A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs.

Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage.

Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1.

The multiple symbiotic partnerships between closely related species of the haptophyte algae and the nitrogen-fixing cyanobacteria Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The diversity of the eukaryotic 18S rDNA phylogenetic gene marker has helped to identify some of these symbiotic haptophyte species, yet we still lack a genetic marker to assess its diversity at a finer scale. One of such genes is the ammonium transporter () gene, which encodes the protein that might be involved in the uptake of ammonium from UCYN-A in these symbiotic haptophytes.

Transcriptional Mechanisms of Thermal Acclimation in .

Low temperature limits the growth and the distribution of the key oceanic primary producer , which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored.

Light and depth dependency of nitrogen fixation by the non-photosynthetic, symbiotic cyanobacterium UCYN-A.

The symbiotic cyanobacterium UCYN-A is one of the most globally abundant marine dinitrogen (N )-fixers, but cultures have not been available and its biology and ecology are poorly understood. We used cultivation-independent approaches to investigate how UCYN-A single-cell N fixation rates (NFRs) and nifH gene expression vary as a function of depth and photoperiod. Twelve-hour day/night incubations showed that UCYN-A only fixed N during the day.

Changes in Population Age-Structure Obscure the Temperature-Size Rule in Marine Cyanobacteria.

The temperature-size Rule (TSR) states that there is a negative relationship between ambient temperature and body size. This rule has been independently evaluated for different phases of the life cycle in multicellular eukaryotes, but mostly for the average population in unicellular organisms. We acclimated two model marine cyanobacterial strains ( MIT9301 and RS9907) to a gradient of temperatures and measured the changes in population age-structure and cell size along their division cycle.

Unexpected presence of the nitrogen-fixing symbiotic cyanobacterium UCYN-A in Monterey Bay, California.

In the last decade, the known biogeography of nitrogen fixation in the ocean has been expanded to colder and nitrogen-rich coastal environments. The symbiotic nitrogen-fixing cyanobacteria group A (UCYN-A) has been revealed as one of the most abundant and widespread nitrogen-fixers, and includes several sublineages that live associated with genetically distinct but closely related prymnesiophyte hosts. The UCYN-A1 sublineage is associated with an open ocean picoplanktonic prymnesiophyte, whereas UCYN-A2 is associated with the coastal nanoplanktonic coccolithophore Braarudosphaera bigelowii, suggesting that different sublineages may be adapted to different environments.

The Transcriptional Cycle Is Suited to Daytime N Fixation in the Unicellular Cyanobacterium " Atelocyanobacterium thalassa" (UCYN-A).

Symbiosis between a marine alga and a N-fixing cyanobacterium ( UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to N-fixing cyanobacteria use different strategies to avoid inhibition of N fixation by the oxygen evolved in photosynthesis.

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled phytoplankton. UCYN-A includes several closely related lineages whose partner fidelity, genome-wide expression and time of evolutionary divergence remain to be resolved. Here we detect and distinguish UCYN-A1 and UCYN-A2 lineages in symbiosis with two distinct prymnesiophyte partners in the South Atlantic Ocean.

Phytoplankton across Tropical and Subtropical Regions of the Atlantic, Indian and Pacific Oceans.

We examine the large-scale distribution patterns of the nano- and microphytoplankton collected from 145 oceanic stations, at 3 m depth, the 20% light level and the depth of the subsurface chlorophyll maximum, during the Malaspina-2010 Expedition (December 2010-July 2011), which covered 15 biogeographical provinces across the Atlantic, Indian and Pacific oceans, between 35°N and 40°S. In general, the water column was stratified, the surface layers were nutrient-poor and the nano- and microplankton (hereafter phytoplankton, for simplicity, although it included also heterotrophic protists) community was dominated by dinoflagellates, other flagellates and coccolithophores, while the contribution of diatoms was only important in zones with shallow nutriclines such as the equatorial upwelling regions. We applied a principal component analysis to the correlation matrix among the abundances (after logarithmic transform) of the 76 most frequent taxa to synthesize the information contained in the phytoplankton data set.

Vertical distribution of major photosynthetic picoeukaryotic groups in stratified marine waters.

Photosynthetic picoeukaryotes (PPEs) are fundamental contributors to oceanic primary production and form diverse communities dominated by prymnesiophytes, chlorophytes, pelagophytes and chrysophytes. Here, we studied the vertical distribution of these major groups in two offshore regions of the northern Iberian Peninsula during summer stratification. We performed a fine-scale vertical sampling (every ∼2 m) across the DCM and used fluorescence in situ hybridization (FISH) to determine the PPE composition and to explore the possible segregation of target groups in the light, nutrient and temperature gradients.

Global distribution and vertical patterns of a prymnesiophyte-cyanobacteria obligate symbiosis.

A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small prymnesiophyte and the clade UCYN-A2 in symbiosis with the larger Braarudosphaera bigelowii. We targeted the prymnesiophyte-UCYN-A1 symbiosis by double CARD-FISH (catalyzed reporter deposition-fluorescence in situ hybridization) and analyzed its abundance in surface samples from the MALASPINA circumnavigation expedition.

Ocean plankton. Determinants of community structure in the global plankton interactome.

Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns.

Polyunsaturated aldehydes from large phytoplankton of the Atlantic Ocean surface (42°n to 33°s).

Polyunsaturated aldehydes (PUAs) are organic compounds mainly produced by diatoms, after cell wounding. These compounds are increasingly reported as teratogenic for species of grazers and deleterious for phytoplanktonic species, but there is still scarce information regarding concentration ranges and the composition of PUAs in the open ocean. In this study, we analyzed the spatial distribution and the type of aldehydes produced by the large-sized (>10 μm) phytoplankton in the Atlantic Ocean surface.

Quorum quenching in cultivable bacteria from dense marine coastal microbial communities.

Acylhomoserine lactone (AHLs)-mediated quorum-sensing (QS) processes seem to be common in the marine environment and among marine pathogenic bacteria, but no data are available on the prevalence of bacteria capable of interfering with QS in the sea, a process that has been generally termed 'quorum quenching' (QQ). One hundred and sixty-six strains isolated from different marine dense microbial communities were screened for their ability to interfere with AHL activity. Twenty-four strains (14.