Article
Marine & Freshwater Biology
Irfana Diah Faryuni, Antoine Saint-Amand, Thomas Dobbelaere, Widyastuti Umar, Jamaluddin Jompa, Abigail Mary Moore, Emmanuel Hanert
Summary: Wakatobi National Park is one of the most biodiverse marine habitats on Earth, but the coral ecosystems within the park are threatened by various anthropogenic stressors. This study evaluated coral connectivity and the contribution of marine protected zones (MPZs) to coral resilience within the park. The results showed limited overlap between MPZs and the reefs identified as best candidates for protection and restoration, suggesting the need for prioritization in coral reef conservation and restoration planning in the park.
Article
Geography
Melody Lynch, Sarah Turner
Summary: This paper examines intersectional resistance to conservation policies in Indonesia's Wakatobi National Park, highlighting how ethnic minority fishers resist conservation measures along lines of gender, ethnicity, and class. The study reveals that fisherwomen, facing cultural gender norms, resist by pursuing livelihood activities against their husband's wishes and utilizing new infrastructure to increase mobility. Park authorities employ 'creative enforcement' techniques, such as accepting bribes and intimidating locals, to regain control, exposing further class, ethnic, and gendered frictions.
GENDER PLACE AND CULTURE
(2022)
Article
Environmental Sciences
Bert W. Hoeksema, Luna M. van der Loos, Godfried W. N. M. van Moorsel
Summary: In this study of the coral reefs around St. Eustatius, it was found that there is no distinct relation between coral diversity and economic value. However, future marine park designs should consider coral diversity.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Environmental Studies
Laurence H. De Clippele, Laura Alonso Diaz, Dominic A. Andradi-Brown, Muhammad Erdi Lazuardi, Mohamad Iqbal, Imam Musthofa Zainudin, Derta Prabuning, Ruben van Hooidonk, Amehr Hakim, Firdaus Agung, Agus Dermawan, Sebastian J. Hennige
Summary: Coral reefs are facing an uncertain future due to global climate change, with increasing occurrences of thermal-induced bleaching. Marine Protected Areas (MPAs) are becoming more important to protect the reefs. A study in Indonesia evaluated the spatial variation of severe bleaching, whether reefs with later bleaching onset are protected within MPAs, and the risk profiles for reefs related to MPAs receiving priority investments.
Article
Environmental Sciences
Yonvitner, Syamsul Bahri Agus, Dea Fauzia Lestari, Riza Pasaribu, Eko Supriyanto, Cahyo Widodo, Ayub Sugara, Jiri Patoka, Surya Gentha Akmal
Summary: This study conducted an investigation on the islands in Kepulauan Seribu Marine National Park in Indonesia and found that coral reef ecosystems are seriously endangered. Measures such as protecting coral reefs from waste threats, controlling overfishing, and regulating tourist behavior are recommended.
COASTAL MANAGEMENT
(2022)
Article
Ecology
Tess Moriarty, Tracy D. Ainsworth, William Leggat
Summary: The prevalence of coral disease has increased significantly under climate change, affecting coral community structure and functionality. The impacts and ecology of coral diseases in high-latitude reefs remain unclear. This study reports the first findings of coral diseases in Lord Howe Island Marine Park, the southernmost coral reef system. Four coral diseases were identified, with a prevalence of 5% and significant variations between time and site.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Environmental Studies
Daniela M. Ceccarelli, Asri P. Lestari, Rudyanto, Alan T. White
Summary: Indonesian coral reefs are facing pressure from various factors such as illegal fishing, destructive fishing practices, pollution, coastal development, and climate change. Marine protected areas (MPAs) are essential for habitat recovery and replenishment of fish stocks. In Indonesia, efforts have been made to improve fisheries productivity and sustainable livelihoods through the establishment of MPAs in three provinces. However, the implementation of regulations to prohibit fishing in these areas is still pending. The study shows a significant decline in target fish species, emphasizing the need for management plans, enforcement, and stakeholder engagement to protect species and secure livelihoods.
