Assessment of fishery resources using environmental DNA: Small yellow croaker (Larimichthys polyactis) in East China Sea

Metabonomics and Transcriptomics Analyses Reveal the Underlying HPA-Axis-Related Mechanisms of Lethality in Larimichthys polyactis Exposed to Underwater Noise Pollution

The problem of marine noise pollution has a long history. Strong noise (>120 dB re 1 µPa) will affects the growth, development, physiological responses, and behaviors of fish, and also can induce the stress response, posing a mortal threat. Although many studies have reported that underwater noise may affect the survival of fish by disturbing their nervous system and endocrine system, the underlying causes of death due to noise stimulation remain unknown. Therefore, in this study, we used the underwater noise stress models to conduct underwater strong noise (50-125 dB re 1 µPa, 10-22,000 Hz) stress experiments on small yellow croaker for 10 min (short-term noise stress) and 6 days (long-term noise stress). A total of 150 fishes (body weight: 40-60 g; body length: 12-14 cm) were used in this study. Omics (metabolomics and transcriptomics) studies and quantitative analyses of important genes (HPA (hypothalamic-pituitary-adrenal)-axis functional genes) were performed to reveal genetic and metabolic changes in the important tissues associated with the HPA axis (brain, heart, and adrenal gland). Finally, we found that the strong noise pollution can significantly interfere with the expression of HPA-axis functional genes (including corticotropin releasing hormone (CRH), corticotropin releasing hormone receptor 2 (CRHR2), and arginine vasotocin (AVT)), and long-term stimulation can further induce metabolic disorders of the functional tissues (brain, heart, and adrenal gland), posing a lethal threat. Meanwhile, we also found that there were two kinds of death processes, direct death and chronic death, and both were closely related to the duration of stimulation and the regulation of the HPA axis.

Large and Small Yellow Croakers Feeding and Living Together Make Large Yellow Croaker Population Recovery Difficult: A Guild Perspective

In recent decades, China's large-scale stock enhancement programs to restore the collapsing large yellow croaker (Larimichthys crocea) fishery resources have not yielded the desired results, and a comprehensive analysis of the underlying reasons for this problem is required. Based on small yellow croaker (Larimichthys polyactis) catch survey data obtained from 15 fishing ports along the coast of the East China Sea, we examined the proportion of large yellow croakers mixed in the small yellow croaker catch and their biological parameters. In addition, we analyzed the differences in the intestinal microbiota and feeding ecology between these two species to explore the reason why the stock enhancement program failed to achieve the desired outcome. The results show that there is a high likelihood of the two species appearing in each other's ecological niches, and there is a significant overlap in their dietary ecology. They may cohabitate and form a guild. The fishing season targeting the small yellow croaker indirectly catches the large yellow croaker population, which puts huge fishing pressure on large yellow croaker resource and shows obvious overfishing. Therefore, it is necessary to optimize and adjust the fishing ban policy and stock enhancement strategies, appropriately reducing the fishing intensity after the fishing ban to facilitate the effective accumulation of resource replenishment effects during the fishing ban period, thus effectively restoring wild large yellow croaker resources.

Metabonomics and Transcriptomics Analyses Reveal the Development Process of the Auditory System in the Embryonic Development Period of the Small Yellow Croaker under Background Noise

Underwater noise pollution has become a potential threat to aquatic animals in the natural environment. The main causes of such pollution are frequent human activities creating underwater environmental noise, including commercial shipping, offshore energy platforms, scientific exploration activities, etc. However, in aquaculture environments, underwater noise pollution has also become an unavoidable problem due to background noise created by aquaculture equipment. Some research has shown that certain fish show adaptability to noise over a period of time. This could be due to fish's special auditory organ, i.e., their "inner ear"; meanwhile, otoliths and sensory hair cells are the important components of the inner ear and are also essential for the function of the auditory system. Recently, research in respect of underwater noise pollution has mainly focused on adult fish, and there is a lack of the research on the effects of underwater noise pollution on the development process of the auditory system in the embryonic development period. Thus, in this study, we collected embryo-larval samples of the small yellow croaker (Larimichthys polyactis) in four important stages of otic vesicle development through artificial breeding. Then, we used metabonomics and transcriptomics analyses to reveal the development process of the auditory system in the embryonic development period under background noise (indoor and underwater environment sound). Finally, we identified 4026 differentially expressed genes (DEGs) and 672 differential metabolites (DMs), including 37 DEGs associated with the auditory system, and many differences mainly existed in the neurula stage (20 h of post-fertilization/20 HPF). We also inferred the regulatory mode and process of some important DEGs (Dnmt1, CPS1, and endothelin-1) in the early development of the auditory system. In conclusion, we suggest that the auditory system development of L. polyactis begins at least in the neurula stage or earlier; the other three stages (tail bud stage, caudal fin fold stage, and heart pulsation stage, 28-35 HPF) mark the rapid development period. We speculate that the effect of underwater noise pollution on the embryo-larval stage probably begins even earlier.

Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations for future use

Background

Over the past decade, environmental DNA (eDNA) has become a resourceful tool in conservation and biomonitoring. Environmental DNA has been applied in a variety of environments, but the application to studies of marine fish, particularly at tropical latitudes, are limited. Since many commercially important Caribbean fishes are overexploited, these species are optimal candidates to explore the use of this method as a biomonitoring tool. Specifically, for many of these species, the formation of fish spawning aggregations (FSAs) marks a critical life history event where fishes will gather in large numbers for reproduction. These FSAs are ephemeral in nature, lasting only a few days, but are predictable in time and space which makes them susceptible to overfishing.

