Tag: marine

A Simple Filter Swap Could Advance Marine eDNA Biomonitoring

A simple adjustment to water filtration methods can dramatically improve the detection of marine animal DNA when using advanced, PCR-free sequencing.

Over the past two decades, environmental DNA (eDNA) analysis has become a crucial tool for monitoring aquatic ecosystems. The most common method, metabarcoding, relies on PCR amplification of a smaller genetic region to identify specific taxa. However, PCR can lead to “significant taxonomic bias” because it often amplifies the DNA of different organisms unequally, making quantitative estimates difficult.

To avoid this, scientists have increasingly explored “shotgun sequencing“- an approach that sequences the DNA in a sample much more broadly – across the entire tree of life and across the genome. Unfortunately, in marine environments, shotgun sequencing is typically overwhelmed by microbial DNA, burying the genetic traces of less abundant macro-organisms such as animals.

Bigger Pores, Better Animal DNA Capture?

In a new study published in Metabarcoding and Metagenomics, researchers investigated if they could capture a higher proportion of eukaryotic (animal and plant) DNA simply by using filters with larger pore sizes.

Filter pore sizes are expected to influence results, since eDNA may be present in many different states, including but not limited to complete organisms, sloughed tissue, feces, free DNA, or gametes.

commented Dr. Adrián Gómez-Repollés, the lead author of the study.

To test this, the team collected 15 seawater samples from Skovshoved Harbour in Denmark and filtered them using pore sizes ranging from 0.2 µm to 8.0 µm. The results showed a stark contrast in the type of DNA captured based on the filter size.

Filters with smaller pore sizes (0.2 µm and 1.2 µm) retained a significantly greater proportion of bacterial reads than eukaryotic reads (63% vs. 28%); conversely, filters with larger pore sizes (5.0 µm and 8.0 µm) retained a significantly greater proportion of eukaryotic reads than bacterial reads (49% vs. 31%).

By switching to 5.0 µm or 8.0 µm filters, the researchers successfully reduced the dominance of bacteria. Of the 19 metazoan (animal) phyla detected using shotgun sequencing, all but one were found to be more abundant when using the larger pore sizes.

Looking to the Future of Biomonitoring

Taxonomic comparison at the kingdom and phylum levels of eukaryotes detected with shotgun sequencing and metabarcoding. A. Number and relative abundance (percentages) of taxonomically classified reads after rarefaction per sample and kingdom for shotgun sequencing; B. Number and relative abundance of taxonomically classified reads after rarefaction per sample and kingdom for metabarcoding. For both heatmaps, sample replicates are ordered along the y-axis by increasing pore size, starting with the enclosed filter type (EN) and continuing with the open pore filter type (OP). Pore sizes are in µm; C. Cladogram of the full set of eukaryotic phyla identified by shotgun sequencing and metabarcoding. Branch colors represent kingdoms (blue, Metazoa; red, Fungi; green, Viridiplantae; pink, other eukaryotes). Three surrounding rings indicate phyla shared between shotgun sequencing and metabarcoding (gray), phyla uniquely detected with metabarcoding (yellow), and phyla uniquely detected with shotgun sequencing (blue). Information in the rings is summarized in a Venn diagram in the upper left corner. Taxa marked with an asterisk are no longer categorized as a phylum. Credit to Gómez-Repollés et al., 2026

When compared alongside traditional 18S rDNA metabarcoding, the shotgun sequencing method successfully shared 39 of the 54 detected eukaryotic phyla, indicating a similar performance in detecting the presence of high-level taxonomic groups.

To test the potential of shotgun sequencing in applied biomonitoring even further, the researchers examined the results at genus-level for a number of well known marine animals such as fish, mussels, crustaceans and bristle worms. Here, they found both DNA matches to native Danish species but also to exotic taxa that were highly unlikely and probably due to the low level of resolution in shotgun sequencing, where genetic regions of low variation and coverage are sequenced.

Water sample collection. Photo by David Stanciu.