Article
Construction & Building Technology
Xiangran Zhao, Qing Wu, Muhammad Akbar, Rongrong Yin, Shiliang Ma, Yong Zhi
Summary: This study investigates the impact of shellfish and marine organism impurities on the mechanical properties and microstructure of coral concrete. The experimental findings show that these impurities have a minimal effect on the mechanical properties of coral concrete when their dosage is below 2%, causing only a decrease of around 6%. The primary factors contributing to the decline in mechanical properties are the weak strength of the impurity shell structure and the formation of numerous small pores within the coral concrete due to the rehydration of internal biomass during the cement hydration process.
Article
Biodiversity Conservation
Agus Sabdono, Endang Sri Lestari, Mada Triandala Sibero
Summary: The Gorgonian corals in Karimunjawa are affected by anthropogenic activities, resulting in changes in the microbial community structure. Bacterial communities associated with Gorgonian corals from Marine Protected Area (MPA) and non-Marine Protected Area (non-MPA) were screened for their potential to combat Urinary Tract Infections (UTIs) pathogens. Results showed that certain bacterial isolates exhibited antimicrobial activity, with higher diversity in the MPA zone compared to the non-MPA zone.
NATURE CONSERVATION-BULGARIA
(2022)
Article
Ecology
Che Din Mohd Safuan, Wan Izatul Asma Wan Talaat, Nazli Aziz, Hafeez Jeofry, Raveena Kim Lai, Husain Khyril-Syahrizan, Aminudin Muhammad Afiq-Firdaus, Ahmad Mohammad Faiz, Mohd Johari Nur Arbaeen, Wei Yien Lua, Xiong-Zhi Xue, Izarenah Md Repin, Zainudin Bachok
Summary: This study aims to assess the health status of coral reefs in Pulau Perhentian Marine Park (PPMP) by using benthic and fish indexes. The study findings reveal significant differences in the percentage cover of biotic and abiotic components among the islands, with algae, dead coral, and sand, silt, or rock being the main contributors. The 2D-CHI classification indicates that the reefs in PPMP range from fair to very degraded, with 55.33% of the reefs in a degraded state. The findings highlight sedimentation, nutrient enrichment, and heavy reliance on coral reefs as potential threats to PPMP reefs.
REGIONAL STUDIES IN MARINE SCIENCE
(2022)
Article
Ecology
Deborah Burn, Samuel Matthews, Chiara Pisapia, Andrew S. Hoey, Morgan S. Pratchett
Summary: Coral abundance metrics do not fully reflect the mortality of coral communities, and the influence of major versus routine disturbances on coral assemblages is not well understood. A study in Australia's Coral Sea Marine Park found that the overall incidence of recent coral injury remained low during a mass bleaching event, but there were significant inter-annual changes in the taxonomic hierarchy for injury incidence. Different coral genera and size classes exhibited varying levels of recent injury, highlighting the vulnerability of large colonies and the possibility of shifts in community size structure. Continued assessment of recent injuries is crucial for understanding the vulnerability of coral communities to future disturbances and changing environmental conditions.
MARINE ECOLOGY PROGRESS SERIES
(2022)
Article
Green & Sustainable Science & Technology
Fery Kurniawan, Luky Adrianto, Dietriech Geoffrey Bengen, Lilik Budi Prasetyo
Summary: This paper evaluates the hypothetical effects of tourism development on water quality using the CWQI and GIS, and finds significant tourism influences on the water quality index in the Marine Tourism Park. The study demonstrates that massive tourism development can reduce water quality and increase vulnerability, highlighting the need for integrated tourism management and environmental protection for sustainable development.
ENVIRONMENT DEVELOPMENT AND SUSTAINABILITY
(2023)
Article
Ecology
Prakas Santoso, Fakhrizal Setiawan, Beginer Subhan, Dondy Arafat, Dietriech G. Bengen, Lalu M. Iqbal Sani, Austin T. Humphries, Hawis Madduppa
Summary: The structural complexity of coral reef habitat plays a critical role in maintaining abundant and diverse reef fish communities. This study found a strong correlation between rugosity, a measure of habitat complexity, and species richness and abundance of fish in marine reserves around Lombok Island in Indonesia.
