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Living Resources of the Deep Sea: Biological Profiles and Environmental...
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Living Resources of the Deep Sea: Biological Profiles and Environmental Linkages

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Marine and Freshwater Biology".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 2955

Special Issue Editors

Prof. Dr. Zuozhi Chen

E-Mail Website
Guest Editor
1. South China Sea Fisheries Research Institute, Guangzhou 510300, China
2. Key Laboratory for Sustainable Utilization of Open-Sea Fishery, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
3. Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
Interests: marine microbiology; fish immunology especially in molecular immunology
Prof. Dr. Longshan Lin

E-Mail Website
Guest Editor
Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
Interests: fishery resources; diversity and spatiotemporal of nekton; fish biology; ichthyological ecology; fish taxonomy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Deep-sea living resources are pivotal to food security, biodiversity conservation, and oceanic carbon cycling; however, their basic biological profiles—and the ways they couple to physical and chemical environments—remain largely undocumented.

This Special Issue addresses two interlinked questions: (1) What are the current status and life-history profiles of deep-ocean biota—including fishes, cephalopods, marine mammals, and microbial communities—covering biomass, diversity, age structure, diet, spawning grounds, migration routes, and reproductive cycles? (2) Which environmental drivers (temperature, oxygen, carbon flux, geomorphology, etc.) shape their distribution patterns, and what physiological, behavioral, and molecular mechanisms enable these organisms to adapt to high pressures, low temperatures, and perpetual darkness?

We welcome the submission of observational, experimental, and modelling contributions that apply traditional vessel surveys, fishery-dependent data, eDNA, acoustic and remote sensing, integrative taxonomy, or comparative genomics to clarify the basic traits of deep-sea organisms and to unravel the environmental factors and mechanisms shaping their distributions. The contribution of studies addressing either theme—or bridging both—is strongly encouraged.

Prof. Dr. Zuozhi Chen
Prof. Dr. Longshan Lin
Guest Editors

Manuscript Submission Information

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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. Biology is an international peer-reviewed open access semimonthly 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 2700 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

  • deep-sea fisheries
  • spawning-ground shifts
  • habitat–environment coupling
  • rare deep-sea biodiversity
  • molecular adaptation
  • environmental DNA (eDNA)
  • acoustic monitoring
  • fishery remote-sensing

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Published Papers (4 papers)

