Tag: ecology

Extensive practical guide to DNA-based biodiversity assessment methods published as a ‘living’ document by DNAqua-Net COST Action

Between 2016 and 2021, over 500 researchers collaborated within the DNAqua-Net international network, funded by the European Union’s European Cooperation in Science and Technology programme (COST), with the goal to develop and advance biodiversity assessment methods based on analysis of DNA obtained from the environment (e.g. river water) or from unsorted collections of organisms.

Such innovative methods are a real game changer when it comes to large-scale assessment of biodiversity and ecological monitoring, as collecting environmental samples that are sent to the lab for analysis is much cheaper, faster and non-invasive, compared with capturing and examining live organisms. However, large-scale adoption has been hindered by a lack of standardisation and official guidance.

Recognising the urgent need to scale up ecological monitoring as we respond to the biodiversity and climate crises, the DNAqua-Net team published a guidance document for the implementation of DNA-based biomonitoring tools.

The guide considers four different types of samples: water, sediments, invertebrate collections and diatoms, and two primary analysis types: single species detection via qPCR and similar targeted methods; and assessment of biological communities via DNA metabarcoding. At each stage of the field and laboratory process the guide sets out the scientific consensus, as well as the choices that need to be made and the trade-offs they entail. In particular, the guide considers how the choices may be influenced by common practical constraints such as logistics, time and budget. Available in an Advanced Book format, the guidelines will be updated as the technology continues to evolve.

Leaders of DNAqua-Net are Prof. Dr. Florian Leese of the University of Duisburg-Essen (Germany) and Dr. Agnès Bouchez of the French National Institute for Agriculture, Food, and Environment (INRAE). The core writing team for the present guide book involves Dr. Micaela Hellström (MIX Research AB, Sweden), Dr. Kat Bruce (NatureMetrics Ltd., UK), Dr. Rosetta Blackman (University of Zurich and EAWAG, Switzerland), Dr. Sarah Bourlat (LIB/Museum Koenig, Germany), and Prof. Kristy Deiner (ETH Zurich and SimplexDNA AG, Switzerland).

“Back in 2016 we realised that all around the globe researchers are testing new eDNA methods, developing individual solutions and products. While this is excellent, we need to reach a consensus and provide this consensus to stakeholders from the applied sectors”,
says Florian Leese.

This video was created as part of EU COST Action DNAqua-Net (CA15219) and shows how environmental DNA (eDNA) can be sampled and analysed from aquatic ecosystems. It shows the whole cycle from the start to final results.
Credit: DNAqua-Net

The guide’s lead author Dr. Kat Bruce adds:

“The urgency of addressing the twin biodiversity and climate crises means that we need to accelerate the adoption of new technologies that can provide data and insights at large scales. In doing so, we walk a tricky line to agree on sufficiently standardised methods that can be usefully applied as soon as they add value, while still continuing to develop them further and innovate within the field. It was a daunting task to seek consensus from several hundred scientists working in a fast-moving field, but we found that our technology is based on a strong foundation of knowledge and there was a high level of agreement on the core principles – even if the details vary and different users make different choices depending on their environmental, financial or logistical constraints.”

Looking back on the last four years that culminated in the publication of a “living” research publication, Prof. Dr. Kristy Deiner says:

“The document took many twists and turns through more than ten versions and passionate discussions across many workshops and late night drinks. All in the days when we could linger at conferences without fear of the pandemic weighing on us. As we worked to find consensus, one thing was clear: we had a lot to say and a standard review paper was not going to cut it. With the knowledge and experience gathered across the DNAqua-Net, it made sense to not limit this flow of information, but rather to try and tackle it head on and use it to address the many questions we’ve all struggled with while developing DNA-based biodiversity survey methods.”

Now that the document – or at least its first version – is publicly available, the researchers are already planning for the next steps and challenges.

“The bottom line is we’ve come a long way in the last ten years. We have a buffet of methods for which many produce accurate, reliable and actionable data to the aid of biodiversity monitoring and conservation. While there is still much work to be done, the many unanswered questions are because the uptake is so broad. With this broad uptake comes novel challenges, but also new insights and a diversity of minds with new ideas to address them. As said this is planned to be a living document and we welcome continued inputs no matter how great or small,” says Deiner.

Dr. Micaela Hellström recalls:

“The book evolved over the four years of COST Action DNAqua-Net which made it possible for the many scientists and stakeholders involved to collaborate and exchange knowledge on an unprecedented scale. Our whole team is well aware of the urgent need to monitor biodiversity loss and to provide accurate species distribution information on large scales, to protect the species that are left. This was a strong driving force for all of us involved in the production of this document. We need consensus on how to coherently collect biodiversity data to fully understand changes in nature.”

