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Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.

Global change experiments often observe shifts in bacterial community composition based on 16S rRNA gene sequences. However, this genetic region can mask a large amount of genetic and phenotypic variation among bacterial strains sharing even identical 16S regions. As such, it remains largely unknown whether variation at the sub-16S level, sometimes termed microdiversity, responds to environmental perturbations and whether such changes are relevant to ecosystem processes. Here, we investigated microdiversity within Curtobacterium, the dominant bacterium found in the leaf litter layer of soil, to simulated drought and nitrogen addition in a field experiment. We first developed and validated Curtobacterium-specific primers of the groEL gene to assess microdiversity within this lineage. We then tracked the response of this microdiversity to simulated global change in two adjacent plant communities, grassland and coastal sage scrub (CSS). Curtobacterium microdiversity responded to drought but not nitrogen addition, indicating variation within the genus of drought tolerance but not nitrogen response. Further, the response of microdiversity to drought depended on the ecosystem, suggesting that litter substrate selects for a distinct composition of microdiversity that is constrained in its response, perhaps related to tradeoffs in resource acquisition traits. Supporting this interpretation, a metagenomic analysis revealed that the composition of Curtobacterium-encoded carbohydrate-active enzymes (CAZymes) varied distinctly across the two ecosystems. Identifying the degree to which relevant traits are phylogenetically conserved may help to predict when the aggregated response of a 16S-defined taxon masks differential responses of finer-scale bacterial diversity to global change. IMPORTANCE Microbial communities play an integral role in global biogeochemical cycling, but our understanding of how global change will affect microbial community structure and functioning remains limited. Microbiome analyses typically aggregate large amounts of genetic diversity which may obscure finer variation in traits. This study found that fine-scale diversity (or microdiversity) within the bacterial genus Curtobacterium was affected by simulated global changes. However, the degree to which this was true depended on the type of global change, as the composition of Curtobacterium microdiversity was affected by drought, but not by nitrogen addition. Further, these changes were associated with variation in carbon degradation traits. Future work might improve predictions of microbial community responses to global change by considering microdiversity.

Global changes such as increased drought and atmospheric nitrogen deposition perturb both the microbial and plant communities that mediate terrestrial ecosystem functioning. However, few studies consider how microbial responses to global changes may be influenced by interactions with plant communities. To begin to address the role of microbial–plant interactions, we tested the hypothesis that the response of microbial communities to global change depends on the plant community. We characterized bacterial and fungal communities from 395 plant litter samples taken from the Loma Ridge Global Change Experiment, a decade-long global change experiment in Southern California that manipulates rainfall and nitrogen levels across two adjacent ecosystems, a grassland and a coastal sage scrubland. The differences in bacterial and fungal composition between ecosystems paralleled distinctions in plant community composition. In addition to the direct main effects, the global change treatments altered microbial composition in an ecosystem-dependent manner, in support of our hypothesis. The interaction between the drought treatment and ecosystem explained nearly 5% of the variation in bacterial community composition, similar to the variation explained by the ecosystem-independent effects of drought. Unexpectedly, we found that the main effect of drought was approximately four times as strong on bacterial composition as that of nitrogen addition, which did not alter fungal or plant composition. Overall, the findings underscore the importance of considering plant–microbe interactions when considering the transferability of the results of global change experiments across ecosystems.

The Indian Ocean accounts for about one fifth of global ocean net primary production but remains undersampled relative to other major ocean basins. The eastern tropical Indian Ocean is characterized by extremely low concentrations of both macronutrients and the micronutrient iron. We measured concentrations of dissolved and particulate trace metals (Fe, Mn, Zn, Pb) in the upper ocean along the GO-SHIP IO9N transect (28˚S to 17˚N, mostly along the 95˚E meridian) during a cruise in April 2016. Cellular quotas (metal/C) of Fe, Mn, Co, Ni, Cu, and Zn were measured in small eukaryotic flagellates (2–7 μm). Deckboard bottle incubation experiments were conducted at one station in each of three putative biogeochemical regions: southern Indian Ocean gyre (SIO, 28-10˚S); equatorial Indian Ocean (EqIO, 10˚S - 5˚N); Bay of Bengal (BoB, 5-17˚N). Nitrate and phosphate were below detection limits in surface waters across the transect. Dissolved and particulate Fe were

El Niño Southern Oscillation (ENSO) influences multi-year variation in sea-surface temperature and the intensity of upwelling in many Pacific regions. However, it is currently unknown how El Niño conditions will affect the concentration and elemental ratios of particulate organic matter (POM). To investigate this, we have quantified POM weekly for 6 years (2012 to 2017) at the MICRO time-series station in the Southern California Bight. We found a strong influence of the 2015 El Niño on sea-surface temperature and phosphate concentration but to a lesser extent on nitrate availability. The 2015 El Niño also resulted in a short-term depression in POC and POP concentrations, whereas PON concentrations displayed an independent long-term decline regardless of the El Niño event. Reduced POM concentrations resulting from the 2015 El Niño occurred in parallel to high C:P and N:P ratios. Following the changes in PON, C:N continued to climb reaching ~9.4 at the end of our sampling period. We suggest that an Eastern Pacific- vs. a Central Pacific-type El Niño as well as a switch in the Pacific Decadal Oscillation phase significantly altered the local response in POM concentrations and ratios.

