In 2022, with the full cooperation of a number of technical support and bioinformatics engineers, the report of Lingen Biology will be upgraded with a major upgrade! The amplicon analysis process items range from 60+ to 120+, which can be described as a value-added update with no price increase! The resulting pictures of the final report can be directly used for the publication of the article, let’s take a look! A small example: In the research paper "Apex Predators Enhance Environmental Adaptation but Reduce Community Stability of Bacterioplankton in Crustacean Aquaculture Ponds" recently published by the Chinese Academy of Fishery Sciences in the "International Journal of Molecular Sciences" (IF=6.208), through The amplicon sequencing of the 16S V4-V5 region revealed the response mechanism of top predators interfering with the bacterioplankton community in aquaculture systems. Teachers, please pay attention to the pictures of the article.
期刊：International Journal of Molecular Sciences
Impact factor: 6.208
Release time: 2022
Sample type: water sample
Client Unit: Chinese Academy of Fishery Sciences
1. Research background
The growing global population has increased the demand for food, and aquatic products are an expanding basic food source in recent years. Aquaculture environments harbor complex bacterial communities that are critical to the growth and health of cultured species. Apex predators occupy positions at the top of food webs and play a key role in ecosystem stability, so apex predators are often added to aquaculture ponds. However, studies exploring the effects of apex predators on the composition and function of bacterioplankton communities, as well as the mechanisms underlying community aggregation, are limited. The research aimed to investigate the aggregation dynamics of bacterioplankton communities in aquaculture systems influenced by apex predator species, and to decipher the mechanisms underlying changes in bacterioplankton populations induced by apex predator disturbance.
2. Experimental design
Eight culture ponds including Chinese mitten crab ( Eriocheir sinensis ) and Japanese giant river prawn ( Macrobrachium niponensis ) were studied in this study. Four of these ponds contained mandarin fish ( Siniperca chuatsi ) as the apex predator (group PC), and the other four ponds had no apex predator (group MC). During the aquaculture process, five water samples were collected and mixed from each pond in four stages, and bacterial cells were collected by 2 L water sample filters for each sample, and environmental factors were determined from the remaining water samples. Subsequently, DNA extraction and 16S rRNA V4-V5 region sequencing were carried out and data analysis was performed.
3. Experimental results
1. Phytoplankton alpha diversity
Four α-diversity indices were calculated to assess the bacterioplankton community. No significant differences were observed for any α-diversity indicator between bacterioplankton populations at different culture stages, or between MC and PC ponds. The results showed that the diversity of the bacterioplankton community tended to be stable during the culture process, and it was not significantly affected by apex predator disturbance.
2. Changes in the bacterioplankton community at different culture stages with or without top predator interference
The PCoA of the Bray–Curtis distance indicated that the bacterioplankton communities at different culture stages were clustered together (Fig. 1a), and that both predator apex disturbance and their interactions significantly affected the bacterioplankton communities. The relative abundance of bacteria at the phylum level is shown in Fig. 1b. Proteobacteria is the most important phylum, followed by Bacteroidetes, Firmicutes and Actinobacteria. As the culture progresses, the bacteria of different phyla have different changes. The results showed that apex predator disturbance did not significantly alter the bacterioplankton composition during culture, but it did affect the magnitude of changes in bacterial abundance.
Using a random forest model, it was determined that the composition of the bacterial community was strongly correlated with the culture stage and apex predator disturbance (Fig. 1c). Combining the results of overall changes in the bacterioplankton community with those from the random forest model analysis revealed that apex predators significantly altered the abundance of low-abundance species, but they did not significantly alter the overall community composition.