“It was a great and intense experience to be a part of the five-person core writing team. In the months prior to submitting the document, we spent countless hours, weekends and late nights researching the field, communicating with researchers and stakeholders, and joining vivid Zoom discussions. As a result, the present book provides solid guidance on multiple eDNA monitoring methods that are – or will soon become – available as the field moves forward.”

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The DNAqua-Net team invites fellow researchers and practitioners to provide their feedback and personal contributions using the contacts below.

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Original source:

Bruce K, Blackman R, Bourlat SJ, Hellström AM, Bakker J, Bista I, Bohmann K, Bouchez A, Brys R, Clark K, Elbrecht V, Fazi S, Fonseca V, Hänfling B, Leese F, Mächler E, Mahon AR, Meissner K, Panksep K, Pawlowski J, Schmidt Yáñez P, Seymour M, Thalinger B, Valentini A, Woodcock P, Traugott M, Vasselon V, Deiner K (2021) A practical guide to DNA-based methods for biodiversity assessment. Advanced Books. https://doi.org/10.3897/ab.e68634

First moth species on Alpenrose discovered

Discovery of the first moth species to mine the leaves of the highly poisonous Alpine rose

Rust-red alpine rose, one of the most popular alpine plants. Photo by Ingrid Huemer

An Austrian-Swiss research team was able to find a previously unknown glacial relic in the Alps, the Alpine rose leaf-miner moth. It is the first known species to have its caterpillars specializing on the rust-red alpine rose, a very poisonous, widely distributed plant that most animals, including moths and butterflies, strictly avoid. The extraordinary record was just published in the peer-reviewed scientific journal Alpine Entomology.

Poisonous host plant

The rust-red alpine rose (Rhododendron ferrugineum) is among the best-known and most attractive plants due to its flowering splendor – at least for humans. It is, in fact, a highly poisonous plant, strictly avoided by grazing animals. For insects, the alpine rose is attractive at most as a nectar plant; insect larvae, on the other hand, develop on it only in exceptional cases. This also applies to Alpine butterflies and moths, which leave Alpine roses largely untouched despite their wide distribution. Therefore, the discovery of a highly specialized species in the Alps came as a complete surprise.

Chance find

Alpine rose leaf-miner moth adults resting on leaves of the host-plant in Ardez, Graubünden, Switzerland. Photos by Jürg Schmid

Since alpine roses are unattractive to caterpillars and no insect the entire Alpine region was previously known to specialize on them, butterfly and moth experts had considered them rather uninteresting and ignored them in their research. The discovery of the alpine rose leaf-miner wasn’t the result of a targeted search: it was a pure stroke of luck.

During a cloudy spell in July this year, researchers surveying the butterflies in Ardez in the Engadine valley, Switzerland, happened to take a break exactly at an infested alpine rose bush.

“The accidental sighting of the first caterpillar in an alpine rose leaf was an absolute adrenaline rush, it was immediately clear that this must be an extraordinary species,”
Peter Huemer, researcher and head of the natural sciences department of the Tyrolean State Museums

Peter Huemer, researcher and head of the natural sciences department of the Tyrolean State Museums, and Swiss butterfly and moth expert Jürg Schmid came back in late July and early August to look for caterpillars and pupae and find out more about this curious insect. The extended search yielded evidence of a stable population of a species that was initially a complete enigma.

Life in the leaf

Leaf-mines of the alpine rose leaf-miner moth on *Rhododendron ferrugineum* in Ardez, Graubünden, Switzerland. Photos by Peter Huemer

The alpine rose leaf-miner moth drills through the upper leaf skin and into the leaf interior immediately after the caterpillar hatches. The caterpillar then spends its entire life until pupation between the intact leaf skins, eating the leaf from the inside. Thanks to this behavior, the caterpillar is just as well protected from bad weather as from many predators such as birds, spiders, or some carnivore insects. The feeding trail, called a leaf mine, begins with a long corridor and ends in a large square-like mine section. The feces are deposited inside this mine. When the time comes for pupation, the caterpillar leaves the infested leaf and makes a typical web on the underside or a nearby leaf. With the help of several fine silk threads, it produces an elaborate “hammock”, in which the pupation finally takes place. In the laboratory, after about 10 days, the successful breeding to a moth succeeded, with a striking result.

Enigmatic glacial relic

Final instar larva of the alpine rose leaf-miner moth on *Rhododendron ferrugineum* in Ardez, Graubünden, Switzerland. Photo by Jürg Schmid

Huemer and Schmid were surprised to find out that the moths belonged to a species that was widespread in northern Europe, northern Asia and North America – the swamp porst leaf-miner butterfly Lyonetia ledi. By looking at its morphological features, such as wing color and pattern, and comparing its DNA barcodes to those of northern European specimens, they were able to confirm its identity.

