Is dinitrogen fixation significant in the Levantine Basin, East Mediterranean Sea?

We report N(2) fixation rates measured from two stations monitored monthly off the Mediterranean coast of Israel during 2006 and 2007, and along a transect from Israel to Crete in September 2008. Analyses of time-series data revealed expression of nifH genes from diazotrophs in nifH clusters I and II, including cyanobacterial bloom-formers Trichodesmium and diatom-Richelia intracellularis associations. However, nifH gene abundance and rates of N(2) fixation were very low in all size fractions measured (> 0.7 µm). Volumetric (15) N uptake ranged from below detection (∼ 36% of > 300 samples) to a high of 0.3 nmol N l(-1) d(-1) and did not vary distinctly with depth or season. Areal N(2) fixation averaged ∼ 1 to 4 µmol N m(-2) d(-1) and contributed only ∼ 1% and 2% of new production and ∼ 0.25% and 0.5% of primary production for the mixed (winter) and stratified (spring-fall) periods respectively. N(2) fixation rates along the 2008 east-west transect were also extremely low (0-0.04 nmol N l(-1) d(-1), integrated average 2.6 µmol N m(-2) d(-1) ) with 37% of samples below detection and no discernable difference between stations. We demonstrate that diazotrophy and N(2) fixation contribute only a minor amount of new N to the P impoverished eastern Mediterranean Sea.

Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts.

In vast areas of the oceans, most of the primary production is performed by cells smaller than 2-3 mum in diameter (picophytoplankton). In recent years, several in situ molecular studies showed a broad genetic diversity of small eukaryotes by sequencing 18S rRNA genes. Compared with photosynthetic cyanobacteria that are dominated by two genera, Prochlorococcus and Synechococcus, marine photosynthetic picoeukaryotes (PPEs) are much more diverse, with virtually every algal class being represented. However, the genetic diversity and ecology of PPEs are still poorly described. Here, we show using in situ molecular analyses of psbA transcripts that PPEs in the Eastern Mediterranean Sea are highly diverse, probably very active, and dominated by groups belonging to the red algal lineages, Haptophyta, Heterokontophyta (also called Stramenopiles), and Cryptophyta.

A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment.

BACKGROUND: Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the photosystem II reaction center (psbA and psbD) were found in cyanophage genomes. This phenomenon suggested that the horizontal transfer of these genes may be involved in increasing phage fitness. To date, a very small percentage of marine bacteria and phages has been cultured. Thus, mapping genomic data extracted directly from the environment to its taxonomic origin is necessary for a better understanding of phage-host relationships and dynamics. RESULTS: To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM) with a codon usage position specific scoring matrix (cuPSSM). Our method has been applied successfully to classify core-photosystem-II gene fragments, including partial sequences coming directly from the ocean, to seven different taxonomic classes. Applying the method on a large set of DNA and RNA psbA clones from the Mediterranean Sea, we studied the distribution of cyanobacterial psbA genes and transcripts in their natural environment. Using our approach, we were able to simultaneously examine taxonomic and ecological distributions in the marine environment. CONCLUSION: The ability to accurately classify the origin of individual genes and transcripts coming directly from the environment is of great importance in studying marine ecology. The classification method presented in this paper could be applied further to classify other genes amplified from the environment, for which training data is available.

Seasonal dynamics of the endosymbiotic, nitrogen-fixing cyanobacterium Richelia intracellularis in the eastern Mediterranean Sea.

Biological nitrogen fixation has been suggested as an important source of nitrogen for the ultra-oligotrophic waters of the Levantine Basin of the Mediterranean Sea. In this study, we identify and characterize the spatial and temporal distribution of the N-fixing (diazotrophic) cyanobacterium Richelia intracellularis. R. intracellularis is usually found as an endosymbiont within diatoms such as Rhizosolenia spp and Hemiaulus spp. and is an important diazotroph in marine tropical oceans. In this study, two stations off the Mediterranean coast of Israel were sampled monthly during 2005-2007. R. intracellularis was identified by microscopy and by reverse transcribed-PCR which confirmed a 98.8% identity with known nifH sequences of R. intracellularis from around the world. The diatom-diazotroph associations were found throughout the year peaking during autumn (October-November) at both stations. Abundance of R. intracellularis ranged from 10 to 55 heterocysts l(-1) and correlated positively with the dissolved Si(OH)(4)/(NO(3)+NO(2)) ratio in surface waters. Although the rates of nitrogen fixation were very low, averaging approximately 1.1 nmol N l(-1) day(-1) for the R. intracellularis size fraction (>10 microm) from surface waters, they correlated positively with heterocyst counts during thermal stratification. The lack of large-scale diatom-diazotroph blooms and the low rates of nitrogen fixation by these diazotrophs may result from the P-starved conditions affecting the Levantine basin.

