The concept of constant elemental ratios in plankton communities—the Redfield ratio—is of central importance to ocean biogeochemistry. Recently, several studies have demonstrated regional differences ...in the plankton C:P and N:P ratio. However, less is known about potential systematic variations in the C:N ratio. Here we present an analysis of the particulate organic carbon to nitrogen ratio of 40,482 globally distributed samples from the upper 200 m of the ocean water column. Particulate organic carbon and nitrogen concentrations are highly correlated (R2 = 0.86) with a median value of 6.5. Using an artificial neural network analysis, we find regional variations in the C:N ratio linked to differences in environmental conditions. The ratio is lower in upper latitude cold water as well as upwelling regions in comparison to the warm oligotrophic gyres. We find substantial differences between ocean gyres that might be associated with differences in the nutrient supply ratio. Using cell sorting, we also quantified the C:N ratio of Prochlorococcus, Synechococcus, and picoeukaryotic field populations. The analysis demonstrates that picophytoplankton lineages exhibit a significantly higher ratio than the bulk particulate material but are only marginally significantly different from each other. Thus, the dominance of picophytoplankton in ocean gyres may contribute to the elevated ratios observed in these regions. Overall, the median C:N ratio derived from 40,482 samples is close to the canonical Redfield ratio, but significant regional deviations from this value are observed. These differences could be important for marine biogeochemistry and the regional coupling between the ocean's carbon and nitrogen cycles.
Key Points
The median upper ocean particulate C:N ratio is broadly constrained at 6.5
The C:N ratio is 7.1 in low compared to 6.2 in high nutrient regions
The C:N ratios in picophytoplankton are greater than global mean
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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
, 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
-specific primers of the
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).
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
-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.
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
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
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.
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.
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.
Microbiomes in light of traits: A phylogenetic perspective Martiny, Jennifer B. H.; Jones, Stuart E.; Lennon, Jay T. ...
Science (American Association for the Advancement of Science),
11/2015, Volume:
350, Issue:
6261
Journal Article
Peer reviewed
Open access
A focus on the phenotypic characteristics of microorganisms-their traits-offers a path for interpreting the growing amount of microbiome data. We review key aspects of microbial traits, as well as ...approaches used to assay their phylogenetic distribution. Recent studies reveal that microbial traits are differentially conserved across the tree of life and appear to be conserved in a hierarchical fashion, possibly linked to their biochemical complexity. These results suggest a predictive framework whereby the genetic (or taxonomic) resolution of microbiome variation among samples provides information about the traits under selection. The organizational parallels seen among human and free-living microbiomes seem to support this idea. Developments in this framework may offer predictions not only for how microbial composition responds to changing environmental conditions, but also for how these changes may alter the health or functioning in human, engineered, and environmental systems.
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The elemental ratios of marine phytoplankton emerge from complex interactions between the biotic and abiotic components of the ocean, and reflect the plastic response of individuals to changes in ...their environment. The stoichiometry of phytoplankton is, thus, dynamic and dependent on the physiological state of the cell. We present a theoretical model for the dynamics of the carbon, nitrogen and phosphorus contents of a phytoplankton population. By representing the regulatory processes controlling nutrient uptake, and focusing on the relation between nutrient content and protein synthesis, our model qualitatively replicates existing experimental observations for nutrient content and ratios. The population described by our model takes up nutrients in proportions that match the input ratios for a broad range of growth conditions. In addition, there are two zones of single-nutrient limitation separated by a wide zone of co-limitation. Within the co-limitation zone, a single point can be identified where nutrients are supplied in an optimal ratio. When different species compete, the existence of a wide co-limitation zone implies a more complex pattern of coexistence and exclusion compared to previous model predictions. However, additional comprehensive laboratory experiments are needed to test our predictions. Our model contributes to the understanding of the global cycles of oceanic nitrogen and phosphorus, as well as the elemental ratios of these nutrients in phytoplankton populations.
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.
