The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

Abstract. Marine N2 fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N2) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N2 fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N2 fixation rate in the global ocean is estimated to be 62 (52–73) Tg N yr−1 and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4–3.1) Tg C from cell counts and to 89 (43–150) Tg C from nifH-based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 ± 9.2 Tg N yr−1, 18 ± 1.8 Tg C and 590 ± 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about ±70%. It was recently established that the most commonly applied method used to measure N2 fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N2 fixation rate upward and may result in significantly higher estimates for the global N2 fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N2 fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future. The database is stored in PANGAEA (doi:10.1594/PANGAEA.774851).

Colonies of the Caribbean coral Montastraea cavernosa (Linnaeus) that harbor endosymbiotic cyanobacteria can fix nitrogen, whereas conspecifics without these symbionts cannot. The pattern of nitrogen fixation is diurnal and maximum rates occur in the early morning and evening. An analysis of δ 15 N stable isotope data showed that the zooxanthellae, but not the animal tissue, from colonies with cyanobacteria preferentially use the products derived from nitrogen fixation, and that these zooxanthellae also have a greater DNA content per cell, suggesting that these cells are in the DNA synthesis (S) and gap (G 2 ) + mitosis (M) phase of their cell cyle and are preparing to undergo cell division. Since nitrogen fixation did not occur during those times of the day when hyperoxia is known to occur, low oxygen concentrations might be required to support cyanobacterial respiration and provide the energy needed to fix nitrogen because the reaction centers of these cyanobacteria are uncoupled from light harvesting accessory pigments and the photosynthetic electron transport chain. Consistent with this were the depleted δ 13 C stable isotope signatures in all compartments of those corals with symbiotic cyanobacteria, which show an increase in heterotrophy compared with samples of M. cavernosa without cyanobacteria. Using modeled underwater light fields and measurements of photosynthesis, we show that the amount of time in which nitrogen fixation in these corals can take place increases with depth and that the distribution of corals with symbiotic cyanobacteria is positively correlated with increasing depth. The results presented here show that the zooxanthellae of M. cavernosa acquire nitrogen from cyanobacterial nitrogen fixation. Given that nitrogen limitation has long been proposed to contribute to the stability of these symbiotic associations, the mechanism by which zooxanthellae symbiosis in these corals is maintained remains an important question and the subject of future study.

N 2 -fixing proteobacteria (␣ and ␥) and unicellular cyanobacteria are common in both the tropical North Atlantic and Pacific oceans. In near-surface waters proteobacterial nifH transcripts were present during both night and day while unicellular cyanobacterial nifH transcripts were present during the nighttime only, suggesting separation of N 2 fixation and photosynthesis by unicellular cyanobacteria. Phylogenetic relationships among unicellular cyanobacteria from both oceans were determined after sequencing of a conserved region of 16S ribosomal DNA (rDNA) of cyanobacteria, and results showed that they clustered together, regardless of the ocean of origin. However, sequencing of nifH transcripts of unicellular cyanobacteria from both oceans showed that they clustered separately. This suggests that unicellular cyanobacteria from the tropical North Atlantic and subtropical North Pacific share a common ancestry (16S rDNA) and that potential unicellular N 2 fixers have diverged (nifH). N 2 fixation rates for unicellular bacterioplankton (including small cyanobacteria) from both oceans were determined in situ according to the acetylene reduction and 15 N 2 protocols. The results showed that rates of fixation by bacterioplankton can be almost as high as those of fixation by the colonial N 2 -fixing marine cyanobacteria Trichodesmium spp. in the tropical North Atlantic but that rates are much lower in the subtropical North Pacific.Growth rates of plankton in open ocean surface waters are often limited by the availability of reduced forms of N. New combined N enters surface waters either by advection, diffusion of NO 3 from deep water, or biological N 2 fixation (15). The last pathway can be significant in tropical and subtropical seas, where large cyanobacteria, Trichodesmium spp., have been considered the major organisms responsible (8,9,11). Ongoing research to identify other sources of N 2 fixation and alternate pathways of reduced N to the trophic chain in the vast oceanic basins has pointed out the potential role of certain N 2 -fixing unicellular bacterioplankton, which could have a significant impact on global biogeochemistry of N and C (14, 16, 44).Previous research has identified the presence of fragments of the unicellular cyanobacterial and proteobacterial nifH genes (which encode one of the peptide molecules that form the dinitrogenase reductase subunit of nitrogenase, the enzyme responsible for N 2 fixation [31]) in the subtropical North Pacific and tropical North Atlantic oceans (16,43,44). Preliminary data on N 2 fixation rates for the 10-to 0.2-m-size fraction of the bacterioplankton have suggested that they could make an important contribution to the global N cycle (14, 44). These studies used 15 N 2 to measure 24-h N 2 fixation rates in 10-m-pore-size-prefiltered water from the subtropical North Pacific. Also, N 2 fixation rates were estimated based on unicellular phytoplankton cell numbers that came from literature values (6). Cyanobacteria are autotrophs and generate ATP necessary for N 2 fixatio...

The members of the Phyllostomidae, the New-World leaf-nosed family of bats, show a remarkable evolutionary diversification of dietary strategies including insectivory, as the ancestral trait, followed by appearance of carnivory and plant-based diets such as nectarivory and frugivory. Here we explore the microbiome composition of different feeding specialists: insectivore Macrotus waterhousii, sanguivore Desmodus rotundus, nectarivores Leptonycteris yerbabuenae and Glossophaga soricina, and frugivores Carollia perspicillata and Artibeus jamaicensis. The V4 region of the 16S rRNA gene from three intestinal regions of three individuals per species was amplified and community composition and structure was analyzed with α and β diversity metrics. Bats with plant-based diets had low diversity microbiomes, whereas the sanguivore D. rotundus and insectivore M. waterhousii had the most diverse microbiomes. There were no significant differences in microbiome composition between different intestine regions within each individual. Plant-based feeders showed less specificity in their microbiome compositions, whereas animal-based specialists, although more diverse overall, showed a more clustered arrangement of their intestinal bacterial components. The main characteristics defining microbiome composition in phyllostomids were species and feeding strategy. This study shows how differences in feeding strategies contributed to the development of different intestinal microbiomes in Phyllostomidae.