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Research

32 pages, 9676 KB  
Article
Comparative Transcriptomics as a Key to Understanding the Adaptation Mechanisms of Baikal Sculpins to the Deep-Water Habitat
by Yulia P. Sapozhnikova, Anastasiya G. Koroleva, Tuyana V. Sidorova, Evgenia A. Vakhteeva, Alexander A. Epifantsev, Sergey A. Potapov, Vera M. Yakhnenko, Lyubov V. Sukhanova, Sergei V. Kirilchik, Tatyana V. Butina, Ivan A. Nebesnykh and Igor V. Khanaev
Biology 2025, 14(12), 1762; https://doi.org/10.3390/biology14121762 - 9 Dec 2025
Viewed by 409
Abstract
Understanding the molecular mechanisms that enable vertebrate adaptation to deep-water environments remains a central goal in evolutionary biology. This study used comparative transcriptomics of skeletal muscle tissue to investigate these mechanisms in four endemic sculpin fish species (Cottoidei) from Lake Baikal, which inhabit [...] Read more.
Understanding the molecular mechanisms that enable vertebrate adaptation to deep-water environments remains a central goal in evolutionary biology. This study used comparative transcriptomics of skeletal muscle tissue to investigate these mechanisms in four endemic sculpin fish species (Cottoidei) from Lake Baikal, which inhabit different depth niches ranging from pelagic to benthic-abyssal zones up to 1642 m. Pelagic species showed increased activity in genes involved in sarcomere structure, calcium handling, and motor proteins, indicating adaptations for sustained locomotion. In contrast, deep-benthic specialists showed enrichment in pathways for glycolytic metabolism, proteasome function, and ubiquitination, reflecting adaptations for energy efficiency and protein homeostasis in a high-pressure environment. We conclude that the colonization of the Baikal abyssal zone by sculpins relies on a suite of shared molecular mechanisms, with distinct ecological pressures driving specific transcriptional changes in motility, metabolic strategy, and cellular integrity. This study provides a systems-level model for deep-water adaptation in vertebrates. Full article
(This article belongs to the Special Issue Living Resources of the Deep Sea: Biological Profiles and Environmental Linkages)
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24 pages, 5039 KB  
Article
Diet Reconstruction Under Limited Prior Information: Dietary Contributions and Isotopic Niche of Metridium senile in the North Yellow Sea
by Yongsong Zhao, Xiujuan Shan, Guangliang Teng, Shiqi Song, Yunlong Chen and Xianshi Jin
Biology 2025, 14(11), 1508; https://doi.org/10.3390/biology14111508 - 28 Oct 2025
Viewed by 584
Abstract
Biomass of the plumose anemone Metridium senile has surged in the benthic ecosystem of the North Yellow Sea in recent years. Understanding its diet and the proportional contributions of food sources is essential for assessing the ecological consequences of this expansion. The species [...] Read more.
Biomass of the plumose anemone Metridium senile has surged in the benthic ecosystem of the North Yellow Sea in recent years. Understanding its diet and the proportional contributions of food sources is essential for assessing the ecological consequences of this expansion. The species is often characterized as a passive suspension feeder, yet laboratory feeding trials have documented shrimp consumption. Because prior dietary information from the region is scarce, conventional stable isotope approaches are poorly constrained. We developed an integrative framework coupling trophic position estimation, isotopic niche metrics, spatial point pattern analysis, and a Bayesian mixing model to improve diet attribution under limited prior information and to test whether M. senile preys on small-bodied and juvenile teleosts and invertebrates under natural conditions. Our analyses showed that: (i) M. senile occupied a high trophic position (TP = 3.09 ± 0.25), exceeding those estimated for putative predators in our dataset, implying weak top-down control; (ii) in isotopic niche analyses, M. senile showed high posterior probabilities of occurring within the niches of cephalopods and medium-sized fishes (78.30% and 63.04%, respectively), consistent with shared prey and inconsistent with a strictly suspension-feeding strategy; (iii) mixing space diagnostics informed by spatial point pattern analysis indicated that including small-sized fishes and shrimps as sources was necessary to reconcile the elevated TP; and (iv) the Bayesian mixing model estimated that small-bodied and juvenile teleosts and invertebrates supplied most long-term nutrition (posterior mean ≈ 0.65), with the remainder from suspension-derived sources, consistent with an opportunistic generalist rather than a strict suspension feeder. Sustained predation on small-bodied and juvenile teleosts and invertebrates could suppress early fish recruitment, impose top-down control on forage species, and alter the local food web structure. Management should monitor M. senile (size structure, population density, and co-occurrence with juveniles and forage biota) and consider targeted removals and seafloor litter cleanups in priority habitats. The framework is applicable to diet studies with limited prior information; adding δ34S, compound-specific amino-acid isotopes (CSIA-AA), and DNA-based dietary evidence should further sharpen source discrimination. Full article
(This article belongs to the Special Issue Living Resources of the Deep Sea: Biological Profiles and Environmental Linkages)
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18 pages, 3350 KB  
Article
Distribution of Summer Zooplankton in the Waters off the Kuril Islands (Northwest Pacific) in Relationship with Environmental Conditions
by Valentina Kasyan
Biology 2025, 14(7), 827; https://doi.org/10.3390/biology14070827 - 8 Jul 2025
Viewed by 753
Abstract
This study covers a large area around the Kuril Islands, one of the longest island arcs in the world, crossing several climatic zones, which allows for observations of longitudinal shifts in planktonic species’ ranges following shifts in the boundaries between the climatic zones. [...] Read more.
This study covers a large area around the Kuril Islands, one of the longest island arcs in the world, crossing several climatic zones, which allows for observations of longitudinal shifts in planktonic species’ ranges following shifts in the boundaries between the climatic zones. We analyzed spatial and vertical changes in the zooplankton community structure and the associated environmental factors from Yuri Island to Onekotan Island both in Pacific and Sea of Okhotsk waters, which are influenced by cold and warm water masses. Species diversity in the Pacific waters was higher than in the Sea of Okhotsk waters, with a peak of diversity recorded from warm waters off the southern Kuril Islands associated with the Soya Current and the Kuroshio Extension. Zooplankton abundance and biomass above the thermocline were higher in the Pacific waters compared to the Sea of Okhotsk area, showing a tendency to increase with higher latitude and lower water temperatures and generally to decline with depth. The water temperature and salinity below the thermocline were the most important explanatory environmental variables responsible for zooplankton abundance variations. The distribution patterns of the large-sized copepods were strongly correlated with temperature and salinity, as well as with dissolved oxygen and chlorophyll a levels. In contrast, small-sized copepods were adapted to or thrived in the areas with elevated temperature and salinity values and a reduced chlorophyll a concentration. Full article
(This article belongs to the Special Issue Living Resources of the Deep Sea: Biological Profiles and Environmental Linkages)
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15 pages, 3061 KB  
Article
Based on the Spatial Multi-Scale Habitat Model, the Response of Habitat Suitability of Purpleback Flying Squid (Sthenoteuthis oualaniensis) to Sea Surface Temperature Variations in the Nansha Offshore Area, South China Sea
by Xue Feng, Xiaofan Hong, Zuozhi Chen and Jiangtao Fan
Biology 2025, 14(6), 684; https://doi.org/10.3390/biology14060684 - 12 Jun 2025
Viewed by 800
Abstract
Overfishing and climate change have led to the depletion of fishery resources in the offshore South China Sea. The purpleback flying squid (Sthenoteuthis oualaniensis) has emerged as a promising alternative due to its ecological and economic value. However, information on its [...] Read more.
Overfishing and climate change have led to the depletion of fishery resources in the offshore South China Sea. The purpleback flying squid (Sthenoteuthis oualaniensis) has emerged as a promising alternative due to its ecological and economic value. However, information on its preferred habitat conditions remains scarce. This study integrates geostatistical and fisheries oceanographic approaches to explore optimal spatial–temporal scales for habitat modeling and to assess habitat changes under warming scenarios. Utilizing fishery data from 2013 to 2017, environmental variables including SST, sea surface temperature anomaly (SSTA), and chlorophyll-a concentration (CHL) were analyzed. Fishing effort data revealed significant seasonal differences, with the highest vessel numbers in summer and the lowest in autumn. Among the six modeling schemes, the combination of 0.5° × 0.5° spatial resolution and seasonal temporal resolution yielded the highest HSI model accuracy (84.02%). Optimal environmental ranges varied by season. Simulations of SST deviations (±0.2 °C, ±0.5 °C, and ±1 °C) showed that extreme warming or cooling could eliminate suitable habitats. These findings highlight the vulnerability of squid habitats to thermal shifts and support adaptive fishery strategies in the South China Sea. Full article
(This article belongs to the Special Issue Living Resources of the Deep Sea: Biological Profiles and Environmental Linkages)
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