The clam Meretrix meretrix (Linnaeus, 1758) is a commercially significant bivalve species widely distributed along China’s coast. To investigate the differences among geoducks from different geographic populations, this study investigated the geographical variations in morphology and key physiological traits among three populations spanning a latitudinal gradient: Liaoning Dandong (north), Jiangsu Rudong (center), and Guangxi Qinzhou (south). We analyzed nine morphological traits and measured physiological indicators—including filtration rate, feeding rate, oxygen consumption, ammonia excretion, and burrowing behavior—at two temperatures (18 °C and 20 °C). The results revealed significant morphological differentiation among the populations. Physiologically, the Guangxi population demonstrated superior adaptation to warmer conditions, exhibiting the highest feeding and metabolic rates at 20 °C. In contrast, the Liaoning population performed better at the lower temperature of 18 °C, while the Jiangsu population showed intermediate characteristics. Furthermore, burrowing capacity varied significantly, with the southern population having the highest burrowing rate. These findings demonstrate clear population-specific adaptations to local thermal environments, likely driven by long-term acclimatization. This study provides a crucial scientific basis for the conservation of genetic resources and informs regionalized aquaculture strategies for M. meretrix, emphasizing the importance of selecting locally adapted populations for cultivation.

(1) Exploring the potential impacts of Mactra veneriformis and Ruditapes philippinarum on the aquaculture of Meretrix meretrix in the tidal flat aquaculture zone is significant for the optimization of bivalve aquaculture structure. (2) In this study, we systematically compared the differences in feeding, metabolic physiological indicators, and energy budgets of the three bivalve species in the M. meretrix aquaculture zone of Rudong County, Jiangsu Province, under the feeding conditions of Isochrysis zhanjiangensis and Platymonas helgolandica. (3) The results indicated that feeding with I. zhanjiangensis could significantly improve the feeding efficiency of the three bivalve species, and M. veneriformis showed the strongest feeding ability. Under I. zhanjiangensis feeding conditions, the clearance rate [1.373 ± 0.177 L/(g·h)] and ingestion rate [9.803 ± 1.264 mg/(g·h)] of M. veneriformis were significantly higher than those of M. meretrix [clearance rate: 0.716 ± 0.046 L/(g·h); ingestion rate: 5.112 ± 0.328 mg/(g·h)] and R. philippinarum [clearance rate: 0.609 ± 0.101 L/(g·h); ingestion rate: 4.351 ± 0.725 mg/(g·h)] (p < 0.05). In terms of energy allocation, the scope for growth (SFG) of M. veneriformis [133.050 ± 15.705 J/(g·h)] was significantly higher than that of the other two bivalve species. M. meretrix [70.550 ± 2.133 J/(g·h)] had the highest energy utilization efficiency, while R. philippinarum [53.688 ± 7.548 J/(g·h)] had the lowest SFG due to high excretion losses. (4) In conclusion, M. veneriformis shows high production potential in the aquaculture system, and its potential impact on M. meretrix is greater than that of R. philippinarum, thus requiring close attention in aquaculture management.

Using a three-factor orthogonal design, we investigated the transcriptomic and histological responses of triploid rainbow trout (Oncorhynchus mykiss) gills across three salinities (10, 20, and 30 ppt) over 60 days, with temperature and body size as background conditions. Results showed that 20 ppt was associated with extensive transcriptional reprogramming, with 3333 differentially expressed transcripts (DETs), whereas 30 ppt induced only 120 DETs; WGCNA further identified salinity-correlated modules involved in ion transport and ribosome biogenesis. Histological alterations remained within physiological ranges with no salinity-dependent severity gradient, as confirmed by semi-quantitative scoring. These findings demonstrate that triploid rainbow trout gills employ distinct molecular strategies at medium versus high salinity. Within the 10–30 ppt range examined, 20 ppt was the salinity at which transcriptional reprogramming was most active, suggesting that this intermediate salinity warrants further investigation as a potential acclimation stage.

