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New Biomonitoring Methodologies for Key Coastal and Estuary Species and...
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New Biomonitoring Methodologies for Key Coastal and Estuary Species and Habitats

A special issue of Journal of Marine Science and Engineering (ISSN 2077-1312). This special issue belongs to the section "Marine Ecology".

Deadline for manuscript submissions: closed (1 October 2024) | Viewed by 2364

Special Issue Editors

Dr. Sofia Duarte

E-Mail Website
Guest Editor
Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
Interests: biomonitoring; aquatic ecosystems; anthropogenic pressures; benthic communities; invasive species; DNA metabarcoding-based monitoring
Dr. María del Pilar Cabezas

E-Mail Website
Guest Editor
Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
Interests: cryptic species; DNA metabarcoding; marine biodiversity; biomonitoring; marine invertebrates; invasive species; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Luis Machado

E-Mail Website
Guest Editor
Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
Interests: biogeography; phylogeography; phylogeny; biomonitoring; DNA metabarcoding; environmental DNA

Special Issue Information

Dear Colleagues,

Coastal and estuarine habitats rank among the world’s most vital ecosystems, fostering unparalleled biodiversity and serving as critical nurseries for juvenile marine life. Moreover, they play pivotal roles in safeguarding coastal communities against erosion and flooding while contributing to climate change mitigation through carbon sequestration. However, in the face of ongoing global change, it is imperative to bolster monitoring efforts in these habitats using cutting-edge methodologies. This Special Issue seeks to address this pressing need by showcasing innovative biomonitoring tools that offer superior accuracy and responsiveness in the biosurveillance of key coastal and estuary species and habitats compared to traditional methods. By leveraging advanced technologies such as high-throughput sequencing, remote sensing, acoustic and photographic assessments, and machine learning algorithms, among others, these approaches deliver more holistic assessments of biodiversity. Furthermore, they enable faster responses to emerging environmental challenges, meeting immediate regulatory and management needs effectively. This collection serves as an invaluable resource, providing a comprehensive overview of the latest advancements in biomonitoring and offering practical guidance for evaluating the health of coastal and estuarine ecosystems. We invite contributions that showcase innovative methodologies, present novel findings, and contribute to the advancement of biomonitoring practices in coastal and estuarine environments.

Dr. Sofia Duarte
Dr. María del Pilar Cabezas
Dr. Luis Machado
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Marine Science and Engineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • coastal and estuarine habitats
  • ecosystem assessment health
  • global change
  • key species
  • DNA-based tools
  • remote sensing
  • machine learning algorithms
  • acoustic assessments
  • photographic assessments
  • biosurveillance

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Published Papers (2 papers)

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Research

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12 pages, 2509 KiB  
Article
Unleashing the Potential of the 360° Baited Remote Underwater Video System (BRUVS): An Innovative Design for Complex Habitats
by Marisa A. Gomes, Catarina M. Alves, Fábio Faria, Regina Neto, Edgar Fernandes, Jesus S. Troncoso and Pedro T. Gomes
J. Mar. Sci. Eng. 2024, 12(8), 1346; https://doi.org/10.3390/jmse12081346 - 8 Aug 2024
Viewed by 1246
Abstract
Coastal ecosystems are vital for numerous demersal and benthopelagic species, offering critical habitats throughout their life cycles. Effective monitoring of these species in complex coastal environments is essential, yet traditional survey methodologies are often impractical due to environmental constraints like strong currents and [...] Read more.
Coastal ecosystems are vital for numerous demersal and benthopelagic species, offering critical habitats throughout their life cycles. Effective monitoring of these species in complex coastal environments is essential, yet traditional survey methodologies are often impractical due to environmental constraints like strong currents and high wave regimes. This study introduces a new cost-effective Baited Remote Underwater Video System (BRUVS) design featuring a vertical structure and 360° cameras developed to overcome limitations of traditional BRUVS, such as system anchoring, overturning, and restricted frame view. The new design was compared against a previous one used on the northwest Iberian coast. Key performance metrics included species detection, habitat identification, and operational efficiency under complex hydrodynamic conditions. Findings reveal that the two designs can effectively identify the common species typically observed in the study area. However, the new design outperformed the previous by significantly reducing equipment losses and anchoring issues. This enhancement in field operations’ simplicity, operability, portability, and resiliency underscores the new system’s potential as a cost-effective and efficient tool for demersal and benthopelagic ecological surveys in challenging coastal seascapes. This innovative BRUVS design offers advanced monitoring solutions, improving habitat assessment accuracy and responsiveness. Full article
(This article belongs to the Special Issue New Biomonitoring Methodologies for Key Coastal and Estuary Species and Habitats)
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Review

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31 pages, 6033 KiB  
Review
Advancements in DNA Metabarcoding Protocols for Monitoring Zooplankton in Marine and Brackish Environments
by Jorge Moutinho, Filipe O. Costa and Sofia Duarte
J. Mar. Sci. Eng. 2024, 12(11), 2093; https://doi.org/10.3390/jmse12112093 - 19 Nov 2024
Viewed by 573
Abstract
Over the past century, numerous studies have proposed various organisms for the biomonitoring of aquatic systems, but only recently has zooplankton emerged as a promising indicator of water quality. The traditional identification methods, however, can be inefficient in the context of monitoring efforts, [...] Read more.
Over the past century, numerous studies have proposed various organisms for the biomonitoring of aquatic systems, but only recently has zooplankton emerged as a promising indicator of water quality. The traditional identification methods, however, can be inefficient in the context of monitoring efforts, as they are often time consuming and costly. DNA metabarcoding offers a powerful alternative, providing a more efficient and reliable approach to monitor zooplankton communities. In this review, we assess the current state-of-the-art methodologies used to evaluate marine and brackish zooplankton communities through the DNA metabarcoding workflow. While several emerging approaches have been reported, no standardization has been achieved so far. The DNA extraction step has gained the most consensus, with the widespread use of commercial kits (DNeasy Blood & Tissue kit employed in ca. 25% of the studies), though there is still a significant variation in kit selection. Additionally, 18S and COI were the main molecular markers employed (ca. 61% and 54%, respectively) though the target region varied in the former. Moreover, many methodologies, particularly those used for processing zooplankton samples, lack practical validation. Some studies also fail to provide sufficient detail in their methodology descriptions hindering reproducibility. Overall, DNA metabarcoding shows great potential for the efficient monitoring of zooplankton communities, but further effort is needed to establish standardized practices and optimize the current approaches across the entire methodological pipeline. Full article
(This article belongs to the Special Issue New Biomonitoring Methodologies for Key Coastal and Estuary Species and Habitats)
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