To better understand mechanisms of carbon (C) and nitrogen (N) dynamics under anthropogenic N enrichment, we examined frequencies of C- and N-targeting genes in litter fungi. In particular, we tested the hypothesis that N enrichment selects for C-targeting genes but against N-targeting genes, if fungi preferentially invest resources in acquisition of growth-limiting nutrients. We conducted a fully-factorial litter and microbial transplant in a N fertilization experiment in Southern California grassland. The transplant design enabled us to contrast direct effects of N fertilization in the environment, indirect effects of N-induced shifts in the microbial community, and indirect effects of N-induced changes in plant litter chemistry. For each treatment, we assessed frequencies of select well-annotated fungal functional genes: cellulose-targeting AA9 genes (for C acquisition) versus ammonium transporter genes and amino acid permease genes (for N acquisition). We found that our hypothesis was upheld only with regard to shifts in the microbial community. Specifically, when grown in the same environment and litter, fungi from the N-fertilized plots displayed greater frequencies of cellulose-targeting AA9 genes from basidiomycetes, but smaller frequencies of ammonium transporter genes and amino acid permease genes, when compared to fungi from the control plots. In contrast, N fertilization in the plot environment was associated with higher frequencies of amino acid permease genes and ammonium transporter genes. Likewise, plant litter from the N-fertilized plots selected for higher frequencies of ammonium transporter genes. Altogether, we found fairly inconsistent effects of N enrichment on fungal functional genes related to C and N acquisition. Even if the genetic capacity of the fungal community to acquire C versus N changes owing to shifts in the microbial community, direct effects of N fertilization and indirect effects of litter chemistry may offset the response.

The ratio of elements such as carbon:nitrogen:phosphorus (C:N:P) in phytoplankton is known to vary substantially within single isolates and across environmental gradients. In addition, C:N:P is known to vary throughout the day due to diel patterns in nutrient acquisition and storage. It has been hypothesized that small phytoplankton such as marine cyanobacteria have relatively invariable elemental ratios during a 24 h period, whereas larger phytoplankton have a greater capacity to store elements and thus a wider diel range of C:N:P. To test this hypothesis, we examined diel variability in cellular C:N:P, using a chemostat culturing system, for one of the most abundant marine cyanobacteria, Synechococcus (WH8102) during two 24 h periods. The cellular C quota nearly doubled during the 14 h light period and was subsequently reduced during the dark period. The cellular N quota also varied considerably, whereas the P quota remained relatively stable. These daily changes in elemental quotas led to highly variable C:Ncell and C:Pcell. Furthermore, the magnitude of variability in cellular elemental stoichiometry of Synechococcus was positively related to the growth rate. We constructed a model to test the extent to which variation in C:Ncell and C:Pcell is related to reserve carbon accumulation and depletion over each light-dark cycle. Results imply that, in addition to growth-related respiratory losses, Synechococcus also purges excess C during the dark period in order to maintain a nutritive balance within cells. Our data suggest that diel variation in C:Ncell and C:Pcell of Synechococcus is of the same order of magnitude as stoichiometric variation within plankton communities between major ocean environments.

Recent studies have revealed clear regional differences in the particulate organic matter composition and stoichiometry of plankton communities. In contrast, less is known about potential mechanisms and patterns of temporal changes in the elemental composition of marine systems. Here, we monitored weekly changes in environmental conditions, phytoplankton abundances, and particulate organic carbon, nitrogen, and phosphorus concentrations over a 3-yr period. We found that variation in the particulate organic matter (POM) concentrations and ratios were related to seasonal oscillations of environmental conditions and phytoplankton abundances. Periods with low temperature, high nutrient concentrations and a dominance of large phytoplankton corresponded to low C: N: P and vice-versa for warmer periods during the summer and fall. In addition to seasonal changes, we observed a multiyear increase in POM C: P and N: P that might be associated with the Pacific Decadal Oscillation. Finally, there was substantial short-term variability in all factors but similar linkages between environmental variability and elemental composition as observed on seasonal and interannual time-scales. Using a feed-forward neural network, we could explain a large part of the variation in POM concentrations and ratios based on changes in environmental conditions and phytoplankton abundances. The apparent links across all time-scales between changes in physics, chemistry, phytoplankton, and POM concentrations and ratios suggest we have identified key controls of the elemental composition of marine communities in this region.