But, when they looked further into the results they observed that the local taxa consistently comprised a higher number of reads. The number of reads could thus be a simple way to initially separate authentic taxa from erroneous matches in eDNA studies based on shotgun sequencing, although the approach needs further testing. 

However, the authors note current limitations with the technology, primarily driven by incomplete public DNA reference databases. In the study, only 0.78% of the total shotgun reads could be definitively assigned to a superkingdom level. Another drawback was the lack of field controls to rule out cross-contamination or input from airborne DNA, coupled with a limited spatiotemporal design involving only a single sampling location. 

Despite these hurdles, shotgun sequencing and filters with larger pore sizes could potentially be a significant step forward for eDNA in marine biology. As global genomic databases continue to expand, “the taxonomic coverage and resolution of shotgun sequencing should improve, likely enhancing the potential of shotgun sequencing for future eDNA research“, says Philip Francis Thomsen, professor and senior author on the study. 

Original study:

Gómez-Repollés A, Sigsgaard EE, Jensen MR, Thomsen PF (2026) Filter pore size influences taxonomic composition of retained eDNA from seawater samples—evidence from shotgun sequencing. Metabarcoding and Metagenomics 10: e164232. https://doi.org/10.3897/mbmg.10.164232

Old specimens establish a new bamboo worm genus and species

Bamboo worms (family Maldanidae) comprise an easily recognizable family of bristle worms (class Polychaeta). Their common name they receive because of their elongated segments, ending with an appendage, which gives them the joint appearance of slender bamboo-shoots. These often fragile marine inhabitants can be found in mud-walled tubes in shelf sediments.

However, bamboo worms are tough to identify from each other. The problem is that to safely recognize them, a researcher needs both anterior and posterior ends from the same specimen. Nevertheless, now PhD student Wang Yueyun and Dr Li Xinzheng from the Marine Biological Museum, Institute of Oceanology, Chinese Academy of Sciences have discovered two new species and a new genus (Paramaldane). The new bamboo worms are described in the open access journal ZooKeys.

Several specimens of the new genus were found during re-examination of specimens collected from South China Sea between 1959 to 1962. The new genus is characterized by the collar-like glandular band on the sixth chaetiger. This is the first discovery of a collar-like structure in the subfamily of Maldaninae. Moreover, there is only one species in this genus till now.

Another discovery, published in the present study, is the second new species, called Maldane adunca, which belongs to another genus within the family. It is similar to the cosmopolitan species Maldane sarsi, yet the differences are clear. The shape of its nuchal grooves, a kind of sense organ, is much more curved, thus resembling hooks. Therefore, it is called adunca, meaning ‘hooked’ in Latin.

Both new species are only found in mud sediment of offshore waters of Hainan Island.

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Original source:

Wang Y, Li X (2016) A new Maldane species and a new Maldaninae genus and species (Maldanidae, Annelida) from coastal waters of China. ZooKeys 603: 1-16. doi: 10.3897/zookeys.603.9125

Zorro, the new Latin American fish species, takes off the mask to show its true identity

Unidentified since its discovery in 2007, a large fish species from Amazonia has failed to give out enough information about itself, leaving only insufficient hints about its genus. Nevertheless, three scientists have now recovered the missing pieces to puzzle out its mysterious identity. In their study, published in the open-access journal ZooKeys, they describe the fish as a new species and name it after the fictional secretive Latin American character Zorro.

The new fish, called Myloplus zorroi, is commonly known among the Brazilians as ‘pacu’ and is a relative to the piranha. The research team, led by Marcelo C. Andrade, Universidade Federal do Para, Brazil, recognised in a fish, collected by sport fishermen from Rio Madeira basin, Brazil, a previously found, yet undescribed species. Following their analysis, it turned out that its discoverers had assumed an incorrect genus for it.

Among the distinctive features of the new fish, which helped its rightful placement, are its characteristic teeth, specialised to crush seeds.

The new pacu species is quite large, growing up to 47,5 cm. It dwells in moderately to rapidly flowing clear rivers, running over rocky or sandy bottoms, and ranging from about 2 to 8 metres in depth. Its basis colour is reddish silver with darker markings running along the upper side of the body. The head is dark and the belly – pale yellow.

