currently used routinely to inventory fish fauna (Wang et al. 2021), molluscs (Klymus et al. 2017) or insects (Uchida et al. 2020). For other groups, such as macrophytes, there is not much information available (Scriver et al. 2015). In plants, identifying suitable eDNA markers been much more challenging, as no single DNA region has been accepted for the purposes of barcoding.
Within this project, we assessed if stoneworts (Charophytes, Characeae) can be detected by using eDNA analysis and if it can be used to support macrophyte monitoring. Charophytes are macroscopic green algae which, because of their role as habitat engineers, are of special importance for aquatic ecosystems. Many charophyte species are bound to clean, nutrient-poor fresh and brackish waters (e.g. Melzer 1999) and are regarded bioindicators for water quality by national and international directives (e.g. Habitats Directive, EU Water Framework Directive). Being sensitive to anthropogenic pressures, a drastic decline in populations with increasing eutrophication has been reported (Sand-Jensen et al. 2017) . However, the diversity of Characeae is often underestimated due to difficulties in morphological determination, and the genetic identification of charophytes has been established only in the recent few years (e.g. Nowak et al. 2016).
We assessed the potential utility of eDNA to document the diversity of charophyte species. eDNA from a fresh water lake (Dreetzsee, Germany, 2018) and from a brackish water site (Darß-Zingst Lagoon System, Germany, 2018) was extracted from filtered or ethanol‐precipitated water samples, and we designed and tested eDNA markers based on four regions of the chloroplast genome - atpB, rbcL, psbC, and matK. Of the four regions, matK and rbcL were most likely to amplify DNA from charophyte species. Both sites exhibit a diverse charophyte flora, which we successfully could identify to species/group level by eDNA analysis.
In a current study, the developed eDNA markers are used to scrutinize the charophyte population of the Schlei estuary (Germany, Schleswig-Holstein). Since conventional monitoring can only be carried out once a year at a few sites, Characeae have not been observed in recent years, or only very sporadically. As it is not possible to survey the entire Schlei, especially due to high water turbidity, the eDNA methodology is tested to assess the presence of Characeae species.
The value of DNA barcoding in a hotspot area: an example of Rhyacophila tristis (Trichoptera) in the Western Carpathians
Authors: Bozáňová Jana , Čiampor Jr Fedor , Mamos Tomasz , Grabowski Michal , Čiamporová-Zaťovičová Zuzana 
Published: March 2021

DNA barcoding has proven to be an essential tool in providing molecular tags for animal species. In addition, the value of DNA barcoding undoubtedly consists in giving information about intraspecific genetic diversity, which is of great importance for biodiversity monitoring and conservation assessments. Such data are especially valuable in case of biodiversity hot-spots. Therefore, the aim of our study was to expand the knowledge of the genetic patterns and distribution of the caddisfly Rhyacophila tristis (Trichoptera, Rhyacophilidae) population in one such biodiversity hotspot - The Western Carpathians.
The W Carpathians include rich freshwater systems of springs and streams, where molecular diversity and phylogeographic patterns of aquatic fauna are yet to be fully explored. Based on the mitochondrial DNA barcoding fragment (COI-5P) of 161 sequences, two BINs representing distinct lineages within R. tristis were identified. BIN BOLD:AAD5574 occurred in 16 localities to the west and BIN BOLD:ADL4166 in 44 localities more to the east, with contact zone in the middle of the mountain system (Fig. 1). BIN BOLD:AAD5574 occurred at a significantly narrower altitudinal interval compared to BIN BOLD:ADL4166, but we did not record significant differences in molecular diversity between BINs. Likewise, past population growth was found in both lineages. Both BINs started to expand demographically at the beginning of the Last Glacial Maximum, however BIN BOLD: ADL4166 increased its demography more sharply compared to BIN BOLD:AAD5574, moreover the effective population size of BIN BOLD:ADL4166 was much higher. BIN BOLD:ADL4166, showing a significantly wider range of altitude, has probably found higher potential for dispersal to various mountain units in the area of the W Carpathians. Our results showed also that BIN BOLD:ADL4166 is more closely related to the separate R. tristis BIN BOLD: ADL4367 recognized in Bulgaria than to the BIN BOLD:AAD5574 occurring geographically in the same mountain system. Additionally, different patterns of population expansion of BIN BOLD:ADL4166 between springs and streams were found. These differences may have occurred due to specific environmental conditions of the karstic springs, which are considered as relatively isolated aquatic habitats.
Our initial study of R. tristis phylogeography in W Carpathians opens several new important questions: Is it possible that BIN BOLD:ADL4166 is expanding from the eastern part of Europe (Bulgaria) to the colder streams in the W Carpathians during the LGM? What role do the W Carpathian springs play in maintaining the genetic diversity and sustainability of R. tristis? Could these relatively isolated aquatic habitats serve as postglacial refugia for R. tristis species? And, maybe also, are they two separate species? This contribution was partially supported by the project VEGA 2/0084/21 and VEGA 1/0127/20.
Sediment eDNA Metabarcoding for monitoring impacts from offshore oil extraction
Authors: Lanzén Anders , Thomassen Hestetun Jon , Bagi Andrea , Dahlgren Thomas 
Published: March 2021

