Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes

Abstract

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.

Feeding strategy and dietary preference shape the microbiome of epipelagic copepods in a warm nutrient‐impoverished ecosystem

“…C. ponticus showed several interactions with both clusters, suggesting that the ability to switch between filter and ambush feeding behavior (Benedetti et al, 2016) might allow this species to harbor a more diverse microbial community. Thus, feeding strategy may shape the copepod microbiota, as has been suggested in previous studies (De Corte et al, 2018;Sadaiappan et al, 2021;Tang et al, 2010). nana are omnivores, targeting a variety of prey types (phytoplankton, detritus, or smaller zooplankton) (Benedetti et al, 2016) while…”

“…Based on the assumption that microbial composition might reflect the host dietary preferences and feeding behavior, it is possible to assume that Calanus and Pleuromamma would display low microbial diversity as does Temora. However, Sadaiappan et al (2021) showed that Calanus and Pleuromamma exhibited more diverse microbial communities than Temora, suggesting that other ecological traits such as diel vertical migration may be contributing to the microbial compositional variation of the copepods. While…”

“…nana were more diverse than those of T. stylifera. Such differences in microbiota diversity can be attributed to the copepod ecological traits such as diel vertical migration, feeding strategy, and dietary preferences (Datta et al, 2018;Sadaiappan et al, 2021), or/and to the changes in the environment (Bickel et al, 2014;Skovgaard et al, 2015).…”

“…Host-associated microbial interactions are essential for the maintenance of any ecosystem (Sadaiappan et al, 2021), thereby examining the ecological associations between copepods, microorganisms, and their environment is imperative for understanding nutrient-limited ecosystems such as the Southeastern Mediterranean Sea, where the copepod-associated microbial communities have not been previously described.…”

Comparative Genomics on Cultivated and Uncultivated Freshwater and Marine “CandidatusManganitrophaceae” Species Implies Their Worldwide Reach in Manganese Chemolithoautotrophy

“…Read pairs were merged and dereplicated and chimera removed with the “pooled” setting using DADA2 ( 52 ). Taxonomic assignments for the resulting amplicon sequencing variants (ASVs) used a pretrained naive Bayes classifier on the full-length 16S rRNA genes in the SILVA 138 SSURef NR99 database ( 53 , 54 ). ASVs assigned to the same level 7 taxonomy were combined, and those assigned to mitochondria or chloroplast or without taxonomy assignments were removed using the –p-exclude mitochondria,chloroplast,“Bacteria;Other;Other;Other;Other;Other,”“Unassigned;Other;Other;Other;Other;Other” setting.…”