Habitat of the alpine rose leaf-miner moth in Engadine/Switzerland with *Rhododendron ferrugineum*. Photo by Jürg Schmid

The Engadine population, however, is located more than 400 km away from the nearest other known populations, which are on the border of Austria and the Czech Republic. Furthermore, the species lives in northern Europe exclusively on swamp porst and Gagel bush – two shrubs that are typical for raised bogs and absent from the Alps. However, the researchers suggest that in earlier cold phases – some 22,000 years ago – the swamp porst and the alpine rose did share a habitat in perialpine lowland habitats north of the Alps. It is very likely that after the last cold period and the melting of the glaciers, some populations of the species shifted their host preference from the swamp porst to the alpine rose. The separation of the distribution areas of the two plants caused by subsequent warm phases inevitably led to the separation of the moth populations.

Extinction risk

Characteristic cocoon with final instar larva and pupa of the alpine rose leaf-miner moth on *Rhododendron ferrugineum* in Ardez, Graubünden, Switzerland. Photos by Jürg Schmid

The Alpine Rose Leaf-miner Moth is so far only known from the Lower Engadine. It lives in a steep, north-exposed, spruce-larch-pine forest at about 1,800 m above sea level. The high snow coverage in winter and the largely shady conditions in summer mean that alpine roses don’t get to bloom there. The scientists suspect that the moth species can still be discovered in places with similar conditions in the northern Alps, such as in neighboring Tyrol and Vorarlberg. Since the moth is likely nocturnal and flies late in the year, probably hibernating in the adult stage, the search for the caterpillars and pupae is more promising. However, the special microclimate of the Swiss location does not suggest that this species, which has so far been overlooked despite 250 years of research, is widespread. On the contrary, there are legitimate concerns that it could be one of the first victims of climate change.

Research article:

Huemer P, Schmid J (2021) Relict populations of Lyonetia ledi Wocke, 1859 (Lepidoptera, Lyonetiidae) from the Alps indicate postglacial host-plant shift to the famous Alpenrose (Rhododendron ferrugineum L.). Alpine Entomology 5: 101-106. https://doi.org/10.3897/alpento.5.76930

The journal Biosystematics and Ecology moves to ARPHA Platform

The scholarly publisher and technology provider Pensoft and its self-developed publishing platform ARPHA welcome Biosystematics and Ecology – a journal by the Austrian Academy of Sciences – to its growing open-access scholarly portfolio. By moving to ARPHA, Biosystematics and Ecology now enjoys a long list of high-tech perks, which dramatically enhance the entire publishing process, from submission to publication, distribution and archiving.

The Austrian Academy of Sciences’ journal Biosystematics and Ecology now boasts an improved publishing infrastructure after moving to the technologically advanced ARPHA Platform and signing with publisher and technology provider Pensoft. The publisher, well-established in the domain of biodiversity-themed journals, is eager to welcome this latest addition to its growing open-access portfolio.

Biosystematics and Ecology is a continuation and replaces the established print-only Biosystematics and Ecology Series of the Austrian Academy of Sciences’s Commission for Interdisciplinary Ecological Studies. It publishes research focused on biodiversity in Central Europe and around the world, a domain of rapidly growing importance as а global biodiversity crisis is looming. A great advantage of Biosystematics and Ecology, in contrast to its predecessor, is the ability to simply update existing checklists and therefore to account for new scientific findings about taxonomic groups or regions.

The peer-reviewed outlet includes contributions on a wide range of ecology and biosystematics topics, aiming to provide biodiversity data, such as catalogi, checklists and interdisciplinary research to the scientific community, while offering the maximum in accessibility, usability, and transparency. The journal is currently indexed in Crossref and archived in CLOCKSS, Portico and Zenodo.

Having already acquired its own glossy and user-friendly website provided by ARPHA, the journal also takes advantage of the platform’s signature fast-track publishing system, which offers an end-to-end publishing solution from submission to publication, distribution and archiving. The platform offers a synergic online space for authoring, reviewing, editing, production and archiving, ensuring a seamlessly integrated workflow at every step of the publishing process.

Thanks to the financial support of the Academy, Biosystematics and Ecology will publish under Diamond Open Access, which means that it is free to read and publish. Opting for ARPHA’s white-label publishing solution, the journal is published under the Academy’s branding and imprint, while benefiting from all signature high-tech features by ARPHA.

Biosystematics and Ecology also makes use of ARPHA Preprints, another platform developed by Pensoft, where authors can post a preprint in a matter of seconds upon submitting a manuscript to the journal. Once the associated manuscript gets published, the preprint is conveniently linked to the formal paper, displaying its citation details.

ARPHA’s easy-to-use, open-access publishing platform offers high-end functionalities such as diverse paper formats (PDF, machine-readable JATS XML, and semantically enriched HTML), automated data export to aggregators, web-service integrations with major global indexing databases, advanced semantics publishing, and automated email notifications and reminders. Features like these make it easy for both humans and machines all over the world to discover, access, cite, and reuse published research.