ENVIRONMENTAL BIOLOGY OF FISHES
(2022)
Article
Ecology
Neus Campanya-Llovet, Amanda E. Bates, Daphne Cuvelier, Eva Giacomello, Diana Catarino, Andrew J. Gooday, Bjorn Berning, Blanca Figuerola, Manuel A. E. Malaquias, Carlos J. Moura, Joana R. Xavier, Tracey T. Sutton, Laurence Fauconnet, Sofia P. Ramalho, Barbara De Moura Neves, Gui M. Machado, Tammy Horton, Andrey V. Gebruk, Kirill Minin, Joel Bried, Tina Molodtsova, Monica A. Silva, Anna Dilman, Antonina Kremenetskaia, Eudriano F. S. Costa, Jameson Clarke, Helen R. Martins, Christopher K. Pham, Marina Carreiro-Silva, Ana Colaco
Summary: Trait-based approaches have become increasingly popular in the scientific community, providing insights into species vulnerability and ecosystem functioning. The FUN Azores trait database, developed collaboratively by 30 researchers, represents a comprehensive assessment of diverse fauna in the Azores Marine Park. The database covers 14 traits for 1,210 species, highlighting gaps in knowledge related to species behavior and life history. The functional maps generated from the database reveal different distribution patterns among size classes and provide a basis for ecological understanding of the marine park.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Review
Environmental Sciences
Ratu Fathia Rahmadyani, Paul Dargusch, Luky Adrianto
Summary: Ecosystem services is a concept used to describe the environmental interrelations with human activities. The Gili Matra Marine Tourism Park (GMMTP) has been extensively researched as a marine protected area focused on marine-based tourism, but there is still a lack of research on the full scope of ecosystem services derived from the coral reef ecosystem. This study aimed to define the services obtained from the GMMTP's coral reef ecosystem, relevant stakeholders, and their activities' impacts on the flow of services and possible implications. Marine tourism, capture fisheries, and land-based activities were identified as services impacting the regulating and supporting services, potentially degrading their utilisation value.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2023)
Review
Biochemistry & Molecular Biology
Tristan Cordier, Laura Alonso-Saez, Laure Apotheloz-Perret-Gentil, Eva Aylagas, David A. Bohan, Agnes Bouchez, Anthony Chariton, Simon Creer, Larissa Fruehe, Francois Keck, Nigel Keeley, Olivier Laroche, Florian Leese, Xavier Pochon, Thorsten Stoeck, Jan Pawlowski, Anders Lanzen
Summary: A decade after the integration of high-throughput sequencing technologies into environmental science, genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems still faces challenges in implementation by regulatory frameworks. Technical limitations, conceptual issues, and diverse implementation strategies may contribute to the perception that routine application of this methodology is premature. Reviewing recent implementations, the strengths and limitations of four general implementation strategies for environmental genomics monitoring are discussed, with emphasis on the potential of integrating meiofauna and microorganisms into biomonitoring.
Article
Fisheries
Konstanze Steiner, Kevin Heasman, Olivier Laroche, Xavier Pochon, Mark Preece, John P. Bowman, Seumas P. Walker, Jane E. Symonds
Summary: The intestinal microbiome of Chinook salmon consists mainly of Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, which are partially shared among feces, surrounding water, and feed. Some bacterial taxa are only present in feces, indicating possible acquisition or growth in the gut rather than the surrounding environment. Inter-individual variation suggests host-specific variability that needs further investigation.
Article
Microbiology
Xavier Pochon, Todd C. LaJeunesse
Summary: The dinoflagellate family Symbiodiniaceae includes numerous genera with diverse species that range from endosymbiotic to free-living. Recent revisions in the family omitted naming some divergent lineages, prompting the description of a new genus and species. The new genus Miliolidium is closely related to Durusdinium and has ecologically distinct lineages found in different locations across the Indo-Pacific.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Olivier Laroche, Xavier Pochon, Susanna A. Wood, Nigel Keeley
Summary: Characterization of microbial assemblages through environmental DNA metabarcoding is becoming more common in monitoring programs, with HSP algorithms inferring functional profiles from 16S rRNA gene data. Despite similarities in functional diversity between HSP-based data and metagenomics, there are differences in taxonomic composition and little correlation in relative abundance of specific functions. HSP-based data shows strong association in functional beta-diversity with metagenomics and responds similarly to environmental impacts, indicating their effectiveness in characterizing and assessing the effects of fish farming on benthic ecosystems.
