Bacterial abundances and chemical water analysis from shrimp farming systems in Indonesia

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.在对虾养殖中，养殖者会审慎设计对虾养殖系统，以规避因胁迫、病害或大规模死亡导致的养殖失败，并实现最优的对虾产量。目前学界对不同养殖系统如何影响养殖水体的环境参数与细菌群落，以及高放养密度（集约化养殖系统）是否会提升病原细菌丰度，尚缺乏足够认知。此外，对虾养殖池塘中悬浮颗粒物含量较高时，其携带的细菌（包括病原细菌）总量往往更多，此类颗粒物可作为对虾养殖环境中潜在病原细菌存在情况的预警指标。因此，本研究在养殖第10、20、30、40、50和70天时，对3个中密度/半集约化养殖池塘（放养密度为40尾虾苗/立方米）与3个高密度/集约化养殖池塘（放养密度为90尾虾苗/立方米）的水体参数、可培养异养细菌（包括潜在致病性弧菌）的丰度进行了测定。此外，本研究通过16S扩增子测序技术，对池塘水体中的游离态细菌群落与附着态细菌群落进行了分析。在测定的环境参数中，悬浮颗粒物含量、盐度、叶绿素a、pH值与溶解氧浓度在集约化与半集约化养殖系统间存在显著差异。但两类养殖系统在无机营养盐含量、异养细菌丰度与潜在致病性弧菌丰度方面未表现出显著差异。细菌群落的优势类群为γ-变形菌纲（Gammaproteobacteria）、α-变形菌纲（Alphaproteobacteria）、黄杆菌纲（Flavobacteria）、芽孢杆菌纲（Bacilli）与放线菌纲（Actinobacteria）。盐单胞菌属（Halomonas）、嗜冷杆菌属（Psychrobacter）与盐格杆菌属（Salegentibacter）的操作分类单元（OTU）在两类养殖系统中均有检出，此类菌群可能参与硝化作用与氨氮去除过程。在附着态组分中，盐单胞菌属（Halomonas）、嗜冷杆菌属（Psychrobacter）与弧菌属（Vibrio）为丰度最高的菌属；而在两类系统的游离态组分中，均检出盐格杆菌属（Salegentibacter）、嗜硫杆菌属（Sulfitobacter）与盐单胞菌属（Halomonas）。此外，集约化养殖系统的颗粒物聚集体中弧菌属的丰度高于半集约化养殖系统。值得注意的是，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，在测定的环境参数中，盐度是解释游离态与附着态细菌群落组成格局的最优因子（解释度分别为R²=15.32%与12.81%）。综上，集约化养殖系统会改变水体水质并提升潜在病原细菌的流行率，但似乎并未促进细菌群落的多样性提升。