One water bucket to find them all: Detecting fish, mammals, and birds from a single sample

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study.

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study

Collection of water samples for eDNA metabarcoding bioassessment.
*Photo by Till-Hendrik Macher.*

In times of exacerbating biodiversity loss, reliable data on species occurrence are essential, in order for prompt and adequate conservation actions to be initiated. This is especially true for freshwater ecosystems, which are particularly vulnerable and threatened by anthropogenic impacts. Their ecological status has already been highlighted as a top priority by multiple national and international directives, such as the European Water Framework Directive.

However, traditional monitoring methods, such as electrofishing, trapping methods, or observation-based assessments, which are the current status-quo in fish monitoring, are often time- and cost-consuming. As a result, over the last decade, scientists progressively agree that we need a more comprehensive and holistic method to assess freshwater biodiversity.

Meanwhile, recent studies have continuously been demonstrating that eDNA metabarcoding analyses, where DNA traces found in the water are used to identify what organisms live there, is an efficient method to capture aquatic biodiversity in a fast, reliable, non-invasive and relatively low-cost manner. In such metabarcoding studies, scientists sample, collect and sequence DNA, so that they can compare it with existing databases and identify the source organisms.

Furthermore, as eDNA metabarcoding assessments use samples from water, often streams, located at the lowest point, one such sample usually contains not only traces of specimens that come into direct contact with water, for example, by swimming or drinking, but also collects traces of terrestrial species indirectly via rainfalls, snowmelt, groundwaters etc.

In standard fish eDNA metabarcoding assessments, these ‘bycatch data’ are typically left aside. Yet, from a viewpoint of a more holistic biodiversity monitoring, they hold immense potential to also detect the presence of terrestrial and semi-terrestrial species in the catchment.

In their new study, reported in the open-access scholarly journal Metabarcoding and Metagenomics, German researchers from the University of Duisburg-Essen and the German Environment Agency successfully detected an astonishing quantity of the local mammals and birds native to the Saxony-Anhalt state by collecting as much as 18 litres of water from across a two-kilometre stretch along the river Mulde.

After water filtration the eDNA filter is preserved in ethanol until further processing in the lab.
*Photo by Till-Hendrik Macher.*

In fact, it took only one day for the team, led by Till-Hendrik Macher, PhD student in the German Federal Environmental Agency-funded GeDNA project, to collect the samples. Using metabarcoding to analyse the DNA from the samples, the researchers identified as much as 50% of the fishes, 22% of the mammal species, and 7.4% of the breeding bird species in the region.

However, the team also concluded that while it would normally take only 10 litres of water to assess the aquatic and semi-terrestrial fauna, terrestrial species required significantly more sampling.

Unlocking data from the increasingly available fish eDNA metabarcoding information enables synergies among terrestrial and aquatic biodiversity monitoring programs, adding further important information on species diversity in space and time.

“We thus encourage to exploit fish eDNA metabarcoding biodiversity monitoring data to inform other conservation programs,”
says lead author Till-Hendrik Macher.

“For that purpose, however, it is essential that eDNA data is jointly stored and accessible for different biodiversity monitoring and biodiversity assessment campaigns, either at state, federal, or international level,”
concludes Florian Leese, who coordinates the project.

Original source:

Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

To combat global change, scientists must prioritize community partnerships

Guest blog post by Kennedy “Ned” Rubert-Nason, Caitlin Mandeville and Kirsten Schwarz

Global change is an immediate, accelerating threat to humanity, and its impacts are perpetuated by human activities. Changes such as climate warming, landscape alteration, pollution, resource extraction and depletion, extreme events, biodiversity loss, and spreading of invasive species including diseases, threaten the natural environment and human society. The consequences of these changes are often disproportionately borne by people who have the least political representation. Despite tremendous investment in research aimed at understanding and developing technological solutions to global change threats, implementing effective science-based solutions remains a major challenge.

Undergraduate students at the University of Maine at Fort Kent learn to study how environmental change affects the growth and physiology of *Populus*. Photo by Kennedy “Ned” Rubert-Nason

An article just published in the open-access, peer-reviewed journal Rethinking Ecology explores how translational science, or the process of putting basic research and technological development into use, can bring about the changes in human behavior that are critical to guiding humanity toward a sustainable future. The engine that drives translational science is a theory of change, or strategic plan, which identifies a global change threat, ties it to a goal (usually eliminating or adapting to the threat), and lays out specific actions needed to achieve that goal along with indicators of success. A theory of change that aims to bring about social and structural changes, as required to address global change threats, must embrace relationship-building, collaboration, engagement, commitment, communication, trust, inclusion, equity, transparency, process, and decision framing.