Curiously enough, although the name of the new fish is chosen as a tribute to Mauricio Camargo-Zorro, a researcher at the Instituto Federal de Educacao, Ciencia e Tecnologia, in recognition of his invaluable contribution to the fish fauna inventory from the Marmelos Conservation Area, zorroi is also a playful reference to the Latin American fictional character Don Diego de la Vega and his secret identity hidden behind the nickname of Zorro.

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Original source:

Andrade MC, Jegu M, Giarrizzo T (2016) A new large species of Myloplus (Characiformes, Serrasalmidae) from the Rio Madeira basin, Brazil. ZooKeys 571: 153-167. doi: http://doi.org/10.3897/zookeys.571.5983.

Long-snouted Amazonian catfishes including three new species to form a new genus

Being close relatives within the same genus, eight catfishes showed enough external differences, such as characteristic elongated mouths, hinting to their separate origin. Following a thorough morphological as well as molecular analysis, a team of researchers suggested that five previously known species along with three new ones, which they have found during their survey, need a new genus to accommodate for their specificity. The study, conducted by a Brazilian research team from Universidade Estadual Paulista and led by Dr. Fabio F. Roxo, is available in the open-access journal ZooKeys.

Among other physical peculiarities, the longer snout-like mouths of the herein discussed catfishes is a characteristic that sets them apart. This is also why the authors have chosen the name of Curculionichthys for the proposed genus, formed by the Latin word for “elongated snout” and the suffix “ichthys” meaning “fishes” in Greek.

Furthermore, one of the new species the researchers describe in the present paper surprises with its several dark-brown spots spread across its body. This colouration is unlike any other in its relatives that have various pigment patterns, yet never dark brown spots.

However, other overlapping morphological features as well as the closeness in the species’ researched habitats suggest they have a common ancestor, once lived in the Amazonian drainages.

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Original source:

Roxo FF, Silva GSC, Ochoa LA, Oliveira C (2015) Description of a new genus and three new species of Otothyrinae (Siluriformes, Loricariidae). ZooKeys 534: 103-134. doi: 10.3897/zookeys.534.6169

New Indonesian crayfish species escapes the decor market to become a freedom fighter

With its orange to greenishly orange motley tip, the new crayfish species has been long-confused with its relatives by the tradesmen who have been collecting them for ornamental purposes. Being exported to countries in Europe, East Asia and America C. snowden specimens inevitably landed in the hands of the scientists from Lukhaup’s team who eventually recognised and proved them as a new crayfish species. Their research is available in the open-access journal ZooKeys.

Although the new crayfish species has probably been sold along with its motley relatives under another name for decades, the scientists figured that it is in fact easily distinguishable by its shape of body and colouration. In order to prove it as a separate species, the team used sequence divergence as well.

Having travelled across the world from its so far only known locality, West Papua, New Guinea, the new freshwater crustacean was given the name of the controversial former CIA employee and government contractor Edward Snowden. Its ‘godfather’ is famous for leaking secretive information from the U.S. National Security Agency, which later led him to a continuous search for political asylum. The authors speak of him as an “American freedom fighter” with “achievements in defence of justice, and freedom.”

In their conclusion the authors note that there could be potential threats to the new species. The freshwater crayfish is being collected in large numbers for both the ornamental fish global market and for food for the locals. Asked about the crustacean’s populations, the collectors spoke about a decline in the last few years.

“Clearly, the continued collection of these crayfish for the trade is not a sustainable practice, and if the popularity of the species continues, a conservation management plan will have to be developed, potentially including a captive breeding program,” the researchers comment.

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Original source:

Lukhaup C, Panteleit J, Schrimpf A (2015) Cherax snowden, a new species of crayfish (Crustacea, Decapoda, Parastacidae) from the Kepala Burung (Vogelkop) Peninsula in Irian Jaya (West Papua), Indonesia. ZooKeys 518: 1-14. doi: 10.3897/zookeys.518.6127