4.4.6. CAB as a source of cyanocobalamin synthesising prokaryotes
Organisms within all domains of life require the cofactor cobalamin (vitamin B12), which is usually produced only by a subset of bacteria and archaea [69]. Previous studies reported that the cobalamin in ocean surface water is due to de nova synthesis by Thaumarchaeota. Moreover, few members of Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes genomes were reported to have the cobalamin synthesising gene [69]. In our analysis, the CAB of Temora spp. was found to have a high proportion of Thaumarchaeota, whereas Alpha-gammaproteobacteria were found to be high in the CAB of Acartia spp., Calanus spp. andPleuromamma spp. In this regard, further studies on CAB diversity from different ocean realms would shine a light on the actual potential of CAB in the global biogeochemical cycles.
5. Conclusion
Herein, five copepod genera viz.Acartia spp., Calanus spp., Centropages sp.,Pleuromamma spp., and Temora spp., and their associated bacteriobiome were investigated. The use of meta-analysis in the present study reveals the difference in bacterial diversity indices within the alpha and beta-diversity. To be more specific, the meta-analysis showed significant variations in the alpha diversity between the copepod genera. Moreover, it revealed that Calanus spp have high Shannon index (H-index) and Pleuromamma spp. have high Faith’s Phylogenetic Diversity. Furthermore, the meta-analysis revealed that the CAB within the phylogenetically closer Pleuromamma spp. andCalanus spp. expressed a mere 7.604% (axis 1) dissimilarity distance in PCoA analysis (Unweighted Unifrac distance matrix based on the phylogenetic index). Likewise, from the meta-analysis, we were able to identify the bacterial taxa which are significantly abundant in each copepod genera in comparison with others.
In earlier studies, the core bacterial OTUs were identified based on their presence/absence [1] as well as by using distribution-based clustering (DBC) algorithms[2]. Herein, machine learning models were used to predict the important copepod associated bacterial genera within the five different copepod genera. In specific, we used supervised machine learning models to predict the important bacterial s-OTUs. We predicted 28 bacterial taxa and one archeael taxon (SML-GBC) as important s-OTUs in the five copepod genera. Among the predicted bacterial genera, in common, Vibrio shilonii, Acinetobacter johnsonii, Piscirickeesiaceae, and Phaeobacter were reported as important s-OTUs in the Calanus spp. and Marinobacter, Limnobacter. Methyloversatilis, Desulfovibrio, Enhydrobacter, Sphingobium, Alteromonas andCoriobacteriaceaewere predicted as important s-OTUs in Pleuromamma spp. for the first time. Additionally, the prediction accuracy (for Calanusspp. and Pleuromamma spp.) of the machine learning models used here showed high accuracy, which indicates the reliability of the predicted important s-OTUs in the copepod genera. Notably, from the machine learning-based classification it was evident that specific bacterial s-OTUs do exist for copepods.
Furthermore, our meta-analysis revealed that the five copepod genera have bacterial communities that are capable of mediating methanogenesis (with evidence of interlinking the methane production, DMSP degradation and phosphate utilisation) and methane oxidation. We also found the five copepod genera to have more potential Assimilatory Sulfur Reducing (ASR) microbial communities than the Dissimilatory Sulfate Reducing (DSR) communities within the CAB. Likewise, the bacterial community with potential genes involved in nitrogen fixation, denitrification and DNRA were also observed among the CAB of these five copepod genera. We also found the potential genes that perform carbon fixation, iron remineralisation and Cyanocobalamin (vitamin B12) synthesis in the CAB of the five copepod genera.