A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Molecular methods such as DNA/eDNA metabarcoding have emerged useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with for genetic marine hard-bottom benthic communities. Here, we present data our first campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved 2018-2020 across 15 observatories along coasts Europe adjacent regions. describe open-access set (image, metadata) explore show its potential ecological research. Our analysis shows that recovered more than 60 eukaryotic phyla capturing diversity up ~5500 amplicon sequence variants ~1800 operational taxonomic units, ~250 ~50 species per observatory cytochrome c oxidase subunit I (COI) 18S rRNA marker genes, respectively. Further, detected threatened, vulnerable non-indigenous often targeted biological monitoring. while deployment duration does not drive estimates, effort sequencing depth do. recommend should be at least 3-6 months during main growth season use resources efficiently possible post-sequencing curation is applied enable statistical comparison entities. suggest used programs long-term research encourage adoption ARMS-MBON protocols.

Language: Английский

---

Benthic Feeding and Diet Partitioning in Red Sea Mesopelagic Fish Resolved Through DNA Metabarcoding and ROV Footage

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

Mesopelagic fish are among the most abundant vertebrates on Earth and play a crucial role in carbon sequestration through their daily vertical migration. However, dietary ecology remains poorly understood, especially Red Sea, limiting our grasp of trophic interactions ecological roles. This study investigates composition two common mesopelagic species lanternfish (Benthosema taxa) endemic lightfish (Vinciguerria mabahiss), using DNA metabarcoding mitochondrial COI marker, supplemented by remotely operated vehicle (ROV) video observations. Our findings show that V. mabahiss exhibits higher prey diversity compared to Benthosema taxa, suggesting more generalist feeding strategy. Both primarily consume copepods, likely due high abundance copepods upper 200 m Sea. Despite this commonality, distinct niches were observed: taxa consumes significant amounts molluscs, followed annelids echinoderms, while occasionally gelatinous such as hydrozoans scyphozoans. Notably, ROV footage demonstrates these engage benthic continental slope, behavior rarely documented. By consuming redistributing organic material diel migrations, contribute biological pump, with important implications for processes ocean. Future studies integrating stable isotope analysis could provide deeper insights into partitioning contributions Sea ecosystem beyond.

Language: Английский

---

Illuminating ecology and distribution of the rare fungus Phellinidium pouzarii in the Bavarian Forest National Park

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 12, 2025

Abstract Due to their cryptic lifestyle, hidden diversity and a lack of ecological knowledge, conservation wood-inhabiting fungi continues be niche interest. Molecular methods are able provide deeper insights into the ecology rare fungal species. We investigated occurrence fungus Phellinidium pouzarii across Bavarian Forest National Park in Germany using fruit body survey, amplicon sequencing qPCR. Additionally, we sequenced genome P. characterized chemical substances responsible for its distinctive scent. Our approach gave matching results between qPCRs, however, found no evidence that is more abundant than can assume based on inventories, underlining species’ critically endangered status. Genomics revealed ’s repertoire ligninolytic enzymes, pointing towards white rot lifestyle. Two main components distinct odour identified (2-phenylethanol, methyl p -anisate) known act as insect attractants and/or possess antimicrobial properties.

Language: Английский

---

Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19158 - e19158

Published: April 14, 2025

DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, their implementation as standardized monitoring is approaching. Evaluating the efficacy reliability these technological crucial for assessments. In this study, we compared three techniques assessing diversity bulk samples from Belgian North Sea. Specifically, amplicon using Illumina MiSeq portable real-time Oxford Nanopore versus shotgun NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served target region analysis. Our results indicate that had similar performances in terms alpha beta diversity, revealing highly location-specific community compositions. metagenomics method also resulted but slightly different compositions approach. Despite differences, were maintained across all platforms. Notably, read counts metagenomic analysis showed weakest correlation size corrected morphological abundance there mismatches between identification DNA based findings which likely caused by a combination factors such primer efficiency an incomplete reference database. underscore critical importance database completeness prior implementing method, especially metagenomics. Nevertheless, our emphasize proves be viable alternative conventional platform monitoring.

Language: Английский

---

A comprehensive assessment of non-indigenous species requires the combination of multi-marker eDNA metabarcoding with classical taxonomic identification

Environment International, Journal Year: 2025, Volume and Issue: 199, P. 109489 - 109489

Published: April 19, 2025

In marine environment, non-indigenous species (NIS) can alter natural habitats and cause biodiversity loss with important consequences for ecosystems socio-economic activities. With more than 1000 NIS introduced over the last century, Mediterranean Sea is one of most threatened regions worldwide, requiring an early identification newly entered alien a proper environmental management. Here, we carried out environmental-DNA (eDNA) metabarcoding analyses, using multiple molecular markers (i.e., 18S rRNA, COI, rbcL) different genetic databases NCBI, PR2, SILVA, MIDORI2, MGZDB, BOLD), on seawater sediment samples collected seasonal basis in three ports located North Adriatic, Ionian Tyrrhenian to identify species, particularly NIS. The use multi-marker eDNA allowed higher number compared morphological analyses (1484 vs. 752 species), minor portion shared by both approaches. Overall, only 4 were consistently identified approaches, whereas 27 17 exclusively detected classical taxonomic respectively. also identifying signatures 5 never reported Italian waters. We conclude that represent highly sensitive tool NIS, but comprehensive census requires combination

Language: Английский

---