Tag: ecosystems

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

Guest Blog Post: New Area of Importance for Bat Conservation in Honduras

The recognition of the “Ceguaca, la Mujer de los Juncos” locality comes as a result of research work – published last year in Subterranean Biology – which produced the first checklist of bats for Santa Bárbara

Guest blog post by Eduardo Javier Ordoñez-Trejo and Manfredo Alejandro Turcios-Casco

Bat populations are threatened due to fragmentation and loss of their habitats. Meanwhile, dry forests are some of the least studied and most threatened ecosystems in Honduras, and similarly, so have been the caves.

We had to walk at least two hours to reach either of the caves in El Peñon or Quita Sueño, so we would take our full equipment: for camping, cooking and studying bats.
Photo by Hefer Ávila

Caves are important reservoirs of species, as they offer perks no other habitat can provide at once: a refuge from predators, inconstant weather, and a critical venue for social interactions, reproduction, hibernation, roosting and nutrients. In order to protect bat populations, the Latin American and Caribbean Web for Bat Conservation (RELCOM) supports the establishment of Areas of Importance for the Conservation of Bats, abbreviated as AICOMS (Spanish for Areas with Importance for the Conservation of Bats) .

It was at least a two-hour walk between the caves of Monte Grueso and the caves of El Peñon. The final stint, though, included a swim across Rio Ulúa, one of most extensive rivers in Honduras.
Photo by Hefer Ávila

Together with biologists of the National Autonomous University of Honduras (UNAH) and local community members, we provided the first ever checklist of bat species in the Dry Forest of Ceguaca, Santa Barbara (Honduras), and described the importance of two caves in the area for bat conservation based on species richness. We published this study last June in Subterranean Biology.

*The* *study* *is openly accessible in Subterranean Biology*

We found that caves in Ceguaca are inhabited by at least 23 bat species of four families, which represents approximately a fifth of all species known from Honduras. Their inhabitants include several threatened species like the hairy-legged vampire bat (Diphylla ecaudata), one of the three existing vampire bats, and rare species with few official records in the area, such as Schmidts’s big-eared bat (Micronycteris schmidtorum). These caves may also represent a critical site for roosting and nursing. During our study, we managed to record pregnant and lactating females of several species, as well as reproductive males.

*The certificate issued by RELCOM recognising the caves in Ceguaca as an Area of Importance for the Conservation of Bats, dated 6th March 2020*

“It feels wonderful to see that our work has had great results and that with our efforts, we established an area where bats will be protected and studied. This certification also includes the name of Roberto Castellano, an elder member of the community of Ceguaca, who helped us during the fieldwork as our guide. He was a great conservationist of this area and protector of the caves. Unfortunately, he passed away during the study, however, due to his enormous contribution, we dedicated our article to him and included him as part of this AICOM success.”
José Alejandro Soler Orellana, co-author of the study.

Using what we learned in Ceguaca’s caves, we approached the Program for Bat Conservation of Honduras (PCMH) and showed them the evidence the locality was indeed a precious place with a spectacular bat diversity. Consequently, thanks to our collaboration with the PCMH, the site was effectively declared as an Area of Importance for the Conservation of Bats by RELCOM on 6th March 2020.

This is an enormous step for bat conservation in the country. Bat conservation efforts should focus on studying and protecting these and other important habitats. We also need to make sure that local people appreciate the important role the bats play in the ecosystem.

A close up of a spider

Description automatically generated — We captured this adult Pallas’s long-tongued bat (*Glossophaga soricina*) female in a cave in Monte Grueso. She must have been returning to the cave after spending the day pollinating local plants. During these surveys, we found trees with opened flowers of Mexican calabash (*Crescentia alata*).
Photo by Hefer Ávila

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Research article:

Turcios-Casco MA, Mazier DIO, Orellana JAS, Ávila-Palma HD, Trejo EJO (2019) Two caves in western Honduras are important for bat conservation: first checklist of bats in Santa Bárbara. Subterranean Biology 30: 41–55. https://doi.org/10.3897/subtbiol.30.35420

19th-century bee cells in a Panamanian cathedral shed light on human impact on ecosystems

About 120 clusters of 19th-century orchid bee nests were found during restoration work on the altarpiece of Basilica Cathedral in Casco Viejo (Panamá). Having conducted the first pollen analysis for these extremely secretive insects, the researchers identified the presence of 48 plant species, representing 23 families.