Routine biological monitoring of the areas affected by offshore oil drilling and extraction is critical for ensuring proper environmental management. In addition to sufficient knowledge of the ecosystem affected, formalised e.g. as biotic indices of indicator species, adequate temporal and spatial resolution is also required, to provide accurate information. As already demonstrated in several types of environments, environmental DNA (eDNA) metabarcoding offers an attractive alternative to current morphology-based assessments, including for impacts of oil extraction or spills.
We have recently studied the influence of different experimental strategies on the accuracy of marine sediment metabarcoding, suggesting minimum criteria for technical and spatial replication (Hestetun et al. 2020). Here, we aim to evaluate the predictive power of this strategy, through agreement with assessments based on physicochemical measurements and current bioindicators. To this end, we targeted the metazoan, and total eukaryotic benthic communities, using COI and 18S V1-V2 markers, respectively. Sampled sites ranged from high to low impacts. The studied areas were located near active production installations and reference sites on the Norwegian continental shelf, in the North Sea and Barents Sea.
As a proxy for accumulated impact, we developed a simple physicochemical pressure index (PI) based on total hydrocarbons, PAH16, barium and copper, all of which agreed well with impact reported from recent routine monitoring. Alpha diversity of both molecular datasets, as well as of morphology data, correlated strongly with this PI. However, the correlation was stronger yet with the macroinvertebrate-based Norwegian Sensitivity Index (NSI) derived from COI metabarcoding data, which also agreed well with NSI values derived from morphology-based monitoring. We also identified a set of bioindicator taxa from each of the two metabarcoding datasets, used to develop two novel metabarcoding-based biotic indeces. Using cross-validation, we demonstrated that predictions based on these indeces agreed well with PI. Predictive performance was better, and similar to NSI, for the COI-based index, but also high for the 18S-based version.
In conclusion, this study demonstrates how de novo biotic indices can be developed, that perform comparably to existing biotic indices. We are confident that, using a larger set of samples, performance can be improved beyond that of current monitoring practices. Thanks to the reduced costs of eDNA analysis in comparison to morphological identifiation, this would also pave the way for improved spatial and temporal resolution employed in routine environmental monitoring. In doing so, it can also provide valuable raw data for improving our understanding of benthic ecology, biodiversity and its sensitivity to anthropogenic pressures.
DNA-based biomonitoring in the tropics: Detection and control of Batrachochytrium dendrobatidis in Ecuadorian ecosystem
Authors: Riascos-Flores Lenin , Carrera Andrea , Naranjo Leopoldo , Yanez Jomira , Goethals Peter , Bonilla Julio , Celi Jorge , Van der heyden Christine , Ortega Mauricio 
Published: March 2021

Batrachochytrium dendrobatidis (Bd) is a fungus that parasites vertebrates, and is associated with population declines worldwide in endemic amphibian species. As such, it is one of several invasive species which pose a serious threat to a variety of vertebrate hosts, in casu: amphibians. Detection of such invasive species is generally based on DNA-based methods where, for instance, swabs or tissue samples of candidate hosts are analysed for their presence. Any management strategy of these invasive species would greatly benefit from sensitive and rapid detection methods which can be applied at a large scale. The analysis of eDNA from the habitat of candidate host organisms may hold significant potential for this purpose. In this study, we compare the ability of eDNA from habitat samples with that of swab and/or tissue samples of candidate hosts to detect the presence of Bd in Ecuador.
We collected individuals from the amphibians: Pristimantis (Anura: Craugastoridae), Rhinella (Anura: Bufonidae), Gastroteca (Anura: Hemiphractidae), from the endangered toad species of the genus Atelopus (Anura: Bufonidae) as well as water samples from different water bodies in Andean and coastal Ecuadorian areas. Samples were processed using a portable field molecular laboratory. Commercial primers for the internal transcribed spacer (ITS), in combination with a new set of primers designed from Bd sequences from tropical countries, were used. Positive PCR results from both types of samples were obtained within eight hours after sampling.
Prevalence of BD was detected in eDNA, swab and tissue samples in four of the six ecosystems monitored -14 out of 26 water samples and 27 out of 43 amphibian of in total 12 species- including three endangered toad species (Atelopus balios, A. nanay, and the rediscovered A. bomolochos). Our results highlight the potential of eDNA-based monitoring to assess the presence and prevalence of Bd in Ecuadorian aquatic ecosystems, in accordance with the National Action Plan for the Conservation of Ecuadorian Amphibians. Furthermore, our field lab approach leads to reliable and fast results for the monitoring of invasive species in a tropical context of a pandemic.
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages
Authors: Bush Alex , Compson Zacchaeus , Kattilakoski Matilda , Rideout Natalie , Levenstein Brianna , Hajibabaei Mehrdad , Monk Wendy , Baird Donald 
Published: March 2021