Methods

In this study, we test the feasibility of using an eDNA sampling approach (water and sediment collection) to detect the presence of known FSAs off the west coast of Puerto Rico, with cytochrome c oxidase subunit 1 (CO1) and 12S rRNA (12S) primers designed to target specific species. A total of 290 eDNA samples were collected and, of those, 206 eDNA samples were processed. All eDNA samples varied in DNA concentration, both between replicates and collection methods. A total of 12 primer sets were developed and tested using traditional PCR and qPCR.

Results

Despite validation of primer accuracy and sample collection during known peak spawning times, the use of traditional PCR and qPCR with both molecular markers failed to produce species-specific amplification. Thus, a trial test was conducted using the CO1 primers in which target fish DNA was 'spiked' at various concentrations into the respective eDNA samples to determine the target species DNA concentration limit of detection. Upon successful amplification of the trial, results indicated that eDNA samples were below the detection threshold of our methods, suggesting that the number of fish present at the spawning aggregations was inadequate for single-species detection methods. In addition, elements such as the unavoidable presence of non-target DNA, oceanic environmental conditions, shedding rates of target fish, among other biotic and abiotic factors could have affected DNA persistence and degradation rates at the sites.

Conclusion

We provide recommendations for species-specific fish detection in lower latitudes, and suggestions for studies aiming to monitor or detect fish spawning aggregations using eDNA sampling.

Dissolved metal assessment in surface seawater: A spatial-seasonal evaluation in the Zhejiang coastal waters, the East China Sea

The spatial-seasonal distributions and variations, correlations with environmental variables and the pollution degrees of dissolved metals in the Zhejiang coastal seawater were investigated. The concentrations of six dissolved metals (i.e. Cu, Pb, Zn, Cd, As and Hg) were in the ranges of 0.10-6.40 (1.6 ± 0.8), 0.16-3.60 (1.2 ± 0.7), 2.50-24.0 (8.5 ± 4.8), 0.011-0.180 (0.07 ± 0.03), 0.85-4.20 (2.1 ± 0.8) and 0.001-0.110 (0.06 ± 0.02) μg/L, throughout the four seasons, respectively. Significant differences in all the dissolved metals were found among seasons, whereas no significant differences were found among stations. The average concentrations of metals were in the following order: Zn > As>Cu > Pb > Cd > Hg. Single metal contamination factor was in the following order: Pb > Hg > Zn > Cu > As>Cd. The pollution level of dissolved metals in the Zhejiang coastal waters (ZCW) was low. Most of the dissolved metals were correlated to temperature, indicating seasonal differences. The redundancy analysis (RDA) indicated that depth, temperature, nitrate and phosphate could best explain the variance pattern of dissolved metals in the ZCW.

Transcriptomic and Behavioral Studies of Small Yellow Croaker (Larimichthyspolyactis) in Response to Noise Exposure

Noise has the potential to induce physiological stress in marine fishes, which may lead to all sorts of ecological consequences. In the current study, we used the RNA-sequencing (RNA-seq) method to sequence the whole transcriptome of the brain in small yellow croaker (Larimichthys polyactis). The animals were exposed to a mix of noises produced by different types of boat played back in a tank, then the brain tissues were collected after the fish had been exposed to a 120 dB noise for 0.5 h. In total, 762 differently expressed genes (DEGs) between the two groups were identified, including 157 up regulated and 605 down regulated genes in the noise exposure group compared with the control group. Gene ontology (GO) enrichment analysis indicated that the most up regulated gene categories included synaptic membranes, receptor-mediated endocytosis and the neurotransmitter secretion process. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways found that endocytosis, cell adhesion molecules and the extracellular matrix (ECM) receptor interaction pathway were over-represented. Specifically, ECM-related genes, including lamin2, lamin3, lamin4, coll1a2, coll5a1 and col4a5 were down regulated in the noise exposure group, implying the impaired composition of the ECM. In addition, the behavioral experiment revealed that L. polyactis exhibited avoidance behaviors to run away from the noise source at the beginning of the noise exposure period. At the end of the noise exposure period, L. polyactis kept motionless on the surface of the water and lost the ability to keep their balance. Taken together, our results indicate that exposure to noise stress contributes to neurological dysfunction in the brain and impaired locomotor ability in L. polyactis.

Detection of an invasive species through an environmental DNA approach: The example of the red drum Sciaenops ocellatus in the East China Sea

Biological invasions are among the most critical threats to local species diversity and ecosystem ecology. The red drum was introduced for marine aquaculture circa 1991 and has become a commercially important maricultural fish species in China and was widely cultured across the coastal areas in mainland China. However, after two decades of maricultural activities, the red drum has been consecutively recorded as escapees along the entire coastal waters of China. Due to the lack of effective monitoring methods, there are not many reports on its distribution in natural seas. In current study, the environmental DNA (eDNA) method was applied. A set of red drum-specific primers and probe were designed, and the distribution and biomass of the red drum were conducted in the East China Sea. The results showed that a total of 47 samples (26.40% of 178 samples) in 27 stations (61.36%) were found to be positive for red drum eDNA. The hotspot was found around the central areas of the East China Sea, especially around the Jiaojiang Estuary and Sanmen Bay area. Significant eDNA concentration differences were found among different stations. Moreover, the presence/absence was also found significantly different among stations. Vertical distribution differences of eDNA presence/absence and concentrations were also found. This study can provide technical support for the monitoring, evaluation, and eradication of invasive species in the future.