The elemental composition of particulate organic matter in the surface ocean significantly affects the efficiency of the ocean's store of carbon. Though the elemental composition of primary producers is an important factor, recent observations from the western North Atlantic Ocean revealed that carbon-to-nitrogen ratios (C:N) of phytoplankton were significantly higher than the relatively homeostatic ratio of the total particulate pool (particulate organic carbon:particulate organic nitrogen; POC:PON). Here we use an idealized ecosystem model to show how interactions between primary and secondary producers maintain the mean composition of surface particulates and the difference between primary producers and bulk material. Idealized physiological models of phytoplankton and microzooplankton, constrained by laboratory data, reveal contrasting autotrophic and heterotrophic responses to nitrogen limitation: under nitrogen limitation, phytoplankton accumulate carbon in carbohydrates and lipids while microzooplankton deplete internal C reserves to fuel respiration. Global ecosystem simulations yield hypothetical global distributions of phytoplankton and microzooplankton C:N ratio predicting elevated phytoplankton C:N ratios in the high-light, low-nutrient regions of the ocean despite a lower, homeostatic POC:PON ratio due to respiration of excess carbon in systems subject to top-down control. The model qualitatively captures and provides a simple interpretation for, a global compilation of surface ocean POC:PON data.

Nitrogen (N) and phosphorus (P) availability, in addition to other macro- and micronutrients, determine the strength of the ocean's carbon (C) uptake, and variation in the N : P ratio of inorganic nutrient pools is key to phytoplankton growth. A similarity between C : N : P ratios in the plankton biomass and deep-water nutrients was observed by Alfred C. Redfield around 80 years ago and suggested that biological processes in the surface ocean controlled deep-ocean chemistry. Recent studies have emphasized the role of inorganic N : P ratios in governing biogeochemical processes, particularly the C : N : P ratio in suspended particulate organic matter (POM), with somewhat less attention given to exported POM and dissolved organic matter (DOM). Herein, we extend the discussion on ecosystem C : N : P stoichiometry but also examine temporal variation in stoichiometric relationships. We have analyzed elemental stoichiometry in the suspended POM and total (POM + DOM) organic-matter (TOM) pools in the upper 100 m and in the exported POM and subeuphotic zone (100-500 m) inorganic nutrient pools from the monthly data collected at the Bermuda Atlantic Time-series Study (BATS) site located in the western part of the North Atlantic Ocean. C : N and N : P ratios in TOM were at least twice those in the POM, while C : P ratios were up to 5 times higher in TOM compared to those in the POM. Observed C : N ratios in suspended POM were approximately equal to the canonical Redfield ratio (C : N : P = 106 : 16 : 1), while N : P and C : P ratios in the same pool were more than twice the Redfield ratio. Average N : P ratios in the subsurface inorganic nutrient pool were ∼ 26 : 1, squarely between the suspended POM ratio and the Redfield ratio. We have further linked variation in elemental stoichiometry to that of phytoplankton cell abundance observed at the BATS site. Findings from this study suggest that elemental ratios vary with depth in the euphotic zone, mainly due to different growth rates of cyanobacterial cells. We have also examined the role of the Arctic Oscillation on temporal patterns in C : N : P stoichiometry. This study strengthens our understanding of the variability in elemental stoichiometry in different organic-matter pools and should improve biogeochemical models by constraining the range of non-Redfield stoichiometry and the net relative flow of elements between pools.

Bacteria and fungi drive the decomposition of dead plant biomass (litter), an important step in the terrestrial carbon cycle. Here we investigate the sensitivity of litter microbial communities to simulated global change (drought and nitrogen addition) in a California annual grassland. Using 16S and 28S rDNA amplicon pyrosequencing, we quantify the response of the bacterial and fungal communities to the treatments and compare these results to background, temporal (seasonal and interannual) variability of the communities. We found that the drought and nitrogen treatments both had significant effects on microbial community composition, explaining 2-6% of total compositional variation. However, microbial composition was even more strongly influenced by seasonal and annual variation (explaining 14-39%). The response of microbial composition to drought varied by season, while the effect of the nitrogen addition treatment was constant through time. These compositional responses were similar in magnitude to those seen in microbial enzyme activities and the surrounding plant community, but did not correspond to a consistent effect on leaf litter decomposition rate. Overall, these patterns indicate that, in this ecosystem, temporal variability in the composition of leaf litter microorganisms largely surpasses that expected in a short-term global change experiment. Thus, as for plant communities, future microbial communities will likely be determined by the interplay between rapid, local background variability and slower, global changes.

