Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry

Abstract

Linking ‘omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as ‘biosensors’ for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

“…We could advocate achieving this via comparative genomics, but this usually necessitates hundreds to thousands of closely related genomes (for review see Read and Massey, 2014;Chen and Shapiro, 2015), as well as a refined phenotypic characterization of the sequenced strains. Alternatively, one could search in situ data for genes or substitutions related to a particular niche or environmental parameter (see e.g., Kent et al, 2016;Grébert et al, 2018;Ahlgren et al, 2019;Garcia et al, 2020). Given the wealth of marine metagenomes that are becoming available for a large variety of environmental niches, such an approach should be particularly powerful to unveil niche adaptation processes in the forthcoming years.…”

High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects

“…Due to their rapid generation times and high diversity, microbial genomes integrate the impact of environmental change 13 and can be used a 'biosensor' of subtle biogeochemical regimes that cannot be identified from physical parameters alone 12,[14][15][16] . Thus, the fields of microbial ecology and oceanography would benefit from coordinated, high resolution measurements of marine 'omics products (i.e., metagenomes, metatranscriptomes, metaproteomes, etc.).…”

Toward Determining the Spatio-Temporal Variability of Upper-Ocean Ecosystem Stoichiometry From Satellite Remote Sensing

“…(E) Satellite-derived C phyto :POC at BATS (solid line) and at HOT (dotted line). stoichiometry models (Garcia et al, 2020) as phytoplankton turnover happens quickly on a time scale of days (Malone et al, 1993). For a complete understanding of the temporal variability of phytoplankton and bulk C:P, measurements of phytoplanktonspecific C:P using high-throughput flow cytometry (Graff et al, 2015;Kirchman, 2016) or single-probe mass spectrometry (Sun et al, 2018) would be necessary.…”

“…For a complete understanding of the temporal variability of phytoplankton and bulk C:P, measurements of phytoplanktonspecific C:P using high-throughput flow cytometry (Graff et al, 2015;Kirchman, 2016) or single-probe mass spectrometry (Sun et al, 2018) would be necessary. Linking metagenomics data with the phytoplankton stoichiometry model and remote sensing may also help improve C:P estimates in the subtropics (Garcia et al, 2020).…”