MOLECULAR ECOLOGY RESOURCES
(2021)
Review
Environmental Sciences
Holly A. Bowers, Xavier Pochon, Ulla von Ammon, Neil Gemmell, Jo-Ann L. Stanton, Gert-Jan Jeunen, Craig D. H. Sherman, Anastasija Zaiko
Summary: The field of eDNA is rapidly expanding to detect rare and invasive species, with developing technologies and protocols addressing challenges in marine environments. This contributes to biosecurity management decisions and aims to facilitate dialogue and innovation in the sector.
Article
Microbiology
Larissa Fruehe, Verena Dully, Dominik Forster, Nigel B. Keeley, Olivier Laroche, Xavier Pochon, Shawn Robinson, Thomas A. Wilding, Thorsten Stoeck
Summary: The analysis of benthic bacterial community structure has proven to be a powerful method for monitoring aquaculture disturbances in coastal environments. By studying the DNA of samples from various salmon-producing countries, core bacterial taxa have been identified that indicate different levels of aquaculture impact, regardless of specific conditions. This research provides valuable insights into the relationship between bacterial groups and benthic processes, contributing to a better understanding of ecosystem functioning in aquaculture sites.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Anastasija Zaiko, Paul Greenfield, Cathryn Abbott, Ulla von Ammon, Jaret Bilewitch, Michael Bunce, Melania E. Cristescu, Anthony Chariton, Eddy Dowle, Jonathan Geller, Alba Ardura Gutierrez, Mehrdad Hajibabaei, Emmet Haggard, Graeme J. Inglis, Shane D. Lavery, Aurelija Samuiloviene, Tiffany Simpson, Michael Stat, Sarah Stephenson, Judy Sutherland, Vibha Thakur, Kristen Westfall, Susanna A. Wood, Michael Wright, Guang Zhang, Xavier Pochon
Summary: Advances in high-throughput sequencing technology are changing marine monitoring by enabling rapid and accurate detection of species in complex samples. An international experiment showed that while there was variation in results from different laboratories, the primary signal in the data was consistent, with samples grouping by geographical origin. Post hoc data clean-up, such as removing low-quality samples, improved sample classification accuracy significantly.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Microbiology
Julien Vignier, Olivier Laroche, Anne Rolton, Pandora Wadsworth, Karthiga Kumanan, Branwen Trochel, Xavier Pochon, Nick King
Summary: The study revealed feeding compromised microalgae to developing oyster larvae caused significant negative effects, including increased deformities, reduced abilities, and slowed development. Analysis of bacterial communities showed certain genera like Halomonas and Marinomonas were strongly associated with impaired larval performance.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Marine & Freshwater Biology
Andrew Barrick, Olivier Laroche, Michael Boundy, John K. Pearman, Tanja Wiles, Juliette Butler, Xavier Pochon, Kirsty F. Smith, Louis A. Tremblay
Summary: This study analyzed the molecular expression pathways of marine copepod Gladioferens pectinatus exposed to copper, benzophenone, and diclofenac across multiple generations. The results showed that these contaminants altered pathways linked to stress, growth, cellular and metabolic processes. Genes associated with oxidative stress and xenobiotic regulation were also impacted.
