Bacterial abundances, water parameters and bacterial community composition of shrimp pond water

In shrimp aquaculture, shrimp farming systems are carefully determined to avoid rearing failure due to stress, disease or mass mortality, and to achieve optimum shrimp production. Little is known about how shrimp farming systems affect environmental parameters and bacterial community in rearing water, whether high stocking densities (intensive system) will increase the abundance of pathogenic bacteria. Moreover, high content of suspended particulate matter in shrimp pond potentially load more bacteria, including pathogenic bacteria, which then can be used as a sentinel of the potential presence of pathogenic bacteria in shrimp farming. Therefore, water parameters and the abundances of cultivable heterotrophic bacteria, including potential pathogenic Vibrio, were measured in three ponds of moderate/semi-intensive (40 post-larvae m-3) and three of high density/intensive shrimp aquaculture (90 post-larvae m-3), at day 10, 20, 30, 40, 50, and 70 of rearing. Additionally, free-living and particle-attached bacterial communities in the pond water were analyzed via 16S amplicon sequencing. Among the observed environmental parameters, suspended particulate matters, salinity, chlorophyll a, pH and dissolved oxygen differed significantly between the intensive and semi-intensive systems. However, no significant difference was observed for inorganic nutrients, abundances of heterotrophic bacteria, and potential pathogenic Vibrio between two systems. Bacterial communities were dominated by Gammaproteobacteria, Alphaproteobacteria, Flavobacteria, Bacilli, and Actinobacteria. Operational taxonomic units (OTUs) of the genera Halomonas, Psychrobacter, and Salegentibacter were present in both systems, where they may be involved in nitrification and ammonium removal. Halomonas, Psychrobacter, and Vibrio were most abundant genera in the particle-attached fractions, while Salegentibacter, Sulfitobacter, and Halomonas were found in the free-living fractions of both systems. Furthermore, aggregates of intensive systems loaded more Vibrio than semi-intensive ones. Interestingly, when the sequence proportion of Halomonas or Psychrobacter decreased, the proportion of Vibrio increased. Redundancy analysis showed that among the observed environmental parameters, salinity was best suited to explain patterns in the composition of both free-living and particle-attached bacterial communities (R²: 15.32% and 12.81%, respectively). In conclusion, intensive systems affected water quality and increased prevalence of potentially pathogenic bacteria, although they did not seem to promote a more diverse bacterial community.

在对虾养殖（shrimp aquaculture）中，养殖从业者会审慎选择对虾养殖系统，以规避因胁迫、病害或大规模死亡导致的养殖失败，并实现最优对虾产量。目前学界对以下问题仍缺乏清晰认知：对虾养殖系统如何影响养殖水体的环境参数与细菌群落，高放养密度的集约化养殖系统是否会提升病原菌的丰度。此外，对虾养殖池塘内悬浮颗粒物含量较高时，可能会携带包括病原菌在内的大量细菌，这类颗粒物可作为对虾养殖环境中潜在病原菌存在情况的指示物。为此，本研究在养殖第10、20、30、40、50和70天，对3个中等/半集约化养殖池塘（放养密度为40尾仔虾/立方米）以及3个高密度/集约化养殖池塘（放养密度为90尾仔虾/立方米）的水体开展采样检测，测定了水体环境参数、可培养异养细菌的丰度，包括潜在致病弧菌（Vibrio）的丰度。同时，通过16S扩增子测序（16S amplicon sequencing）分析了养殖水体中游离态与颗粒附着态细菌群落的组成。检测的环境参数中，悬浮颗粒物、盐度、叶绿素a、pH值与溶解氧在集约化与半集约化养殖系统间存在显著差异。然而，两类系统间的无机营养盐含量、异养细菌丰度以及潜在致病弧菌丰度均未出现显著差异。细菌群落以γ-变形菌纲（Gammaproteobacteria）、α-变形菌纲（Alphaproteobacteria）、黄杆菌纲（Flavobacteria）、芽孢杆菌纲（Bacilli）和放线菌纲（Actinobacteria）为主。盐单胞菌属（Halomonas）、嗜冷杆菌属（Psychrobacter）以及盐生拟杆菌属（Salegentibacter）的操作分类单元（OTUs）在两类养殖系统中均有检出，它们可能参与硝化作用与氨氮去除过程。在颗粒附着态组分中，丰度最高的菌属为盐单胞菌属、嗜冷杆菌属与弧菌属；而在两类系统的游离态组分中，均检出了盐生拟杆菌属、嗜硫杆菌属（Sulfitobacter）与盐单胞菌属。此外，集约化养殖系统的颗粒物聚集体携带的弧菌数量多于半集约化系统。有趣的是，当盐单胞菌属或嗜冷杆菌属的序列占比下降时，弧菌属的序列占比会随之上升。冗余分析（redundancy analysis, RDA）结果显示，在检测的环境参数中，盐度最能解释游离态与颗粒附着态细菌群落的组成模式（分别解释了15.32%与12.81%的群落变异）。综上，集约化养殖系统会改变养殖水体水质，并提升潜在病原菌的流行率，尽管其似乎并未促进细菌群落的多样性提升。