Differences in relative availability of nitrate vs. phosphate may contribute to regional variations in plankton elemental stoichiometry. As a representative of the globally abundant marine Synechococcus, strain WH8102 was grown in 16 chemostats up to 52 d at a fixed growth rate with nitrogen-phosphorus ratios (N : Psupply) of 1-50. Initially, the phosphate and nitrate concentrations in the vessel decreased when the respective nutrient was limiting. Cell growth generally stabilized, although several chemostats had apparent oscillations in biomass. We observed extensive plasticity in the elemental content and ratios. N : Pcell matched the supply values between N : Psupply 5 and 20. The C : Pcell followed a similar trend. In contrast, the mean C : Ncell was 6.8 and did not vary as a function of supply ratios. We also observed that induction of alkaline phosphatase, the fraction of P allocated to nucleic acids, and the lipid sulfoquinovosyldiacylglycerol : phosphatidyglycerol ratio inversely correlated with P availability. Our results suggest that this extensive plasticity in the elemental content and ratios depends both on the external nutrient availability as well as past growth history. Thus, our study provides a quantitative understanding of the regulation of the elemental stoichiometry of an abundant ocean phytoplankton lineage.

Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ∼17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.

The ratio of carbon (C) to phosphorus (P) in marine phytoplankton is thought to be constant throughout the worlds'oceans. Known as the Redfield ratio, this relationship describes the links between carbon and phosphorus cycling and marine ecosystems. However, variations in the stoichiometry of phytoplankton have recently been identified, in particular strong latitudinal variability. Here we assess the impact of this variability in the C:P ratio of biomass on the C:P ratio of organic matter that is exported to the deep ocean using a biogeochemical inverse-model based on a data-constrained ocean circulation model and a global database of dissolved inorganic carbon and phosphate measurements. We identify global patterns of variability in the C:P ratios of exported organic matter, with higher values in the nutrient-depleted subtropical gyres, where organic matter export is relatively low, and lower ratios in nutrient-rich upwelling zones and high-latitude regions, where organic matter export is high. This suggests that total carbon export is relatively constant throughout the oceans, in agreement with recent estimates of carbon fluxes. We conclude that the latitudinal patterns of C:P in exported organic matter are consistent with the large-scale stoichiometric variations in phytoplankton C:P. We suggest that a future expansion of nutrient-depleted waters could result in a shift to more efficient C export that compensates for the expected decline in productivity.

Marine microbial communities mediate many biogeochemical transformations in the ocean. Consequently, processes such as primary production and carbon (C) export are linked to nutrient regeneration and are influenced by the resource demand and elemental composition of marine microbial biomass. Laboratory studies have demonstrated that differential partitioning of element resources to various cellular components can directly influence overall cellular elemental ratios, especially with respect to growth machinery (i.e., ribosomal RNA) and phosphorus (P) allocation. To investigate whether allocation to RNA is related to biomass P content and overall C: P biomass composition in the open ocean, we characterized patterns of P allocation and C: P elemental ratios along an environmental gradient of phosphate supply in the North Atlantic subtropical gyre (NASG) from 35.67° N, 64.17° W to 22.676° N, 65.526° W. Because the NASG is characterized as a P-stressed ecosystem, we hypothesized that biochemical allocation would reflect sensitivity to bioavailable phosphate, such that greater phosphate supply would result in increased allocation toward P-rich RNA for growth. We predicted these changes in allocation would also result in lower C: P ratios with increased phosphate supply. However, bulk C: P ratios were decoupled from allocation to nucleic acids and did not appear to vary systematically across a phosphate supply gradient of 2.2-14.7 μ4mol m-2 d-1. Overall, we found that C: P ratios ranged from 188 to 306 along the transect, and RNA represented only 6-12% of total particulate P, whereas DNA represented 11-19%. We did find that allocation to RNA was positively correlated with phosphate supply rate, suggesting a consistent physiological response in biochemical allocation to resource supply within the whole community. These results suggest that community composition and/or nonnucleic acid P pools may influence ecosystem-scale variation in C: P stoichiometry more than nucleic acid allocation or P supply in diverse marine microbial communities. ©Author(s) 2014.

Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms in oligotrophic waters and responsible for a significant percentage of the earth's primary production. Here we developed a method for metagenomic sequencing of sorted Prochlorococcus and Synechococcus populations using a transposon-based library preparation technique. First, we observed that the cell lysis technique and associated amount of input DNA had an important role in determining the DNA library quality. Second, we found that our transposon-based method provided a more even coverage distribution and matched more sequences of a reference genome than multiple displacement amplification, a commonly used method for metagenomic sequencing. We then demonstrated the method on Prochlorococcus and Synechococcus field populations from the Sargasso Sea and California Current isolated by flow cytometric sorting and found clear environmentally related differences in ecotype distributions and gene abundances. In addition, we saw a significant correspondence between metagenomic libraries sequenced with our technique and regular sequencing of bulk DNA. Our results show that this targeted method is a viable replacement for regular metagenomic approaches and will be useful for identifying the biogeography and genome content of specific marine cyanobacterial populations. © 2014, American Society for Microbiology.