Casco Viejo, Panamá in 1875, as seen from the summit of Cerro Ancón.
A white tower of the Cathedral where bees were nesting is visible in the distant background in the centre of the peninsula.
Photo by Eadweard Muybridge, courtesy of the Smithsonian American Art Museum; gift of Mitchell and Nancy Steir.

Despite being “neotropical-forest-loving creatures,” some orchid bees are known to tolerate habitats disturbed by human activity. However, little did the research team of Paola Galgani-Barraza (Smithsonian Tropical Research Institute) expect to find as many as 120 clusters of nearly two-centuries-old orchid bee nests built on the altarpiece of the Basilica Cathedral in Casco Viejo (Panamá). Their findings are published in the open-access Journal of Hymenoptera Research.

Locations of nest cell aggregations of Eufriesea surinamensis within the Cathedral in Casco Viejo, Panamá
Photo by Paola Galgani-Barraza

This happened after restoration work, completed in 2018 in preparation for the consecration of a new altar by Pope Francis, revealed the nests. Interestingly, many cells were covered with gold leaf and other golden material applied during an earlier restoration following an 1870 fire, thus aiding the reliable determination of the age of the clusters. The cells were dated to the years prior to 1871-1876.

The bee species, that had once constructed the nests, was identified as the extremely secretive Eufriesea surinamensis. Females are known to build their nests distant from each other, making them very difficult to locate in the field. As a result, there is not much known about them: neither about the floral resources they collect for food, nor about the materials they use to build their nests, nor about the plants they pollinate.

However, by analysing the preserved pollen for the first time for this species, the researchers successfully detected the presence of 48 plant species, representing 43 genera and 23 families. Hence, they concluded that late-nineteenth century Panama City was surrounded by a patchwork of tropical forests, sufficient to sustain nesting populations of what today is a forest-dwelling species of bee.

Not only did the scientists unveil important knowledge about the biology of orchid bees and the local floral diversity in the 19th century, but they also began to uncover key information about the functions of natural ecosystems and their component species, where bees play a crucial role as primary pollinators. Thus, the researchers hope to reveal how these environments are being modified by collective human behaviour, which is especially crucial with the rapidly changing environment that we witness today.

The orchid bee Eufriesea surinamensis
Photo by Paola Galgani-Barraza

Original source:

Galgani-Barraza P, Moreno JE, Lobo S, Tribaldos W, Roubik DW, Wcislo WT (2019) Flower use by late nineteenth-century orchid bees (Eufriesea surinamensis, Hymenoptera, Apidae) nesting in the Catedral Basílica Santa María la Antigua de Panamá. Journal of Hymenoptera Research 74: 65-81. https://doi.org/10.3897/jhr.74.39191

Revolutionary method could bring us much closer to the description of hyperdiverse faunas

A novel approach relying on a short sequence of mitochondrial DNA in conjunction with a lateral image of the holotype specimen was proposed to greatly accelerate species identification and description, especially when it comes to hyperdiverse taxa, such as parasitic wasps.

At today’s rate, it could take another two millennia for science to document all currently existing species of multicellular life

Two hundred and sixty-one years ago, Linnaeus formalized binomial nomenclature and the modern system of naming organisms. Since the time of his first publication, taxonomists have managed to describe 1.8 million of the estimated 8 to 25 million extant species of multicellular life, somewhere between 7% and 22%. At this rate, the task of treating all species would be accomplished sometime before the year 4,000. In an age of alarming environmental crises, where taking measures for the preservation of our planet’s ecosystems through efficient knowledge is becoming increasingly urgent, humanity cannot afford such dawdling.

“Clearly something needs to change to accelerate this rate, and in this publication we propose a novel approach that employs only a short sequence of mitochondrial DNA in conjunction with a lateral image of the holotype specimen,”
explain the researchers behind a new study, published in the open-access journal Deutsche Entomologische Zeitschrift (DEZ).

Description rate of parasitic wasps species (superfamily
Ichneumonoidea).
Data from Taxapad (Yu et al. 2016).

In standardized practices, it is required that experts conduct plenty of time- and labor-consuming analyses, in order to provide thorough descriptions of both the morphology and genetics of individual species, as well as a long list of characteristic features found to differentiate each from any previously known ones. However, the scientists argue, at this stage, it is impossible to pinpoint distinct morphological characters setting apart all currently known species from the numerous ones not yet encountered. To make matters worse, finding human and financial resources for performing this kind of detailed research is increasingly problematic.

