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.

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.

Understanding niche differentiation and interspecific coexistence patterns of macrobenthos provides critical references for ecological assessment of bivalve aquaculture. Seasonal field surveys (Autumn 2023–Summer 2024) across 12 sampling sites were conducted in an intensive Meretrix meretrix tidal flat farm in Rudong, Jiangsu. Synchronous water depth, sediment grain size and total organic carbon (TOC), and salinity were measured at each station to characterize habitat gradients; no unfarmed reference tidal flats were included, so all community patterns only reflect within-farm variation. The study area has sustained 10-year continuous bottom culture with baseline juvenile stocking density of 250 ind./m² and twice-yearly manual harvesting. A total of 58 macrobenthic taxa were identified, and 13 dominant species were screened with a dominance index threshold Y > 0.02. All abundance data were fourth-root-transformed before Bray–Curtis community analysis to reduce bias of hyper-abundant taxa. Standardized Shannon niche breadth (0–1 normalized, r = 48 site–season composite units) and permutation-tested (999 replicates) Pianka niche overlap/similarity coefficients were calculated to quantify resource utilization similarity. Niche breadth ranged from 0.018 to 0.971, with farmed M. meretrix showing the maximum value, indicating broader seasonal resource adaptation. High niche overlap (>0.50) was detected between M. meretrix and four wild dominant species (Nephtys californiensis, Moerella iridescens, Lingula anatina, Umbonium thomasi). Notably, niche metrics derived solely from spatial abundance data cannot directly confirm interspecific competition or trophic segregation; the stable coexistence observed in our assemblage is tentatively hypothesized to be driven by vertical sediment partitioning and divergent feeding guilds based on published functional studies, without direct in situ trophic or stratified sediment evidence from this work. Hierarchical UPGMA clustering (0.35 Bray–Curtis distance threshold) and corrected NMDS ordination (48 site–season units, dominant-species fitted vectors) illustrated distinct functional groups. Based on the observed niche convergence among filter-feeding bivalves under local farming conditions, the range of 230–280 ind./m² is presented as an observational reference. Controlled manipulative experiments with gradient stocking densities are needed to test whether this range can balance aquaculture yield and benthic biodiversity.