In most terrestrial environments, our knowledge of the elemental composition and stoichiometry of microorganisms stems from indirect whole community analyses. In contrast, we have little direct knowledge of the elemental composition of specific microorganisms and the variation between and within Fungi and Bacteria. To address this issue, we isolated and identified the elemental content of 87 strains of Fungi and Bacteria isolated from grassland leaf litter. The isolated strains were affiliated with a broad range of diversity including Ascomycota and Basidiomycota for Fungi, and Proteobacteria, Bacteroidetes, and Actinobacteria for Bacteria. The C:P and C:N but not N:P ratios were significantly higher in Fungi than in Bacteria. Extensive strain variation in elemental composition was partly linked to phylogeny and growth rate. Across all strains, the geometric mean C:N:P was 88:15:1. This overall ratio was significantly higher than reported for other leaf litter and terrestrial whole communities but closer to the canonical Redfield ratio characterizing marine microorganisms. This result warrants further investigation into the discrepancy between whole community and isolated strain elemental ratios. © 2014 Elsevier Ltd.

Abstract. Marine microbial communities mediate many biogeochemical transformations in the ocean. Consequently, processes such as primary production and carbon (C) export are linked to nutrient regeneration and are influenced by the resource demand and elemental composition of marine microbial biomass. Laboratory studies have demonstrated that differential partitioning of element resources to various cellular components can directly influence overall cellular elemental ratios, especially with respect to growth machinery (i.e., ribosomal RNA) and phosphorus (P) allocation. To investigate whether allocation to RNA is related to biomass P content and overall C : P biomass composition in the open ocean, we characterized patterns of P allocation and C : P elemental ratios along an environmental gradient of P-supply in the North Atlantic subtropical gyre (NASG) from 35.67° N 64.17° W to 22.67° N 65.52° W. Because the NASG is characterized as a P-stressed ecosystem, we hypothesized that biochemical allocation would reflect sensitivity to bioavailable P, such that greater P supply would result in increased allocation toward P-rich RNA for growth. We expected these changes in allocation to also result in lower C : P ratios with increased P supply. In contrast to our predictions however, bulk C : P ratios were decoupled from allocation to nucleic acids and did not vary systematically across a P supply gradient of 2.2–14.7 μmol m–2 d–1. Overall, we found that C : P ratios ranged from 188–306 along the transect, and RNA represented only 6–12% of total particulate P, whereas DNA represented 11–19%. However, we did find that allocation to RNA was positively correlated with SRP supply rate, suggesting a consistent physiological response in biochemical allocation to resource supply within the whole community. These results suggest that community composition or non-nucleic acid P pools may influence ecosystem scale variation in C : P stoichiometry more than nucleic acid allocation or prevailing environmental conditions in diverse marine microbial communities.

Factors controlling the spatial distribution of bacterial diversity have been intensely studied, whereas less is known about temporal changes. To address this, we tested whether the mechanisms that underlie bacterial temporal b-diversity vary across different scales in three marine microbial communities. While seasonal turnover was detected, at least 73% of the community variation occurred at intra-seasonal temporal scales, suggesting that episodic events are important in structuring marine microbial communities. In addition, turnover at different temporal scales appeared to be driven by different factors. Intra-seasonal turnover was significantly correlated to environmental variables such as phosphate and silicate concentrations, while seasonal and interannual turnover were related to nitrate concentration and temporal distance. We observed a strong link between the magnitude of environmental variation and bacterial b-diversity in different communities. Analogous to spatial biogeography, we found different rates of community changes across temporal scales. © 2013 by the Ecological Society of America.

Nearly 75 years ago, Alfred C. Redfield observed a similarity between the elemental composition of marine plankton in the surface ocean and dissolved nutrients in the ocean interior. This stoichiometry, referred to as the Redfield ratio, continues to be a central tenet in ocean biogeochemistry, and is used to infer a variety of ecosystem processes, such as phytoplankton productivity and rates of nitrogen fixation and loss2-4. Model, field and laboratory studies have shown that different mechanisms can explain both constant and variable ratios of carbon to nitrogen and phosphorus among ocean plankton communities. The range of C/N/P ratios in the ocean, and their predictability, are the subject of much active research. Here we assess global patterns in the elemental composition of phytoplankton and particulate organic matter in the upper ocean, using published and unpublished observations of particulate phosphorus, nitrogen and carbon from a broad latitudinal range, supplemented with elemental data for surface plankton populations. We show that the elemental ratios of marine organic matter exhibit large spatial variations, with a global average that differs substantially from the canonical Redfield ratio. However, elemental ratios exhibit a clear latitudinal trend. Specifically, we observed a ratio of 195:28:1 in the warm nutrient-depleted low-latitude gyres, 137:18:1 in warm, nutrient-rich upwelling zones, and 78:13:1 in cold, nutrient-rich high-latitude regions. We suggest that the coupling between oceanic carbon, nitrogen and phosphorus cycles may vary systematically by ecosystem. © 2013 Macmillan Publishers Limited. All rights reserved.