AQUATIC TOXICOLOGY
(2022)
Review
Environmental Sciences
J. Pawlowski, K. Bruce, K. Panksep, F. Aguirre, S. Amalfitano, L. Apotheloz-Perret-Gentil, T. Baussant, A. Bouchez, L. Carugati, K. Cermakova, T. Cordier, C. Corinaldesi, F. O. Costa, R. Danovaro, A. Dell'Anno, S. Duarte, U. Eisendle, B. J. D. Ferrari, F. Frontalini, L. Fruehe, A. Haegerbaeumer, V Kisand, A. Krolicka, A. Lanzen, F. Leese, F. Lejzerowicz, E. Lyautey, I Macek, M. Sagova-Mareckova, J. K. Pearman, X. Pochon, T. Stoeck, R. Vivien, A. Weigand, S. Fazi
Summary: Environmental DNA (eDNA) metabarcoding is transforming aquatic biomonitoring by sequencing DNA/RNA to identify entire communities within a targeted group. Most studies have focused on water eDNA and macroinvertebrate samples, but eDNA metabarcoding has also been applied to soft sediment samples, especially for microbial or meiofaunal communities. Compared to traditional methods, eDNA metabarcoding offers advantages for assessing sediment environmental quality. However, there is a need for standardization to improve robustness and comparability. This review focuses on sampling, preservation, and DNA extraction protocols for sediment eDNA metabarcoding, aiming to identify best practices and promote harmonization for future benthic monitoring.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Georgia Thomson-Laing, Russleigh Parai, Laura T. Kelly, Xavier Pochon, Rewi Newnham, Marcus J. Vandergoes, Jamie D. Howarth, Susanna A. Wood
Summary: Freshwater eels such as the New Zealand long-finned eel and short-finned eel are crucial apex predators in rivers and lakes, but their populations are declining due to habitat destruction and commercial harvest. The development of species-specific ddPCR assays provides a new method for detecting their DNA in water and sediment samples, offering valuable insights into their spatial distributions in different environments. The ddPCR analyses showed a positive correlation between gene copies and eel sequence reads, suggesting the potential for more accurate assessments of eel populations.
Article
Microbiology
Mailys Picard, Susanna A. Wood, Xavier Pochon, Marcus J. Vandergoes, Lizette Reyes, Jamie D. Howarth, Ian Hawes, Jonathan Puddick
Summary: Understanding the historical onset of cyanobacterial blooms in freshwater bodies can help identify their potential drivers. Lake sediments are valuable archives for exploring these records. In this study, we compared the results obtained from a droplet digital PCR assay and high-performance liquid chromatography to analyze cyanobacterial DNA and pigments in sediment cores. Our findings suggest that the biphasic approach of combining these two methods can provide complementary information for studying changes in the cyanobacterial community.
Article
Environmental Sciences
John K. Pearman, Susanna A. Wood, Marcus J. Vandergoes, Javier Atalah, Sean Waters, Janet Adamson, Georgia Thomson-Laing, Lucy Thompson, Jamie D. Howarth, David P. Hamilton, Xavier Pochon, Laura Biessy, Katie A. Brasell, Jenny Dahl, Riki Ellison, Sean J. Fitzsimons, Henry Gard, Tania Gerrard, Rose Gregersen, McKayla Holloway, Xun Li, David J. Kelly, Reece Martin, Kiely McFarlane, Nicholas P. McKay, Adelaine Moody, Chris M. Moy, Sebastian Naeher, Rewi Newnham, Russleigh Parai, Mailys Picard, Jonathan Puddick, Andrew B. H. Rees, Lizette Reyes, Marc Schallenberg, Claire Shepherd, Julia Short, Kevin S. Simon, Konstanze Steiner, Charlotte Sunde, Marianna Terezow, John Tibby
Summary: Efficient monitoring methods for lakes are necessary for proactive protection and management. Using bacterial communities in lake surface sediments provides a rapid and cost-effective way to assess trophic states.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Ecology
Anastasija Zaiko, Ulla von Ammon, Jacqui Stuart, Kirsty F. Smith, Richard Yao, Melissa Welsh, Xavier Pochon, Holly A. Bowers
Summary: A study compared different filter membranes for capturing NAs, with results showing that larger pore size cellulose membranes were more efficient, while positively charged nylon membranes enhanced capture of naked NAs and eRNA signal. Using coarse pore size filters can efficiently capture target DNA and RNA signals, saving processing time.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Ulla von Ammon, Tessa Averink, Karthiga Kumanan, Cara L. Brosnahan, Xavier Pochon, Kate S. Hutson, Jane E. Symonds
Summary: A tetraplex ddPCR assay was developed for monitoring priority salmon diseases in New Zealand aquaculture farms. The assay showed high sample throughput and immediate results, but also demonstrated some cross-reactivity issues.
FRONTIERS IN MICROBIOLOGY
(2022)