Researchers at Ringve Botanical Garden in Trondheim, Norway, regularly involve the local community in research and stewardship related to urban biodiversity.” Photo by Ringve Botanical Garden, Norwegian University of Science and Technology University Museum

To overcome global change threats, ecologists and other scientists need to prioritize building partnerships with communities that help bring science into practice. These partnerships are critically needed to combat misinformation, build public trust in science, bring about equitable and evidence-informed policies that are accountable to communities’ priorities, and empower people to respond effectively to challenges posed by climate change, pollution, landscape change, extreme events and pandemics.

New Hampshire Sea Grant scientists lead a community outing to survey potential erosion impacts associated with coastal storms. Photo by Caitlin Mandeville

The authors of the paper identified four priority areas for ecologists to engage in translational science:

forging partnerships,
garnering public support,
building strong communities,
and protecting natural resources.

While fundamental research remains vital, there needs to be greater emphasis on the communication, policy, education, leadership and role modeling dimensions that help bring the findings from that research into practice. Interdisciplinary scientists like ecologists are particularly well-suited to this line of work, although they can face barriers such as inadequate training, time, funding and institutional support. Lowering these barriers, and creating a culture that values science-based solutions, must be key priorities in future measures aimed at combating global change threats. Many organizations, including the Union of Concerned Scientists and the Ecological Society of America, provide training and support for ecologists to engage more deeply in translational science.

Community science is a powerful tool researchers can use to partner with communities. Here, volunteers work with the New Hampshire Sea Grant Beach Profile Monitoring program to collect regular data on beach dynamics and erosion that can be used for managing the shoreline. Photo by Caitlin Mandeville

Original source:

Rubert-Nason K, Casper AMA, Jurjonas M, Mandeville C, Potter R, Schwarz K (2021) Ecologist engagement in translational science is imperative for building resilience to global change threats. Rethinking Ecology 6: 65-92. https://doi.org/10.3897/rethinkingecology.6.64103

Failure to respond to a coral disease epizootic in Florida: causes and consequences

By 2020, losses of corals have been observed throughout Florida and into the greater Caribbean basin in what turned out to be likely the most lethal recorded case of Stony Coral Tissue Loss Disease. A Perspectives paper, published in the open-access peer-reviewed journal Rethinking Ecology, provides an overview of how Florida ended up in a situation, where the best that could be done is rescuing genetic material from coral species at risk of regional extinction.

Guest blog post by William F. Precht

A colony of the large grooved brain coral, Colpophyllia natans, infected by Stony Coral Tissue Loss Disease. The photo shows the progressive, rapid advance of disease, left-to-right, across the colony.
Image by William Precht.

Dredging projects conducted in association with coral reefs typically generate concern by environmental groups, resulting in careful monitoring by government agencies. Even though the aim of those dredge projects is to widen or deepen existing ship channels, while minimizing damage to coral reef resources, there are often the intuitive negative assumptions that dredging kills corals.

The recent Port Miami Dredge Project started as an uncomplicated case story. However, significant problems arose, caused by a concurrent and unprecedented coral disease epidemic that killed large numbers of corals, which was initiated following a regional thermal anomaly and coral bleaching event.

The coral disease, known as Stony Coral Tissue Loss Disease (SCTLD), was first observed in September 2014 near Virginia Key, Florida. In roughly six years, the disease has spread throughout Florida and into the greater Caribbean basin. The high prevalence of SCTLD and the resulting high mortality in coral populations, coupled with the large number of susceptible species affected, suggest that this disease outbreak is one of the most lethal ever recorded on contemporary coral reefs. The disease is still presently active and continues to ravage coral reefs throughout the region.

The initial response to this catastrophic disease by resource managers with purview over the ecosystem in Southeast Florida was slow. There is generally a noticeably short window of opportunity to intervene in disease amelioration or eradication in the marine environment. This slow response enabled the disease to spread unchecked. Why was the response to the loss of our coral reefs to a coral disease epidemic such a massive failure? This includes our failure as scientists, regulators, resource managers, local media, and policy makers alike. With this Perspectives paper, published in Rethinking Ecology, my intention was to encapsulate the numerous reasons for our failures during the first few years of the outbreak, reminiscent of the early failures in the U.S. response to the COVID-19 pandemic.

First, the Port Miami dredging project was ongoing when the coral disease epidemic began. Some managers and local environmental groups blamed dredging, rather than SCTLD for the coral losses, reported in the project’s compliance monitoring program. Second, this blame was amplified in the media, because dredging projects are intuitively assumed to be bad for coral reefs. Third, during this same time, the State of Florida prohibited government employees from acknowledging global warming in their work. This was problematic because ocean warming is a proximal cause of many coral diseases.

As a result, some managers ignored the well-known links between warming and coral disease. A consequence of this policy was that the dredging project provided an easy target to blame for the coral mortality noted in the monitoring program, despite convincing data that suggested otherwise.