Anaerobic bacteria were isolated from a 1700-year-old wooden spear shaft, excavated from an archaeological site that dates from the iron age, in the southern part of Jutland, Denmark. The bacteria were cultivated in glucose- and xylose-supplemented media at 14°C and 20°C. A gene library with 21 clones was constructed by extracting and amplifying 16S rDNA sequences from the individual cultures. One clone was phylogenetically affiliated to the Spirochaeta. Eleven clones affiliated to an unidentified member of the α-Proteobacteria were present in all culture samples. Three clones were affiliated to the β-Proteobacteria. Four clones were clustered among the Geobacteriaceae, in the δ-Proteobacteria. A single clone was clustered with gram-positives. All the identified bacterial families are commonly found in soil or bog environments and many are able to utilize cellulose as their carbon or energy source. © 2003 Elsevier Ltd. All rights reserved.

In this study, the construction a model distribution system suitable for studies of attached and suspended microbial consisted of two loops connected in series with a total of 140 biofilm sampling points. The biofilm from the system was studied using 11 different microbial methods and the results were compared and discussed. The methods were used for biomass quantification (AODC, HPC and ATP determination), visualisation of structure (CLSM), activity measurement (leucine incorporation, AOC removal rate, respiration of benzoic acid, CTC and live/dead stains), and microbial diversity profiling (clone libraries and DGGE).

Cyanobacterial diazotrophs, specifically the genera Trichodesmium and UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution of Trichodesmium and UCYN-A using the nitrogenase gene ( nifH ) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera. Trichodesmium exhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution. Trichodesmium clades were primarily influenced by temperature and nutrient availability, and particularly frequent in regions of phosphorus stress. In contrast UCYN-A was found in regions of iron stress. UCYN-A clades demonstrated a more homogeneous distributions, with a single sequencing variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations of Trichodesmium and UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. This study underscores the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing cyanobacteria.

Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms., Competing Interests: The authors declare no conflict of interest.

Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy., Competing Interests: The authors declare no conflict of interest.

Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16-25°C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Harcourt et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the "translation-compensation hypothesis" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N:P., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Historically, our understanding of bacterial ecology in the Indian Ocean has been limited to regional studies that place emphasis on community structure and function within oxygen minimum zones. Thus, bacterial community dynamics across the wider Indian Ocean are largely undescribed. As part of Bio-GO-SHIP, we sequenced the 16S rRNA gene from 465 samples collected on sections I07N and I09N. We found that (i) there were 23 distinct bioregions within the Indian Ocean, (ii) the southeastern gyre had the largest gradient in bacterial alpha-diversity, (iii) the Indian Ocean surface microbiome was primarily composed of a core set of taxa, and (iv) bioregions were characterized by transitions in physical and geochemical conditions. Overall, we showed that bacterial community structure spatially delineated the surface Indian Ocean and that these microbially-defined regions were reflective of subtle ocean physical and geochemical gradients. Therefore, incorporating metrics of in-situ microbial communities into marine ecological regions traditionally defined by remote sensing will improve our ability to delineate warm, oligotrophic regions.

The life history strategies of soil microbes determine their metabolic potential and their response to environmental changes. Yet these strategies remain poorly understood. Here we use shotgun metagenomes from terrestrial biomes to characterize overarching covariations of the genomic traits that capture dominant life history strategies in bacterial communities. The emerging patterns show a triangle of life history strategies shaped by two trait dimensions, supporting previous theoretical and isolate-based studies. The first dimension ranges from streamlined genomes with simple metabolisms to larger genomes and expanded metabolic capacities. As metabolic capacities expand, bacterial communities increasingly differentiate along a second dimension that reflects a trade-off between increasing capacities for environmental responsiveness or for nutrient recycling. Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution. Our findings provide a trait-based framework to compare life history strategies of soil bacteria., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus., (© 2023. The Author(s).)