Viral photosynthetic reaction center genes and transcripts in the marine environment.

Cyanobacteria of the genera Synechococcus and Prochlorococcus are important contributors to photosynthetic productivity in the open ocean. The discovery of genes (psbA, psbD) that encode key photosystem II proteins (D1, D2) in the genomes of phages that infect these cyanobacteria suggests new paradigms for the regulation, function and evolution of photosynthesis in the vast pelagic ecosystem. Reports on the prevalence and expression of phage photosynthesis genes, and evolutionary data showing a potential recombination of phage and host genes, suggest a model in which phage photosynthesis genes help support photosynthetic activity in their hosts during the infection process. Here, using metagenomic data in natural ocean samples, we show that about 60% of the psbA genes in surface water along the global ocean sampling transect are of phage origin, and that the phage genes are undergoing an independent selection for distinct D1 proteins. Furthermore, we show that different viral psbA genes are expressed in the environment.

Molecular ecology of nifH genes and transcripts in the eastern Mediterranean Sea.

The eastern Mediterranean Sea is one of the most extreme oligotrophic oceanic regions on earth in terms of nutrient concentrations and primary productivity. Nitrogen fixation has been suggested to contribute to the high N : P molar ratios of approximately 28:1 found in this region. Surprisingly, no molecular biological work has been performed in situ to assess whether N(2) fixation genes actually occur in the eastern Mediterranean Sea, or to determine which organisms are responsible for this process. In this study, we examined the presence and expression of nitrogenase genes (nifH) in the upper water layer of the eastern Mediterranean. Clone libraries constructed from both DNA and reverse-transcribed PCR-amplified mRNA were examined and compared. We observed different nifH genes from diverse microbial groups, such as Cyanobacteria, Proteobacteria and methanogenic Archaea. Interestingly, numerous phylotypes were observed in coastal stations at the DNA level but none were active. However, in far offshore stations, the phylotypes observed at the DNA level were the ones that were actually active. Our preliminary study revealed diverse diazotrophs that possess and express nifH genes, which may support N(2) fixation in the eastern Mediterranean Sea.

Characterization of RS29, a blue-green proteorhodopsin variant from the Red Sea.

Using structural modeling comparisons and mutagenesis, amino acid residue 105 was found to function as a spectral tuning switch in marine proteorhodopsins (PR). Changes at this position account for most of the spectral difference between blue-absorbing PRs (B-PRs), and green-absorbing PRs (G-PRs). Here we analyzed a Red Sea variant (RS29) from a new family of PRs that is composed of G-PR type variants that possess glutamine instead of leucine at position 105 like in B-PRs. The absorption spectrum as well as photocycle of RS29 variant were measured and compared to point-mutated 'position 105' PRs. Unexpectedly, the absorption maximum of RS29 was 515 nm, a smaller blue shift compared to the 498 nm maximum of G-PR_L105Q. We found that two additional residues at positions 65 and 70 each contribute a small red shift to the absorption spectrum of G-PR and therefore appear to account for the intermediate absorption maximum of RS29 by their opposing influences on the spectrum. Our results show that in addition to the retinal pocket position 105 determinant, other residues predicted to be outside the retinal pocket fine-tune the absorption spectra of marine PRs. The RS29 photochemical reaction cycle was found to be 2 orders of magnitude slower than that of G-PR with a t(1/2) of >600 ms. This result raises the possibility of regulatory (i.e. sensory) rather than energy harvesting functions for some members of the PR family.