The Cyanobacteria Prochlorococcus and Synechococcus account for a substantial fraction of marine primary production. Here, we present quantitative niche models for these lineages that assess present and future global abundances and distributions. These niche models are the result of neural network, nonparametric, and parametric analyses, and they rely on >35,000 discrete observations from all major ocean regions. The models assess cell abundance based on temperature and photosynthetically active radiation, but the individual responses to these environmental variables differ for each lineage. The models estimate global biogeographic patterns and seasonal variability of cell abundance, with maxima in the warm oligotrophic gyres of the Indian and the western Pacific Oceans and minima at higher latitudes. The annual mean global abundances of Prochlorococcus and Synechococcus are 2.9 ± 0.1 × 10 27 and 7.0 ± 0.3 × 10 26 cells, respectively. Using projections of sea surface temperature as a result of increased concentration of greenhouse gases at the end of the 21st century, our niche models projected increases in cell numbers of 29% and 14% for Prochlorococcus and Synechococcus, respectively. The changes are geographically uneven but include an increase in area. Thus, our global niche models suggest that oceanic microbial communities will experience complex changes as a result of projected future climate conditions. Because of the high abundances and contributions to primary production of Prochlorococcus and Synechococcus, these changes may have large impacts on ocean ecosystems and biogeochemical cycles.climate change | marine biogeochemistry | microbial biogeography M arine phytoplankton contribute roughly one-half of the global net primary production and play a key role in regulating global biogeochemical cycles (1). Marine phytoplankton are very diverse (2), including phylogenetic, biochemical, metabolic, and ecological variability (3-6). Thus, understanding the contribution of different phytoplankton groups to ecosystem functioning is central to predicting the biogeochemical impact of future environmental changes (7). However, our limited quantitative understanding of the global distribution and abundance of most phytoplankton groups constrains our ability to incorporate phytoplankton diversity into ocean biogeochemical models.The marine Cyanobacteria Prochlorococcus and Synechococcus are abundant in many ocean regions. The known geographical distributions of the two lineages are based primarily on individual cruises or time series observations and secondarily on macroecological descriptions, indicating central tendencies and boundary constraints related to light, temperature, nutrients, and chlorophyll a concentration (8-10). Prochlorococcus is present from the surface to a depth of ∼150 m in the open ocean between 40°N and 40°S. The population size declines beyond these latitudinal limits, and Prochlorococcus is thought to be absent at temperatures below 15°C (11). Furthermore, the lineage is believed to be out...

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.

Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild.

A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metricconsenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (s D ), ranging from a few deep to many shallow clades (average s D : 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.

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 1 . 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 loss [2][3][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 [5][6][7][8][9][10][11][12] . 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.A. C. Redfield first noted the similarity between the particulate nutrient ratios of plankton living in the surface ocean and that of dissolved nutrients in the deep ocean 1 . He predicted that deep-ocean nutrient ratios were controlled by the uniform nutrient requirements of sinking, and subsequently remineralized, surface plankton. This concept remains a central tenet in our understanding of ocean biogeochemistry. However, model, field and laboratory studies have shown that different mechanisms can explain both constant and variable C/N/P ratios among ocean plankton communities, but the range of ratios in the ocean and the relative importance of each mechanism are subject to much research [5][6][7][8][9][10]13,14 . Despite this continued lack of understanding of global patterns, the N/P ratio is routinely used to draw conclusions about ocean ecosystem processes, particularly related to nutrient limitation of phytoplankton production and the net magnitude of N 2 fixation and denitrification. 2,3 . Alas, these ratios are of critical importance to study, model and predict ocean biogeochemical cycles. Equally important is the C/P ratio of ocean plankton