Rainbow trout (Oncorhynchus mykiss) is a globally cultured cold-water salmonid, yet triploid larvae often develop spinal ventral lordosis and conjoined twin malformations with unclear molecular mechanisms. Here, RNA-seq of 15 dph normal (N), spinal-deformed (SD) and conjoined (CT) triploid larvae yielded 54.13 Gb of valid data, identifying 4292, 3601 and 2699 DEGs for SD vs. N, CT vs. SD and CT vs. N groups, respectively. Five shared disrupted cascades (cell adhesion, neuroactive ligand-receptor interaction, phagosome, cytokine-receptor interaction, and PI3K-Akt signaling) were identified, while potential calcium/MAPK and steroid-biosynthesis-related pathways were predominantly perturbed in SD and CT larvae, respectively. Filtered PPI sub-networks displayed distinct predicted topological phenotype-associated candidate transcripts, with coagulation and complement transcripts forming core hubs in SD larvae and steroid-related transcripts showing weak connectivity in CT groups. Three discriminative transcripts with inverse expression patterns were screened. This study reveals conserved and phenotype-specific transcriptional phenotype-associated candidate transcripts of the two malformations and provides candidate phenotype-associated transcripts for subsequent functional verification of larval malformations. It should be noted that all transcriptomic data originate from whole-larval homogenates; expression signatures of conjoined-twin larvae may be confounded by altered tissue-type proportions rather than malformation-exclusive regulatory mechanisms.

This study examined the sediment microbial communities at 12 stations within the Meretrix meretrix farming area in Rudong, Jiangsu Province, utilising high-throughput sequencing. It elucidates the ecological relationships between the sediment microbial communities and the primary physical and chemical factors influencing the farming water and sediment. The results indicated that the microbial communities comprised 55 phyla. The Shannon index ranged from a minimum of 8.97 to a maximum of 9.96, while the Simpson index varied from 0.996 to 0.997, indicating a uniform species distribution. β diversity analysis revealed significant spatial diversity among the communities. Dominant bacterial groups included Proteobacteria (25.2–38%) and Desulfobacterota (10.4–14.4%), with Desulfobacterota reaching a peak of 14.4% at tidal creek station S2, reflecting the sulphate reduction process associated with organic pollution input. At the genus level, Woesia (9.15–17.16%), Desulfobacterota, and Subgroup_22 were identified as core functional bacteria. Redundancy analysis indicated that phosphate and nitrate were the primary drivers of community variation, accounting for a cumulative interpretation rate of 43.2%. Spearman correlation analysis confirmed that fine-grained sediments were more likely to store organic matter, significantly promoting the colonisation of AQS1 (p < 0.05) and Cohaesibacter (p < 0.05), while inhibiting Puniceispirillales (p < 0.01). An alkaline environment positively selects for sulphur-cycling bacteria, such as Desulfatiglans (p < 0.05). This study provides technical support for the regulation of sediment environments and the promotion of healthy clam culture practices.

The hard clam Meretrix meretrix is a commercially important bivalve species in China, yet its aquaculture industry is increasingly threatened by germplasm degradation and recurrent mass summer mortality events associated with elevated temperatures and Vibrio infections. To characterize candidate germplasm resources with potential value for heat-tolerance breeding and to elucidate the genetic basis of adaptive differentiation, we integrated genotyping-by-sequencing (GBS) and gill transcriptome sequencing across five wild populations spanning the entire latitudinal range of China: Dandong (LD), Weihai (SW), and Rudong (JR) in the north, and Beihai (GB) and Qinzhou (GQ) in the south. Phylogenetic and population structure analyses resolved the five populations into two distinct genetic lineages corresponding to northern and southern clusters, with the Beihai population exhibiting the highest genetic diversity and the Weihai population showing signs of inbreeding that were elevated relative to the other populations. Comparative transcriptomic analysis revealed that differentially expressed genes between northern and southern populations were significantly enriched in immune-related pathways (including NOD-like receptor and IL-17 signaling pathways) and lipid metabolic pathways (including cholesterol and steroid biosynthesis). Notably, populations with similar genomic backgrounds still displayed pronounced transcriptional divergence, indicating that transcriptional divergence can arise even in the absence of strong genomic differentiation; because this conclusion is based on observational data, it cannot fully separate long-term genetic adaptation from environmentally induced transcriptional plasticity. These findings provide fundamental data for germplasm conservation and for future selective breeding programs targeting stress resistance in M. meretrix.