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent., (© 2023 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

Establishing links between microbial diversity and environmental processes requires resolving the high degree of functional variation among closely related lineages or ecotypes. Here, we implement and validate an improved metagenomic approach that estimates the spatial biogeography and environmental regulation of ecotype-specific replication patterns (R Obs ) across ocean regions. A total of 719 metagenomes were analyzed from meridional Bio-GO-SHIP sections in the Atlantic and Indian Ocean. Accounting for sequencing bias and anchoring replication estimates in genome structure were critical for identifying physiologically relevant biological signals. For example, ecotypes within the dominant marine cyanobacteria Prochlorococcus exhibited distinct diel cycles in R Obs that peaked between 19:00-22:00. Additionally, both Prochlorococcus ecotypes and ecotypes within the highly abundant heterotroph Pelagibacter (SAR11) demonstrated systematic biogeographies in R Obs that differed from spatial patterns in relative abundance. Finally, R Obs was significantly regulated by nutrient stress and temperature, and explained by differences in the genomic potential for nutrient transport, energy production, cell wall structure, and replication. Our results suggest that our new approach to estimating replication is reflective of gross population growth. Moreover, this work reveals that the interaction between adaptation and environmental change drives systematic variability in replication patterns across ocean basins that is ecotype-specific, adding an activity-based dimension to our understanding of microbial niche space., (© 2022. The Author(s).)

Concentrations and elemental stoichiometry of suspended particulate organic carbon, nitrogen, phosphorus, and oxygen demand for respiration (C:N:P:-O 2 ) play a vital role in characterizing and quantifying marine elemental cycles. Here, we present Version 2 of the Global Ocean Particulate Organic Phosphorus, Carbon, Oxygen for Respiration, and Nitrogen (GO-POPCORN) dataset. Version 1 is a previously published dataset of particulate organic matter from 70 different studies between 1971 and 2010, while Version 2 is comprised of data collected from recent cruises between 2011 and 2020. The combined GO-POPCORN dataset contains 2673 paired surface POC/N/P measurements from 70°S to 73°N across all major ocean basins at high spatial resolution. Version 2 also includes 965 measurements of oxygen demand for organic carbon respiration. This new dataset can help validate and calibrate the next generation of global ocean biogeochemical models with flexible elemental stoichiometry. We expect that incorporating variable C:N:P:-O 2 into models will help improve our estimates of key ocean biogeochemical fluxes such as carbon export, nitrogen fixation, and organic matter remineralization., (© 2022. The Author(s).)

Oceanic nutrient cycles are coupled, yet carbon-nitrogen-phosphorus (C:N:P) stoichiometry in marine ecosystems is variable through space and time, with no clear consensus on the controls on variability. Here, we analyze hydrographic, plankton genomic diversity, and particulate organic matter data from 1970 stations sampled during a global ocean observation program (Bio-GO-SHIP) to investigate the biogeography of surface ocean particulate organic matter stoichiometry. We find latitudinal variability in C:N:P stoichiometry, with surface temperature and macronutrient availability as strong predictors of stoichiometry at high latitudes. Genomic observations indicated community nutrient stress and suggested that nutrient supply rate and nitrogen-versus-phosphorus stress are predictive of hemispheric and regional variations in stoichiometry. Our data-derived statistical model suggests that C:P and N:P ratios will increase at high latitudes in the future, however, changes at low latitudes are uncertain. Our findings suggest systematic regulation of elemental stoichiometry among ocean ecosystems, but that future changes remain highly uncertain., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2022.)

The activation of unrecognized antibiotic resistance genes in the bacterial cell can give rise to antibiotic resistance without the need for major mutations or horizontal gene transfer. We hypothesize that bacteria harbor an extensive array of diverse cryptic genes that can be activated in response to antibiotics via adaptive resistance. To test this hypothesis, we developed a plasmid assay to randomly manipulate gene copy numbers in Escherichia coli cells and identify genes that conferred resistance when amplified. We then tested for cryptic resistance to 18 antibiotics and identified genes conferring resistance. E. coli could become resistant to 50% of the antibiotics tested, including chloramphenicol, d-cycloserine, polymyxin B, and 6 beta-lactam antibiotics, following this manipulation. Known antibiotic resistance genes comprised 13% of the total identified genes, where 87% were unclassified (cryptic) antibiotic resistance genes. These unclassified genes encoded cell membrane proteins, stress response/DNA repair proteins, transporters, and miscellaneous or hypothetical proteins. Stress response/DNA repair genes have a broad antibiotic resistance potential, as this gene class, in aggregate, conferred cryptic resistance to nearly all resistance-positive antibiotics. We found that antibiotics that are hydrophilic, those that are amphipathic, and those that inhibit the cytoplasmic membrane or cell wall biosynthesis were more likely to induce cryptic resistance in E. coli. This study reveals a diversity of cryptic genes that confer an antibiotic resistance phenotype when present in high copy number. Thus, our assay can identify potential novel resistance genes while also describing which antibiotics are prone to induce cryptic antibiotic resistance in E. coli. IMPORTANCE Predicting where new antibiotic resistance genes will rise is a challenge and is especially important when new antibiotics are developed. Adaptive resistance allows sensitive bacterial cells to become transiently resistant to antibiotics. This provides an opportune time for cells to develop more efficient resistance mechanisms, such as tolerance and permanent resistance to higher antibiotic concentrations. The biochemical diversity harbored within bacterial genomes may lead to the presence of genes that could confer resistance when timely activated. Therefore, it is crucial to understand adaptive resistance to identify potential resistance genes and prolong antibiotics. Here, we investigate cryptic resistance, an adaptive resistance mechanism, and identify unknown (cryptic) antibiotic resistance genes that confer resistance when amplified in a laboratory strain of E. coli. We also pinpoint antibiotic characteristics that are likely to induce cryptic resistance. This study may help detect novel antibiotic resistance genes and provide the foundation to help develop more effective antibiotics.

Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed "YAS" framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β -glucosidase (BG), β -xylosidase (BX), and N-acetyl- β - D -glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Alster, Allison, Glassman, Martiny and Treseder.)

Nutrient supply regulates the activity of phytoplankton, but the global biogeography of nutrient limitation and co-limitation is poorly understood. Prochlorococcus adapt to local environments by gene gains and losses, and we used genomic changes as an indicator of adaptation to nutrient stress. We collected metagenomes from all major ocean regions as part of the Global Ocean Ship-based Hydrographic Investigations Program (Bio-GO-SHIP) and quantified shifts in genes involved in nitrogen, phosphorus, and iron assimilation. We found regional transitions in stress type and severity as well as widespread co-stress. Prochlorococcus stress genes, bottle experiments, and Earth system model predictions were correlated. We propose that the biogeography of multinutrient stress is stoichiometrically linked by controls on nitrogen fixation. Our omics-based description of phytoplankton resource use provides a nuanced and highly resolved description of nutrient stress in the global ocean., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or "Bio-GO-SHIP." One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.

In the California Current Ecosystem, El Niño acts as a natural phenomenon that is partially representative of climate change impacts on marine bacteria at timescales relevant to microbial communities. Between 2014-2016, the North Pacific warm anomaly (a.k.a., the "blob") and an El Niño event resulted in prolonged ocean warming in the Southern California Bight (SCB). To determine whether this "marine heatwave" resulted in shifts in microbial populations, we sequenced the rpoC1 gene from the biogeochemically important picocyanobacteria Prochlorococcus and Synechococcus at 434 time points from 2009-2018 in the MICRO time series at Newport Beach, CA. Across the time series, we observed an increase in the abundance of Prochlorococcus relative to Synechococcus as well as elevated frequencies of ecotypes commonly associated with low-nutrient and high-temperature conditions. The relationships between environmental and ecotype trends appeared to operate on differing temporal scales. In contrast to ecotype trends, most microdiverse populations were static and possibly reflect local habitat conditions. The only exceptions were microdiversity from Prochlorococcous HLI and Synechococcus Clade II that shifted in response to the 2015 El Niño event. Overall, Prochlorococcus and Synechococcus populations did not return to their pre-heatwave composition by the end of this study. This research demonstrates that extended warming in the SCB can result in persistent changes in key microbial populations., Competing Interests: The authors have declared that no competing interests exist.

Climate-driven depletion of ocean oxygen strongly impacts the global cycles of carbon and nutrients as well as the survival of many animal species. One of the main uncertainties in predicting changes to marine oxygen levels is the regulation of the biological respiration demand associated with the biological pump. Derived from the Redfield ratio, the molar ratio of oxygen to organic carbon consumed during respiration (i.e., the respiration quotient, [Formula: see text]) is consistently assumed constant but rarely, if ever, measured. Using a prognostic Earth system model, we show that a 0.1 increase in the respiration quotient from 1.0 leads to a 2.3% decline in global oxygen, a large expansion of low-oxygen zones, additional water column denitrification of 38 Tg N/y, and the loss of fixed nitrogen and carbon production in the ocean. We then present direct chemical measurements of [Formula: see text] using a Pacific Ocean meridional transect crossing all major surface biome types. The observed [Formula: see text] has a positive correlation with temperature, and regional mean values differ significantly from Redfield proportions. Finally, an independent global inverse model analysis constrained with nutrients, oxygen, and carbon concentrations supports a positive temperature dependence of [Formula: see text] in exported organic matter. We provide evidence against the common assumption of a static biological link between the respiration of organic carbon and the consumption of oxygen. Furthermore, the model simulations suggest that a changing respiration quotient will impact multiple biogeochemical cycles and that future warming can lead to more intense deoxygenation than previously anticipated., Competing Interests: The authors declare no competing interest.

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'.