Longitudinal variability of diazotroph abundances in the subtropical North Atlantic Ocean

Diazotrophy-related studies in the North Atlantic have largely focused on its western tropical area, leaving the subtropics and the east undersampled. We studied the longitudinal distribution of Trichodesmium, UCYN-A, UCYN-B, the putative Gammaproteobacterium g-24774A11 and Richelia (Het1) along 24.58N, using quantitative polymerase chain reaction on different size fractions (10, 10–3 and 3–0.2 mm) and additional filament counts for Trichodesmium. Trichodesmium was the most abundant phylotype, followed by UCYN-A, g-24774A11 and Het1, with maximum abundances of 8.8 ! 105, 2.0 ! 105, 3.3 ! 103 and 3.4 ! 102 nifH copies L21, respectively, whereas UCYN-B was mostly undetected. A clear shift in the diazotroph community was observed at !308W, coinciding with the transition between the North Atlantic Subtropical Gyre boundary and inner core. This transition zone divided the transect into an eastern half dominated by UCYN-A and western half dominated by Trichodesmium and g-24774A11. g-24774A11 was only detected in the 10–3 mm fraction, suggesting their association with larger microbes or aggregates. Our results indicate that typical size fractionation by 10 mm is not optimal for reconciling diazotroph phylotypes to N2 fixation rates and that non-cyanobacterial diazotrophs may contribute importantly to bulk diazotrophic activity in the western subtropical North Atlantic.Consolider-Malaspina (CSD2008-00077), CAIBEX (CTM2007-66408- CO2-02). HOTMIX (CTM2011-30010-CO2-01)Versión del editor1,749

Copepod-Associated Gammaproteobacteria Respire Nitrate in the Open Ocean Surface Layers

Microbial dissimilatory nitrate reduction to nitrite, or nitrate respiration, was detected in association with copepods in the oxygenated water column of the North Atlantic subtropical waters. These unexpected rates correspond to up to 0.09 nmol N copepod−1 d−1 and demonstrate a previously unaccounted nitrogen transformation in the oceanic pelagic surface layers. Genes and transcripts for both the periplasmic and membrane associated dissimilatory nitrate reduction pathways (Nap and Nar, respectively) were detected. The napA genes and transcripts were closely related with sequences from several clades of Vibrio sp., while the closest relatives of the narG sequences were Pseudoalteromonas spp. and Alteromonas spp., many of them representing clades only distantly related to previously described cultivated bacteria. The discovered activity demonstrates a novel Gammaproteobacterial respiratory role in copepod association, presumably providing energy for these facultatively anaerobic bacteria, while supporting a reductive path of nitrogen in the oxygenated water column of the open ocean

A reference map of the human binary protein interactome.

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships(1,2). Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome(3), transcriptome(4) and proteome(5) data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes

Microbial Interactions With Cnidarians In Massachusetts Coastal Waters

Jellyfish are an important component of many coastal ecosystems and recent work has shown they can interact with microbial communities. Studies have shown that gelatinous and crustaceous zooplankton can not only release dissolved organic matter (DOM) that can alter the respiration and community structure of bacteria in the surrounding water, but also can harbor microbial communities that differ from the surrounding seawater. Such studies have not been conducted in Massachusetts waters with a Scyphomedusa (Aurelia aurita) and Hydromedusa (Nemopsis bachei). Nemopsis Bachei is a colonial coastal hydrozoan native to the East Coast of the United States, and within the past 20 years these hydrozoans have invaded the European waters of the Atlantic and German Bight. A. aurita is a cosmopolitan schyphozoa capable of producing large blooms in the Atlantic, Pacific, and Indian Oceans. This study furthers our knowledge on this gelatinous zooplankton by comparing DOC effects of hydrozoans against known results of scyphomedusa, both classes being of the Cnidarian phylum, as well as examining the microbial communities of two Cnidarians within Massachusetts coastal waters. Laboratory experiments show that N. bachei releases labile dissolved organic carbon (DOC) into the surrounding water such that bacterial abundance increases and the microbial community shifts. Using the molecular fingerprinting method of terminal restriction fragment length polymorphism (T-RFLP) it was found that Gammaproteobacteria and Bacteroidetes became more dominant in the bacterial community in response to N. bachei produced dissolved organic matter (DOM). Cloning and sequencing results from hydromedusa directly picked from the water support these trends. Both Nemopsis bachei and Aurelia aurita had significantly different bacterial communities than that of the surrounding seawater. N. bachei bacterial sequences were dominated by Gammaproteobacteria, Bacteroidetes, and Alphaproteobacteria whereas A. aurita was dominated by Cyanobacteria, Tenericutes, and bacteria that could not be classified. These cnidarian-associated bacteria are suggestive of symbiotic associations that could be of importance in nutrient cycling or potential pathogenic abilities

Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome

<div><p>Copepod-bacteria interactions include permanent and transient epi- and endobiotic associations that may play roles in copepod health, transfer of elements in the food web, and biogeochemical cycling. Microbiomes of three temperate copepod species (<i>Acartia longiremis</i>, <i>Centropages hamatus</i>, and <i>Calanus finmarchicus</i>) from the Gulf of Maine were investigated during the early summer season using high throughput amplicon sequencing. The most prominent stable component of the microbiome included several taxa within Gammaproteobacteria, with <i>Pseudoalteromonas</i> spp. especially abundant across copepod species. These Gammaproteobacteria appear to be promoted by the copepod association, likely benefitting from nutrient enriched microenvironments on copepods, and forming a more important part of the copepod-associated community than <i>Vibrio</i> spp. during the cold-water season in this temperate system. Taxon-specific associations included an elevated relative abundance of Piscirickettsiaceae and Colwelliaceae on <i>Calanus</i>, and <i>Marinomonas</i> sp. in <i>Centropages</i>. The communities in full and voided gut copepods had distinct characteristics, thus the presence of a food-associated microbiome was evident, including higher abundance of Rhodobacteraceae and chloroplast sequences in the transient communities. The observed variability was partially explained by collection date that may be linked to factors such as variable time since molting, gender differences, and changes in food availability and type over the study period. While some taxon-specific and stable associations were identified, temporal changes in environmental conditions, including food type, appear to be key in controlling the composition of bacterial communities associated with copepods in this temperate coastal system during the early summer.</p></div

Bacterial associations with the hydromedusa <i>Nemopsis bachei</i> and scyphomedusa <i>Aurelia aurita</i> from the North Atlantic Ocean

<p>Recent studies suggest that jellyfish influence the community composition of marine microorganisms, but few studies have been conducted contrasting communities among different jellyfish taxa. In this study microbial communities were compared between two cnidarians found in North Atlantic Ocean coastal waters during the spring–summer months. Microbial communities associated with the invasive hydrozoan <i>Nemopsis bachei</i> and the cosmopolitan scyphozoan <i>Aurelia aurita</i> (Cnidaria) were characterized based on the 16S rRNA gene sequence. The bacterial communities associated with the jellyfish were significantly different from the communities in seawater, and <i>N. bachei</i> and <i>A. aurita</i> hosted taxon-specific bacterial groups. Gammaproteobacteria, Bacteroidetes and Alphaproteobacteria dominated bacterial sequences on <i>N. bachei</i>, the dominant orders including Vibrionales, Flavobacteriales, Rhizobiales and Rickettsiales. <i>Vibrio</i> spp. and <i>Photobacterium</i> spp. were abundant in <i>N. bachei</i>, and <i>Tenacibaculum</i> sp. (Bacteroidetes) had a host-specific association with <i>N. bachei</i>. Mycoplasmatales was a prominent, unique, and potentially host-promoted association in <i>A. aurita</i>, and overall Cyanobacteria, Tenericutes and unclassified bacteria dominated the sequences in <i>A. aurita</i>. This is the first description of the microbial community composition in <i>N. bachei</i>, which has been reported as an invasive species in eastern North Atlantic waters. Overall these results suggest that different cnidarians in North Atlantic coastal waters promote growth of distinct microbial communities. Jellyfish could thus differentially influence microbially mediated biogeochemical cycles and food webs in regions where they proliferate.</p

Groups from phylum to genus level determined to be significant representatives of their sample type from the LefSe analysis.

<p>In the graph, each ring represents a taxonomic level, with phylum, class, order, family, and genus from center to the periphery, respectively. Each circle is a taxonomic unit found in the dataset, with circles or nodes shown in color where the taxon was a significantly more abundant group. F, full gut; S, starved. ug, unidentified genus; a. ug_Microbacteriaceae b. ug_family NS11_12, c. family NS_12, d. <i>Veillonella</i> spp., e. Veillonellaceae, f. Fusobacteriales, g. ug_Pirellulaceae, h. Pirellulaceae, i. Pirellulales, j. ug_Bradyrhizobiaceae, k. Bradyrhizobiaeae, l. Rhizobiales, m. <i>Paracoccus</i> spp., n. ug_Rhodobacteraceae, o. Rhodobacteraceae, p. Rhodobacterales, q. ug_Colwelliaceae, r. Colwelliaceae, s. <i>Marinomonas</i> spp., t. <i>Acitenobacter</i> spp., u. ug_Piscirickettsiaceae, v. Piscirickettsiaceae, w. Thiotrichales, x. <i>Pseudoalteromonas</i> spp., y. Pseudoalteromonadaceae, z. <i>Photobacterium</i> spp.</p

Average distribution of the community composition in samples discriminated at the phylum/sub-phylum level.

<p>F, full gut; S, starved; Ac, <i>Acartia</i>; Ce, <i>Centropages</i>; Ca, <i>Calanus</i>. <i>Acartia</i> F (n = 9), <i>Acartia</i> S (n = 6), <i>Calanus</i> F (n = 5), <i>Centropages</i> F (n = 4), <i>Centropages</i> S (n = 8), water (n = 5).</p

Selected taxa that were significantly more abundant in specific copepod types (LefSe, p<0.05).

<p>*, sample type in which the relative abundance of the taxon was significantly elevated. F, full gut; S, starved; Ac, <i>Acartia</i>; Ce, <i>Centropages</i>; Ca, <i>Calanus</i>. In <i>Acartia</i> S, no significantly more abundant groups were detected.</p

Heatmap with dendrograms (hierarchical clustering based on Bray-Curtis distance) for genus level groupings and samples.

<p>F, full gut; S, starved. The dendrogram at the top demonstrates the similarity of communities in several samples of starved <i>Acartia</i> and <i>Centropages</i>, although time-dependent variability is also present. Several co-varying genera with higher relative abundance in water samples are driving the separation from the other sample types. Higher relative abundance of <i>Pseudoalteromonas</i> sp. and several other bacterial genera is seen in copepods in comparison to water samples.</p