Specifically, the intensive compliance monitoring program, conducted by trained scientific divers, was statistically significant. SCTLD that was killing massive numbers of corals throughout the region was also killing corals at the dredge site. Further, this was happening in the same proportions and among the same suite of species.

Finally, when the agencies responded to the outbreak, their efforts were too little and much too late to make a meaningful difference. While eradication of the disease was never a possibility, early control measures may have slowed its spread, or allowed for the rescue of significant numbers of large colonies of iconic species. Because of the languid management response to this outbreak, we are now sadly faced with a situation where much of our management efforts are focused on the rescue of genetic material from coral species already at risk of regional extinction.

The delayed response to this SCTLD outbreak in Southeast Florida has many similarities to the COVID-19 pandemic response in the United States and there are lessons learned from both that will improve disease response outcomes in the future, to the benefit of coral reefs and human populations.

Publication:

Precht W (2021) Failure to respond to a coral disease epizootic in Florida: causes and consequences. Rethinking Ecology 6: 1-47. https://doi.org/10.3897/rethinkingecology.6.56285

Eurasian eagle owl diet reveals new records of threatened giant bush-crickets

Bird diets provide a real treasure for research into the distribution and conservation of their prey, conclude scientists after studying the Eurasian Eagle Owl in southeastern Bulgaria. In their paper, published in the open-access, peer-reviewed journal Travaux du Muséum National d’Histoire Naturelle “Grigore Antipa”, they report the frequent presence of the threatened Big-Bellied Glandular Bush-Cricket, and conclude that studies on the Eurasian Eagle Owl could be used to identify biodiversity-rich areas in need of protection.

Male specimen of the Big-Bellied Glandular Bush-Cricket (Bradyporus macrogaster)
Photo by Dragan Chobanov

Bird diets provide a real treasure for research into the distribution and conservation of their prey, such as overlooked and rare bush-cricket species, point out scientists after studying the diet of the Eurasian Eagle Owl (Bubo bubo) in southeastern Bulgaria.

In their paper, published in the open-access, peer-reviewed journal Travaux du Muséum National d’Histoire Naturelle “Grigore Antipa”, Dr Dragan Chobanov (Institute of Biodiversity and Ecosystem Research, Bulgaria) and Dr Boyan Milchev (University of Forestry, Bulgaria) report the frequent presence of the threatened with extinction Big-Bellied Glandular Bush-Cricket (Bradyporus macrogaster) in the diet of Eurasian Eagle Owls, and conclude that the predatory bird could be used to identify biodiversity-rich areas in need of protection.

While the Balkan Peninsula has already been recognised as the area with the highest diversity of orthopterans (grasshoppers, crickets and bush-crickets) in Europe and one of the generally most biologically diverse areas in the whole Palearctic realm, it is also home to a worrying number of threatened species. Additionally, a thorough and updated country assessment of the conservation status of the orthopterans found in Bulgaria is currently lacking. This is why the Bulgarian team undertook a study on the biodiversity of these insects by analysing food remains from pellets of Eurasian Eagle Owls, collected from 53 breeding sites in southeastern Bulgaria.

As a result, the scientists reported three species of bush crickets that have become a significant part of the diet of the studied predatory birds. Curiously enough, all three species are rare or threatened in Bulgaria. The case of the Big-Bellied Glandular Bush-Cricket is of special concern, as it is a species threatened by extinction. Meanwhile, the local decline in mammals and birds that weigh between 0.2 and 1.9 kg, which are in fact the preferred prey for the Eurasian Eagle Owl, has led the highly opportunistic predator to increasingly seek large insects for food. The researchers even suspect that there might be more overlooked species attracting the owls.

Taking into account the hereby reported interconnected inferences of conservation concern, as well as the vulnerability of the Big-Bellied Glandular Bush-Cricket, a species with a crucial role in the food chain, the scientists call for the newly provided data to prompt the designation of a new Natura 2000 site. Additionally, due to the species’ requirements for habitats of low disturbance and high vegetation diversity, and its large size and easy location via singing males, they point out that it makes a suitable indicator for habitat quality and species community health.

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Original source:

Chobanov D, Milchev B (2020) Orthopterans (Insecta: Orthoptera) of conservation value in the Eurasian Eagle Owl Bubo bubo food in Bulgaria. Travaux du Muséum National d’Histoire Naturelle “Grigore Antipa” 63(2): 161-167. https://doi.org/10.3897/travaux.63.e53867

Scientists took a rare chance to prove we can quantify biodiversity by ‘testing the water’

Recent study conducted at a UK fishery farm provides new evidence that DNA from water samples can accurately determine fish abundance and biomass

Organisms excrete DNA in their surroundings through metabolic waste, sloughed skin cells or gametes, and this genetic material is referred to as environmental DNA (eDNA).

