Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries

Abstract

Global oceanographic monitoring initiatives started by measuring abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling. There is, however, a large gap between the taxonomic information produced by bacterial genomic analyses and information on bacterial functions, which is sought by biogeochemists, ecologists, and modellers. Here, we provide a mechanistic understanding of how a bacterial marker gene (16S rRNA) can be used to derive latitudinal trends for core metabolic pathways and, ultimately, be used for mapping ecosystem function change in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we identified ten metabolic pathways, which were related to ecological processes of primary productivity, temperature-regulated growth, coping strategies for nutrient limitation, energy metabolism, and degradation. We compared and contrasted these metabolic pathways with measured physico-biochemical parameters within and between oceanographic provinces, and found that functional diversity is as affected by oceanographic boundaries as is taxonomic composition. This study demonstrates that bacterial marker gene data, sampled and analysed with low costs and high throughput, can be used to infer on metabolic changes at the community scale. Such analyses may provide insight into the drivers of ecological changes and, overall, into the effects of biodiversity on marine ecosystem functioning.

Particle‐associated and free‐living bacterial communities in an oligotrophic sea are affected by different environmental factors

“…An important, yet speculative, observation is that predicted pathways for the metabolism of anthropogenic pollutants, including pesticides, petroleum products and plastics, are enriched in the PA community versus the FL one. These results are based on an inference of community metagenomes, an approach that has recently been proposed to identify metabolic changes underlying bacterioplankton biogeography (Raes et al ., 2021). Nevertheless, this approach may be biased by many factors, including unequal representation of different heterotrophic bacterial lineages in the genomic databases and genomic variability between taxa with closely related 16S rRNA sequences (e.g.…”

Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries

“…For a list of all analyses performed and detailed information and citations regarding the software versions of the R packages used in analyses, please refer to the Supplementary methods. The workflow code for the analyses reported in our study are available on GitHub 68 .…”

“…pangaea.de/10.1594/PANGAEA.884052. All the code, key data files, and workflows to reproduce the analyses and figures are available on GitHub 68 .…”