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).

Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.

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Bacterial community composition, enzymatic activities, and carbon dynamics were examined during diatom blooms in four 200-liter laboratory seawater mesocosms. The objective was to determine whether the dramatic shifts in growth rates and ectoenzyme activities, which are commonly observed during the course of phytoplankton blooms and their subsequent demise, could result from shifts in bacterial community composition. Nutrient enrichment of metazoan-free seawater resulted in diatom blooms dominated by a Thalassiosira sp., which peaked 9 days after enrichment (Ϸ24 g of chlorophyll a liter ؊1 ). At this time bacterial abundance abruptly decreased from 2.8 ؋ 10 6 to 0.75 ؋ 10 6 ml ؊1, and an analysis of bacterial community composition, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments, revealed the disappearance of three dominant phylotypes. Increased viral and flagellate abundances suggested that both lysis and grazing could have played a role in the observed phylotype-specific mortality. Subsequently, new phylotypes appeared and bacterial production, abundance, and enzyme activities shifted from being predominantly associated with the <1.0-m size fraction towards the >1.0-m size fraction, indicating a pronounced microbial colonization of particles. Sequencing of DGGE bands suggested that the observed rapid and extensive colonization of particulate matter was mainly by specialized ␣-Proteobacteria-and Cytophagalesrelated phylotypes. These particle-associated bacteria had high growth rates as well as high cell-specific aminopeptidase, ␤-glucosidase, and lipase activities. Rate measurements as well as bacterial population dynamics were almost identical among the mesocosms indicating that the observed bacterial community dynamics were systematic and repeatable responses to the manipulated conditions. During phytoplankton blooms in the ocean, primary productivity and its processing by the food web create a heterogeneous environment of particulate, colloidal, and dissolved organic matter in a continuum of size classes and concentrations (2,4,35,76). Major changes in organic matter concentration and composition are expected to occur at different stages of the bloom. The variations in the organic matter regime are typically accompanied by pronounced changes in bacterial abundance, productivity, ectohydrolase activities, and colonization of particles (48,68). In one recent mesocosm experiment (68), growth rates, colonization, and enzyme activities generally increased following the peak of a diatom bloom but different enzymes were found to peak at different times. In principle, these changes could have occurred without major shifts in the phylogenetic composition of the bacterial community. Shifts in activity and surface attachment would represent plasticity in the bacterial phenotypes, with enzyme expression and growth being regulated in response to the available organic substrates. Alternatively, the observed changes could have resulted from community succession, with bacteria with...

Variation in traits causes bacterial populations to respond in contrasting ways to environmental drivers. Learning about this will help us understand the ecology of individual populations in complex ecosystems. We used 454 pyrosequencing of the hypervariable region V6 of the 16S rRNA gene to study seasonal dynamics in Baltic Sea bacterioplankton communities, and link community and population changes to biological and chemical factors. Comparing the abundance profiles of operational taxonomic units at different phylogenetic distances revealed a weak but significant negative correlation between abundance profile similarity and genetic distance, potentially reflecting habitat filtering of evolutionarily conserved functional traits in the studied bacterioplankton.

Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.amoA | ureC | Beaufort Sea | Ross Sea | Amundsen Sea

ABSTRACT:The relationship between bacterial 16S rRNA gene composition and carbon metabolism was analyzed during an intense dinoflagellate bloom off the Southern California coast during the spring of 1997. Bacterial numbers and rate processes, chlorophyll a, and the dissolved and particulate organic matter pools were measured during the bloom to provide a framework within which to assess bacterial community composition. Free bacteria were numerically dominant, generally comprising > 90% of the total, and were responsible for > 70% of bacterial production. Attached bacteria had higher cell-specific growth rates than free bacteria (range = 0.5 to 15.1 and 0.7 to 2.5 d -1 , respectively) and had hydrolytic ectoenzyme activities at times more than an order of magnitude higher on a per cell basis. Denaturing gradient gel electrophoresis analysis of bacterial community composition indicated that: (1) the free and attached communities were distinct, and (2) marked shifts in bacterial community structure occurred concomitant with the peaks in attached enzyme activities, specific growth rates and DOC concentration. Of the 24 16S rDNA clones analyzed, 7 were related to the Cytophaga-like bacteria (CLB), 6 to the α-subclass and 5 to the γ-subclass of the Proteobacteria; 3 were related to oxygenic phototrophs, 2 were heteroduplexes and 1 was a possible chimera. While the α-and γ-Proteobacteria predominated in the <1.0 µm fraction, CLB were identified in both the free and attached fractions as well as among bacteria cultured from the same water, without overlap among these groups. The observation that distinct Cytophaga group sequences were present in the free versus attached fractions is counter to the current understanding that these organisms occupy a principally 'particle-specialist' niche. Our results suggest that some CLB are also important in the decomposition of polymeric organic matter in the dissolved phase with implications for the accumulation of dissolved organic matter and pathways of carbon flow during phytoplankton blooms.KEY WORDS: Bacteria· Community composition · DGGE · Cell-specific activity · Algal bloom Resale or republication not permitted without written consent of the publisher

Cyanobacteria are thought to be the main N2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.