As eDNA can be collected directly from water, soil or air, and analysed using molecular tools with no need to capture the organisms themselves, this genetic information can be used to report biodiversity in bulk. For instance, the presence of many fish species can be identified simultaneously by sampling and sequencing eDNA from water, while avoiding harmful capture methods, such as netting, trapping or electrofishing, currently used for fish monitoring.

While the eDNA approach has already been applied in a number of studies concerning fish diversity in different types of aquatic habitats: rivers, lakes and marine systems, its efficiency in quantifying species abundance (number of individuals per species) is yet to be determined. Even though previous studies, conducted in controlled aquatic systems, such as aquaria, experimental tanks and artificial ponds, have reported positive correlation between the DNA quantity found in the water and the species abundance, it remains unclear how the results would fare in natural environments.

However, a research team from the University of Hull together with the Environment Agency (United Kingdom), took the rare opportunity to use an invasive species eradication programme carried out in a UK fishery farm as the ultimate case study to evaluate the success rate of eDNA sampling in identifying species abundance in natural aquatic habitats. Their findings were published in the open-access, peer-reviewed journal Metabarcoding and Metagenomics.

“Investigating the quantitative power of eDNA in natural aquatic habitats is difficult, as there is no way to ascertain the real species abundance and biomass (weight) in aquatic systems, unless catching all target organisms out of water and counting/measuring them all,”
explains Cristina Di Muri, PhD student at the University of Hull.

Drained pond after fish translocation.
Photo by Dr. Watson H.V.

During the eradication, the original fish ponds were drained and all fish, except the problematic invasive species: the topmouth gudgeon, were placed in a new pond, while the original ponds were treated with a piscicide to remove the invasive fish. After the eradication, the fish were returned to their original ponds. In the meantime, all individuals were counted, identified and weighed from experts, allowing for the precise estimation of fish abundance and biomass.

“We then carried out our water sampling and ran genetic analysis to assess the diversity and abundance of fish genetic sequences, and compared the results with the manually collected data. We found strong positive correlations between the amount of fish eDNA and the actual fish species biomass and abundance, demonstrating the existence of a strong association between the amount of fish DNA sequences in water and the actual fish abundance in natural aquatic environments,”
reports Di Muri.

Environmental DNA sampling using water collection bottles
Photo by Dr. Peirson G.

The scientists successfully identified all fish species in the ponds: from the most abundant (i.e. 293 carps of 852 kg total weight) to the least abundant ones (i.e. one chub of 0.7 kg), indicating the high accuracy of the non-invasive approach.

“Furthermore, we used different methods of eDNA capture and eDNA storage, and found that results of the genetic analysis were comparable across different eDNA approaches. This consistency allows for a certain flexibility of eDNA protocols, which is fundamental to maintain results comparable across studies and, at the same time, choose the most suitable strategy, based on location surveyed or resources available,”
elaborates Di Muri.

“The opportunity of using eDNA analysis to accurately assess species diversity and abundance in natural environments will drive a step change in future species monitoring programmes, as this non-invasive, flexible tool is adaptable to all aquatic environments and it allows quantitative biodiversity surveillance without hampering the organisms’ welfare.”

***

Original publication:

Di Muri C, Lawson Handley L, Bean CW, Li J, Peirson G, Sellers GS, Walsh K, Watson HV, Winfield IJ, Hänfling B (2020) Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds. Metabarcoding and Metagenomics 4: e56959. https://doi.org/10.3897/mbmg.4.56959

Notice me! Neglected for over a century, Black sea spider crab re-described

After the revision of available type specimens from all available collections in the Russian museums and the Senckenberg Museum in Frankfurt-on-Main, as well as newly collected material in the Black Sea and the North-East Atlantic, a research team of scientists, led by Dr Vassily Spiridonov from Shirshov Institute of Oceanology of Russian Academy of Sciences, re-described Macropodia czernjawskii and provided the new data on its records and updated its ecological characteristics.

Even though recognised in the Mediterranean Sea, the Macropodia czernjawskii spider crab was ignored by scientists (even by its namesake Vladimir Czernyavsky) in the regional faunal accounts of the Black Sea for more than a century. At the same time, although other species of the genus have been listed as Black sea fauna, those listings are mostly wrong and occurred either due to historical circumstances or misidentifications.Now, scientists re-describe this, most likely, only species of the genus occurring in the Black Sea in the open-access journal Zoosystematics and Evolution.

The studied spirder crab species *Macropodia czernjawskii* in the wild, Tuaphat (near Gelendzhik), Caucasus, Black Sea.
Photo by Sergey Anosov

The spider crab genus Macropodia was discovered in 1814 and currently includes 18 species, mostly occurring in the Atlantic and the Mediterranean. The marine fauna of the Black Sea is predominantly of Mediterranean origin and Macropodia czernjawskii was firstly discovered in the Black Sea in 1880, but afterwards, its presence there was largely ignored by the scientists.