Metabarcoding is capable of delivering consistent and accurate fine-resolution biodiversity data, and offers great promise for improving aspects of environmental assessment and research. Even so, many ecologists are keen to make further inferences about species’ abundances and the number of sequence reads has proven to be a poor proxy for abundance. The conservative interpretation has been to treat metabarcoding data as presence/absence, and although such data are less rich, occurrence and abundance are only different expressions of the same phenomenon. Interestingly if we assume the probability of detecting individuals is constant, it should be possible to use changes in the frequency of detection to infer changes in the underlying abundance. We tested the possibility that changes in the abundance structure of benthic macroinvertebrate communities could be recovered using replicated metabarcoding.
We conducted 5 monthly surveys from Jun-Nov 2019 at the Catamaran Brook, a small tributary of the Little Southwest Miramichi River in New Brunswick, Canada. Each survey collected 30 benthic samples divided between control and treatment cages that excluded predatory fish. A further 6 samples were taken for traditional microscopic identification and counting.
Analysis of the metabarcoding data demonstrated that we could recover plausible changes in abundance from occurrence data, including significant responses to both seasonal dynamics and the experimental exclusion of predators. The microscopy samples merely confirmed that count data are highly stochastic, and therefore while specific estimates of expected abundance from our model are highly uncertain, they capture those differences we could validate. In summary, while we confirmed that occurrence data are more robust for routine bioassessment, it is possible to recover fine-resolution changes in abundance that can inform ecological studies using metabarcoding.
Developing DNA Based Methods for Environmental Regulation and Management- UK Insights
Authors: Duncan Willie 
Published: March 2021

DNA assessments are revolutionising biomonitoring opportunities across the globe, including the monitoring of rare and invasive species, creating biodiversity inventories, and developing pollution diagnostic and ecosystem resilience assessment methods. To date pollution and ecosystem resilience assessments have been based on assessing the diversity of familiar taxonomic groups but the introduction of DNA based methods will significantly increase the opportunities to exploit groups not previously used for this work.
Environmental regulators and managers can derive many benefits from the adoption of these methods, such as improved understanding of environmental conditions, cost effective sample processing, overcoming taxonomic bottlenecks, either through shortages in trained taxonomists or utilising biota with challenging taxonomies. In addition to creating diversity based metrics DNA monitoring also allows for the assessment of functional attributes such as those that support important ecosystem services.
The UK has been an early adopter of this technology and this paper will explore how the alignment of scientific advances have coincided with operational needs to create a fertile arena for the development of DNA based assessment methods that will be used in environmental regulation and management. Development projects advanced in the UK will be examined to identify the common and specific issues associated with them that have led to early engagement and adoption.
Évaluons, évoluons
Authors: Delaye Pierre , Savy Hervé 
Published: March 2021

Expérimentés à partir des années 1980, les dispositifs en unités capitalisables (UC) se sont développés progressivement et occupent aujourd’ hui une place centrale dans les formations diplômantes du ministère de l’Agriculture destinées aux apprentis et aux stagiaires de la formation professionnelle continue. La démarche d’ élaboration des référentiels, fondée sur une analyse des métiers ainsi que les espaces d’ autonomie confiés aux centres en matière de formation et d’ évaluation permettent une liaison précise avec les emplois visés sur le territoire. L’ organisation en unités indépendantes et l’ évaluation par objectifs facilitent la construction de plans de formation et d’ évaluation, adaptés aux besoins diversifiés des apprenants. Un rôle important est confié aux jurys en charge du suivi des centres de formation et aux directions régionales de l’ alimentation, de l’ agriculture et de la forêt, chargées d’ encadrer, d’ organiser et d’ animer l’ ensemble du dispositif régional. Sur le terrain, des organisations diverses ont été déployées en fonction du contexte. Au travers des dernières rénovations de diplômes, le ministère a réaffirmé la place donnée aux dispositifs par UC, adaptés aux enjeux actuels. Cette orientation constitue une opportunité pour relancer une dynamique autour de ce dispositif : ajustement et clarification des règles de mise en œuvre, animation en région et formation des acteurs, réflexion plus fondamentale sur les évolutions futures à envisager.
Les grandes décisions de l’histoire de France
Authors: Le Naour Jean-Yves 
Published: March 2021

En décrétant la mobilisation générale le 1er août 1914, le gouvernement français prend la lourde responsabilité de faire entrer le pays dans la guerre contre les empires centraux. On imagine que cette grave décision, si difficile à prendre, si lourde de conséquences, a été mûrement réfléchie et longuement débattue… mais il n’en est rien. En réalité, la France, ballottée par les événements, a décidé de ne pas choisir et a choisi de ne pas décider. Spectatrice largement impuissante de la crise diplomatique de juillet 1914, elle se tient en retrait, silencieuse, avec au fond plus de calculs que d’indécision, à la différence du précédent de 1870 où la montée aux extrêmes avait été portée par un parti de la guerre qui avait eu raison des réticences de Napoléon III 1 . Liée par son alliance avec la Russie, elle n’avait aucun moyen de la renier, sauf à perdre toute crédibilité et à se trouver isolée sur l’échiquier international lors de la prochaine crise. Voici le récit d’une dizaine de jours édifiants qui ont défait « le monde d’hier » cher à Stefan Zweig .