Plankton Ecology Lab, Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Panaji, Goa, 403004, India.
Department of Bioengineering, Imperial College London, South Kensington, London, SW72AZ, UK.
Sci Rep. 2021 Feb 8;11(1):3312. doi: 10.1038/s41598-021-82482-z.
Copepods are the dominant members of the zooplankton community and the most abundant form of life. It is imperative to obtain insights into the copepod-associated bacteriobiomes (CAB) in order to identify specific bacterial taxa associated within a copepod, and to understand how they vary between different copepods. Analysing the potential genes within the CAB may reveal their intrinsic role in biogeochemical cycles. For this, machine-learning models and PICRUSt2 analysis were deployed to analyse 16S rDNA gene sequences (approximately 16 million reads) of CAB belonging to five different copepod genera viz., Acartia spp., Calanus spp., Centropages sp., Pleuromamma spp., and Temora spp.. Overall, we predict 50 sub-OTUs (s-OTUs) (gradient boosting classifiers) to be important in five copepod genera. Among these, 15 s-OTUs were predicted to be important in Calanus spp. and 20 s-OTUs as important in Pleuromamma spp.. Four bacterial s-OTUs Acinetobacter johnsonii, Phaeobacter, Vibrio shilonii and Piscirickettsiaceae were identified as important s-OTUs in Calanus spp., and the s-OTUs Marinobacter, Alteromonas, Desulfovibrio, Limnobacter, Sphingomonas, Methyloversatilis, Enhydrobacter and Coriobacteriaceae were predicted as important s-OTUs in Pleuromamma spp., for the first time. Our meta-analysis revealed that the CAB of Pleuromamma spp. had a high proportion of potential genes responsible for methanogenesis and nitrogen fixation, whereas the CAB of Temora spp. had a high proportion of potential genes involved in assimilatory sulphate reduction, and cyanocobalamin synthesis. The CAB of Pleuromamma spp. and Temora spp. have potential genes accountable for iron transport.
桡足类是浮游动物群落中的优势成员，也是最丰富的生命形式。为了确定与桡足类相关的细菌生物群（CAB）中与桡足类相关的特定细菌分类群，并了解它们在不同桡足类之间的变化，了解桡足类相关的细菌生物群（CAB）是至关重要的。分析 CAB 中的潜在基因可能揭示它们在生物地球化学循环中的内在作用。为此，使用机器学习模型和 PICRUSt2 分析方法对属于五个不同桡足类属的 CAB 的 16S rDNA 基因序列（约 1600 万条读取）进行了分析，这五个桡足类属分别是：真刺唇角水蚤属、磷虾属、中剑水蚤属、胸刺水蚤属和长刺水蚤属。总体而言，我们预测在五个桡足类属中有 50 个亚 OTU（梯度提升分类器）很重要。在这些亚 OTU 中，有 15 个被预测在磷虾属中很重要，20 个在胸刺水蚤属中很重要。有四个细菌亚 OTU（约翰逊不动杆菌、噬菌杆菌、希氏弧菌和鱼立克次体科）被鉴定为磷虾属中的重要亚 OTU，而 Marinobacter、副球菌、脱硫弧菌、利姆诺杆菌、黄杆菌、甲基盐单胞菌、产甲烷菌和 Coriobacteriaceae 被预测为胸刺水蚤属中的重要亚 OTU，这是首次报道。我们的荟萃分析表明，胸刺水蚤属的 CAB 中具有高比例的潜在基因，这些基因与甲烷生成和固氮有关，而长刺水蚤属的 CAB 中则具有高比例的与同化硫酸盐还原和钴胺素合成有关的潜在基因。胸刺水蚤属和长刺水蚤属的 CAB 中都具有与铁运输有关的潜在基因。