Fig.1 Variation of bacterioplankton community with culture stage and predator distribution apex
3. Environmental adaptation of bacterioplankton communities
测量了八个环境因素，以评估培养阶段和顶端捕食者的影响。MC和PC池塘中浮游细菌群落的65.89%的变异可由选定的环境因素解释（图2a）。除溶解氧、亚硝酸盐和总磷外，大多数环境因素与浮游细菌群落之间存在显著相关性。不同培养阶段的浮游细菌群落被环境因素明显区分。从第一阶段开始，水温与浮游细菌群落呈正相关，而氨和pH值与菌群成负相关。此外，硝酸盐和TN浓度分别与第二阶段和第三阶段至第四阶段的浮游细菌群落呈负相关。
此外，还研究了关键属的相对丰度与环境因素之间的相关性（图2b），利用环境广度研究了浮游细菌对环境因素的响应，PC池塘中浮游细菌群落的环境广度比MC池塘大（图2c）。这一结果表明，在具有捕食者干扰的养殖池塘中，浮游细菌群落具有更强的环境适应能力。
图2 浮游细菌群落的环境适应
4、顶端捕食者影响的浮游细菌群落组成机制
基于零模型估计了确定性过程和随机过程对MC和PC池塘浮游细菌群落聚集的相对贡献，群落聚集以随机过程为主（图3a）。与MC样本相比，确定性过程更有助于PC池塘中浮游细菌群落的聚集（图3b）。均质扩散是一个随机过程，是形成MC和PC池塘中浮游细菌群落的主要生态过程，PC样本中漂变的相对贡献率显著低于MC池塘中的漂变贡献率（图3c）。这些发现表明，顶端捕食者干扰通过改善环境过滤和减少漂移，增强了确定性过程对浮游细菌群落聚集的相对贡献。
图3浮游细菌群落的聚集受到顶端捕食者的影响
5、顶端捕食者对浮游细菌生态功能的影响
利用FAPROTAX软件预测了浮游细菌群落的功能特征，并确定了各组之间的显著差异。在MC和PC池塘中，与化能异养相关的功能在浮游细菌群落中占主导地位，第二阶段的浮游细菌群落的发酵功能显著提高（图4a）。
Tax4Fun2的KEGG功能分析结果（图4b）表明，随着捕食者干扰的加剧，养殖池塘中浮游细菌的功能冗余减少。此外，βNTI与MC池塘中浮游细菌的FRI变化显著正相关，而PC池塘中则无明显相关（图4c），这意味着生态群落过程对具有顶端捕食者的养殖池塘中浮游细菌的功能影响很小。
图4 受顶端捕食者影响的浮游细菌群落的生态功能
6、顶端捕食者对浮游细菌群落稳定性的影响
为了调查水产养殖池塘中的浮游细菌模式，构建了MC和PC样本的MEN（图5），这两个MEN之间的拓扑特性差异表明，它们与PC池塘中的浮游细菌略有关联。所有指标都表明，在没有捕食者顶端干扰的养殖池塘中，浮游细菌的MEN具有较高的稳定性。
图5 浮游细菌群落的稳定性受到顶端捕食者的影响
7、顶端捕食者形成细菌浮游生物的机制
水温、pH、氨和TN与MC池塘浮游细菌的βMNTD显著相关，同时，水温、氨、氮和硝酸盐与PC池塘中浮游细菌的βMNTD显著相关。其中，只有硝酸盐浓度与PC池塘中浮游细菌的系统发育差异显著相关，而MC池塘中则没有相关关系（图6a）。
基于数据构建了一个概念框架来描述有和没有顶端捕食者的水产养殖池塘中浮游细菌群落的变化过程（图6b）。最终，具有顶端捕食者的养殖池塘中的浮游细菌表现出较高的环境适应能力，但功能冗余度和群落稳定性较低。
图6 具有顶端捕食者的浮游细菌群落的形成机制
四、研究结论
研究结果表明，甲壳动物养殖池塘不同养殖阶段浮游细菌群落的组成和功能存在显著差异。有捕食者的养殖池塘提供了更好的养殖环境。在顶端捕食者干扰下，硝酸盐在调节浮游细菌群落聚集的随机过程和确定性过程之间的平衡方面起着决定性作用，同时，顶端捕食者导致了更广泛的环境适应，但功能冗余度和群落稳定性较低。
参考文献
Apex Predators Enhance Environmental Adaptation but Reduce Community Stability of Bacterioplankton in Crustacean Aquaculture Ponds. Int J Mol Sci. 2022;23
Doi 10.3390/ijms231810785