Molecular Biodiversity Assessment in the Deep-Sea

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Marine Diversity".

Deadline for manuscript submissions: closed (31 January 2020) | Viewed by 5535

Special Issue Editors


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Guest Editor
1. Department of Life Sciences, University of Trieste, Trieste, Italy
2. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Sgonico, Italy
Interests: mollusc comparative genomics; biodiversity assessment with molecular tools; DNA metabarcoding; environmental DNA; gene expression; transcriptomics; molecular immunology; marine biotechnology
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Special Issue Information

Dear Colleagues,

The deep sea is the largest biome on Earth, yet we have little knowledge of the ecosystems that harbor such a spectacular diversity of life—from tiny microbes to large corals and fishes. Around 97% of the Ocean’s biome occurs below 200 meters in depth, and this life performs many key ecosystem functions. Deep sea habitats offer unique ecosystem services to mankind, such as mineral resources, fisheries, and the as of yet almost unexplored sources of bioactive molecules. The deep sea may also provide solutions to societal challenges, such as finding alternatives to mining on land, and options for sequestering carbon to mitigate anthropogenic climate change.

Notwithstanding its natural capital and its remoteness, this environment is already showing clear signs of anthropogenic impacts. Many vulnerable deep-sea habitats and communities are being destroyed by destructive fishing practices and are under threat from the increasing exploitation of their mineral and living resources.

The changes of deep-sea biodiversity and ecosystem functioning provide information about how these habitats respond when they are affected or threatened by the existing or emerging human activities, and by climate change.

In the last two decades, new technologies have enabled scientists to start exploring this final frontier. The rapid advancing of molecular biology techniques has allowed scientists to understand this extreme environment in an unprecedented way; high-throughput sequencing platforms are nowadays widely used to unravel deep-sea biodiversity, adaptive strategies, and ecosystem functions. As a complement to the standard monitoring programs, the adoption of molecular methods either targeting whole marine organisms or environmental DNA offer powerful tools to assess biodiversity in these remote environments, and are becoming fundamental in order to better understand the changes that may reduce ecosystem productivity with a potential loss of ecosystem services.

Dr. Sergio Stefanni
Prof. Alberto Pallavicini
Guest Editors

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Keywords

  • Deep-sea
  • Genetic diversity
  • Ecosystem services
  • Molecular ecology
  • Mining
  • Management

Published Papers (1 paper)

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Research

24 pages, 4667 KiB  
Article
DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA
by Sara Atienza, Magdalena Guardiola, Kim Præbel, Adrià Antich, Xavier Turon and Owen Simon Wangensteen
Diversity 2020, 12(4), 123; https://doi.org/10.3390/d12040123 - 26 Mar 2020
Cited by 24 | Viewed by 5058
Abstract
Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its [...] Read more.
Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900–1750 m) at two seasons, and used a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a metabarcoding marker. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing MOTU richness and diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, which was significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs and in the most diverse taxa. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, the broad spatio-temporal patterns elucidated from both datasets coincided, with both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high-resolution method to detect ecological shifts. We also highlight that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques. Full article
(This article belongs to the Special Issue Molecular Biodiversity Assessment in the Deep-Sea)
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