This holds especially true when it comes to hyperdiverse groups, such as ichneumonoid parasitoid wasps: a group of tiny insects believed to comprise up to 1,000,000 species, of which only 44,000 were recognised as valid, according to 2016 data. In their role of parasitoids, these wasps have a key impact on ecosystem stability and diversity. Additionally, many species parasitise the larvae of commercially important pests, so understanding their diversity could help resolve essential issues in agriculture.

Meanwhile, providing a specific species-unique snippet of DNA alongside an image of the specimen used for the description of the species (i.e. holotype) could significantly accelerate the process. By providing a name for a species through a formal description, researchers would allow for their successors to easily build on their discoveries and eventually reach crucial scientific conclusions.

“If this style were to be adopted by a large portion of the taxonomic community, the mission of documenting Earth’s multicellular life could be accomplished in a few generations, provided these organisms are still here,”
say the authors of the study.

To exemplify their revolutionary approach, the scientists use their paper to also describe a total of 18 new species of wasps in two genera (Zelomorpha and Hemichoma) known from Área de Conservación Guanacaste, Costa Rica. Currently, the team works on the treatment of related species, which still comprise only a portion of the hundreds of thousands that remain unnamed.

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Original source:

Meierotto S, Sharkey MJ, Janzen DH, Hallwachs W, Hebert PDN, Chapman EG, Smith MA (2019) A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment. Deutsche Entomologische Zeitschrift 66(2): 119-145. https://doi.org/10.3897/dez.66.34683

Scientists dive into museum collections to reveal the invasion route of a small crustacean

Biological invasions are widely recognised as one of the most significant components of global change. Far-reaching and fast-spreading, they often have harmful effects on biodiversity.

Therefore, acquiring knowledge of potentially invasive non-native species is crucial in current research. In particular, it is important that we enhance our understanding of the impact of such invasions.

To do so, Prof Sabrina Lo Brutto and Dr Davide Iaciofano, both working at the Taxonomy Laboratory of the University of Palermo, Italy, performed research on an invasive alien crustacean (Ptilohyale littoralis) known to have colonised the Atlantic European Coast. Their findings are published in the open access journal ZooKeys.

The studied species belongs to a group of small-sized crustaceans known as amphipods. These creatures range from 1 to 340 mm in length and feed on available organic matter, such as dead animals and plants. Being widely distributed across aquatic environments, amphipods have already been proven as excellent indicators of ecosystem health.

While notable for their adaptability and ecological plasticity, which secure their abundance in various habitats, these features also make amphipods especially dangerous when it comes to playing the role of invaders.

Having analysed specimens stored at the Museum of Natural History of Verona and the Natural History Museum in Paris, the scientists concluded that the species has colonised European waters 24 years prior to the currently available records.

The problem was that, back in 1985, when the amphipod was first collected from European coasts, it was misidentified as a species new to science instead of an invader native to the North American Atlantic coast.

A closer look into misidentified specimens stored in museum collections revealed that the species has been successfully spreading along the European coastlines.

Male of the invasive amphipod species (*Ptilohyale littoralis*), sampled in October 2015, from Bay of Arcachon, France.

Moreover, it was predicted that the amphipod could soon reach the Mediterranean due to the high connectivity between the sea and the eastern Atlantic Ocean through the Straits of Gibraltar – a route already used by invasive marine fauna in the past.

In the event that the invader reaches the Mediterranean, it is highly likely for the crustacean to meet and compete with a closely related “sister species” endemic to the region. To make matters worse, the two amphipods are difficult to distinguish due to their appearance and behaviour both being extremely similar.

However, in their paper, the scientists have also provided additional information on how to distinguish the two amphipods – knowledge which could be essential for the management of the invader and its further spread.

The authors believe that their study demonstrates the importance of taxonomy – the study of organism classification – and the role of natural history collections and museums.

“Studying and monitoring biodiversity can acquire great importance in European aquatic ecosystems and coastal Mediterranean areas, where biodiversity is changing due to climate change and invasions of alien species,” Prof Lo Brutto says. “In this context, specific animal groups play a crucial role in detecting such changes and they, therefore, deserve more attention as fundamental tools in biodiversity monitoring.”

“Regrettably, the steadily diminishing pool of experts capable of accurately identifying species poses a serious threat in this field.”

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Original source:

Lo Brutto S, Iaciofano D (2018) A taxonomic revision helps to clarify differences between the Atlantic invasive Ptilohyale littoralis and the Mediterranean endemic Parhyale plumicornis(Crustacea: Amphipoda). ZooKeys, 754: 47-62. https://doi.org/10.3897/zookeys.754.22884