Key Points
Mean surface ocean particulate organic carbon:nitrogen ratios (POC:PON) are relatively homeostatic
Under nitrogen limitation, phytoplankton have elevated carbon‐to‐nitrogen (C:N) ratios
Interactions between primary and secondary producers control average POC:PON of surface particulates
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Rates of ecosystem processes such as decomposition are likely to change as a result of human impacts on the environment. In southern California, climate change and nitrogen (N) deposition in ...particular may alter biological communities and ecosystem processes. These drivers may affect decomposition directly, through changes in abiotic conditions, and indirectly through changes in plant and decomposer communities. To assess indirect effects on litter decomposition, we reciprocally transplanted microbial communities and plant litter among control and treatment plots (either drought or N addition) in a grassland ecosystem. We hypothesized that drought would reduce decomposition rates through moisture limitation of decomposers and reductions in plant litter quality before and during decomposition. In contrast, we predicted that N deposition would stimulate decomposition by relieving N limitation of decomposers and improving plant litter quality. We also hypothesized that adaptive mechanisms would allow microbes to decompose litter more effectively in their native plot and litter environments. Consistent with our first hypothesis, we found that drought treatment reduced litter mass loss from 20.9% to 15.3% after six months. There was a similar decline in mass loss of litter inoculated with microbes transplanted from the drought treatment, suggesting a legacy effect of drought driven by declines in microbial abundance and possible changes in microbial community composition. Bacterial cell densities were up to 86% lower in drought plots and at least 50% lower on litter derived from the drought treatment, whereas fungal hyphal lengths increased by 13-14% in the drought treatment. Nitrogen effects on decomposition rates and microbial abundances were weaker than drought effects, although N addition significantly altered initial plant litter chemistry and litter chemistry during decomposition. However, we did find support for microbial adaptation to N addition with N-derived microbes facilitating greater mass loss in N plots than in control plots. Our results show that environmental changes can affect rates of ecosystem processes directly through abiotic changes and indirectly through microbial abundances and communities. Therefore models of ecosystem response to global change may need to represent microbial biomass and community composition to make accurate predictions.
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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 μmol 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.
Light penetration through the ocean creates underwater light color niches and photosynthetic organisms use specific strategies to capture light in these niches. The selection pressure for some ...cyanobacteria strains in the genus Synechococcus that change color to absorb either blue or green light (chromatic acclimaters, or generalists) is not well understood. Here, we tested the hypothesis that changes in ocean spectra brought about by mixing preferentially selects for generalists within a Synechococcus population. We investigated ocean conditions that led to high proportions of Synechococcus generalists versus specialists in a model ocean column, and compared simulations with in situ metagenomic and physical oceanographic data from major Bio‐GO‐SHIP cruises, supplemented with GEOTRACES and TARA Oceans, as well as the GOOS Argo Program and sea surface height from AVISO. We found that greater mixed layer depths selected for generalists in simulated Synechococcus populations, but did not account for much of the variance in the partitioning of light‐harvesting strategies in situ. Rather, oceanographic signatures for upwelling areas and ocean fronts explained more of the variation between Synechococcus generalists and specialists in the ocean. Our results motivate further study of the in situ light environments of upwelling zones and ocean fronts, which are currently understudied as potential light‐driven niche habitats.
Plain Language Summary
The variety of pigments used by cyanobacteria to capture light for photosynthesis increases the colors of light available for use in the ocean. Some members of the cyanobacterial genus, Synechococcus, can change color to absorb either blue or green light (generalists), adding to the variety of light‐harvesting strategies. Though the reason for this color change is believed to be fluctuations in the underwater blue/green light field, this has not been tested directly. Using a mathematical model of the ocean column, we find the highest percentages of generalists in the Synechococcus population in deep ocean mixed layers. Comparison of model results to actual distributions of generalists indicate that deep mixing plays a smaller role than our model suggested, and that upwelling zones, where water is vertically moved to the surface, and ocean fronts, where major ocean currents meet, are also important habitats for Synechococcus generalists in the ocean.
Key Points
Despite high correlation with modeled deep mixing, Synechococcus blue‐green acclimaters do not correlate with open ocean mixed layer depths
A high percentage of Synechococcus chromatic acclimaters correlate with low surface temperatures and low sea surface height
A high percentage of Synechococcus chromatic acclimaters are observed along paths of major ocean fronts, and upwelling zones
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