After the revision of available type specimens from all available collections in the Russian museums and the Senckenberg Museum in Frankfurt-on-Main, as well as newly collected material in the Black Sea and the North-East Atlantic, a research team of scientists, led by Dr Vassily Spiridonov from Shirshov Institute of Oceanology of Russian Academy of Sciences, re-described Macropodia czernjawskii and provided the new data on its records and updated its ecological characteristics.

“The analysis of the molecular genetic barcode (COI) of the available material of Macropodia species indicated that M. czernjawskii is a very distinct species while M. parva should be synonimised with M. rostrata, and M. longipes is a synonym of M. tenuirostris”,
states Dr Spiridonov sharing the details of the genus analysis.

All Macropodia species have epibiosis and M. czernjawskii is no exception: almost all examined crabs in 2008-2018 collections had significant epibiosis. It normally consists of algae and cyanobacteria and, particularly, a non-indigenous species of red alga Bonnemaisonia hamifera, officially reported in 2015 at the Caucasian coast of the Black Sea, was found in the epibiosis of M. czernjawskii four years earlier.

“It improves our understanding of its invasion history. Museum and monitoring collections of species with abundant epibiosis (in particular inachid crabs) can be used as an additional tool to record and monitor introduction and establishments of sessile non-indigenous species,”
suggests Dr Spiridonov.

The spider crab species *Macropodia czernjawskii* in the wild, Tuaphat (near Gelendzhik), Caucasus, Black Sea.
Photo by Sergey Anosov

***

Original source:

Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342

Bulgarian Academy of Sciences signs with Pensoft to move Silva Balcanica journal to ARPHA

The first 2020 issue of the journal by the Academy’s Forest Research Institute is already online on a brand new and user-friendly website

The scholarly publisher and technology provider Pensoft welcomes the open-access, peer-reviewed international journal in forest science concerning the Balkan Peninsula, Central and Southern Europe Silva Balcanica to its self-developed publishing platform ARPHA. Having become the latest addition to the lengthy portfolio of scholarly outlets dedicated to the fields of ecology and biology for Pensoft and ARPHA, Silva Balcanica is now offering a wide range of benefits and services to its readers, authors, reviewers and editors alike.

Having already acquired its own glossy and user-friendly website provided by ARPHA, Silva Balcanica also takes advantage of the platform’s signature fast-track, end-to-end publishing system. In addition, the published content enjoys automated export of data to aggregators, as well as web-service integrations with major global indexing and archiving databases.

*Silva Balcanica’s new website on ARPHA Platform. Visit at****https://silvabalcanica.pensoft.net***

Ever since its inception in 2001, the journal by the Forest Research Institute at the Bulgarian Academy of Sciences (FRI-BAS), has been providing open access to the latest research in all aspects of forest ecosystems and landscapes of the Balkan Peninsula, and also Central and Southern Europe.

Silva Balcanica invites scientific analysis of practical results, as well as investigations, in the forest sciences, including forest ecology; forest soil science; forest genetics, tree breeding and plantation forestry; biometry and sylviculture; forest economy and management; forest entomology and pathology; ecology and management of game fauna, urban forestry and green infrastructure. Constructive critique addressing scientific publications or events in the field of forestry and forest science are also accepted.

In the first 2020 issue of Silva Balcanica, we can find a total of eight research papers, dealing with a range of various topics, including studies on local plant diversity, genetics, application of experimental designs for forestry research, ecosystem services, population dynamics, invasive pathogens and previously unknown populations of forest-dwelling insects. It brings together single-authored research contributions as well as international collaborative projects, with input from authors from Bulgaria, Greece, Northern Macedonia and Italy.

CEO and founder of both Pensoft and ARPHA Platform Prof. Lyubomir Penev comments:

“Silva Balcanica is an important scholarly outlet and also a remarkable example of international cooperation, inspired and maintained by curiosity, care and responsibility towards the unique, but fragile ecosystems this part of Europe hosts. This is why we take pride in having this particular journal joining our portfolio,”

Silva Balcanica’s Editorial Board says:

“The Scientific Council of the Forest Research Institute at the Bulgarian Academy of Sciences decided to begin publishing Silva Balcanica as an international series in 2001 and since 2014, Silva Balcanica has been published as an international journal.

We are honored to have as members of our Editorial Advisory Board eminent European professors and researchers in forestry and related sciences that join our efforts in pursuit of high quality scientific publishing.

We are confident that Silva Balcanica will unite the research of scientists and specialists in forestry from Southeastern, Central and Eastern Europe and beyond, and will help them in the processes of their European integration.”

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Visit the new website of Silva Balcanica at https://silvabalcanica.pensoft.net.