Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity and dynamics remain largely unexplored. In this study, we monitored the interannual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a nonlocal seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota marine group I and Euryarchaeota group II.B in winter and Euryarchaeota group II.A in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.ong-term dynamic | dormancy | taxonomic diversity | microbial observatory | Somlit

Prochlorococcus, the most abundant genus of photosynthetic organisms, owes its remarkably large depth distribution in the oceans to the occurrence of distinct genotypes adapted to either low- or high-light niches. The pcb genes, encoding the major chlorophyll-binding, light-harvesting antenna proteins in this genus, are present in multiple copies in low-light strains but as a single copy in high-light strains. The basis of this differentiation, however, has remained obscure. Here we show that the moderate low-light-adapted strain Prochlorococcus sp. MIT 9313 has one iron-stress-induced pcb gene encoding an antenna protein serving photosystem I (PSI)--comparable to isiA genes from cyanobacteria--and a constitutively expressed pcb gene encoding a photosystem II (PSII) antenna protein. By comparison, the very low-light-adapted strain SS120 has seven pcb genes encoding constitutive PSI and PSII antennae, plus one PSI iron-regulated pcb gene, whereas the high-light-adapted strain MED4 has only a constitutive PSII antenna. Thus, it seems that the adaptation of Prochlorococcus to low light environments has triggered a multiplication and specialization of Pcb proteins comparable to that found for Cab proteins in plants and green algae.

Little is known about the dynamics of dissolved phosphate in oligotrophic areas of the world's oceans, where concentrations are typically in the nanomolar range. Here, we have budgeted phosphate uptake by the dominant microbial groups in order to assess the effect of the microbial control of this depleted nutrient in the North Atlantic gyre. Low concentrations (2.2 +/- 1.2 nM) and rapid microbial uptake (2.1 +/- 2.4 nM day(-1)) of bioavailable phosphate were repeatedly determined in surface waters of the North Atlantic oligotrophic gyre during spring and autumn research cruises, using a radiotracer dilution bioassay technique. Upper estimates of the concentration of bioavailable phosphate were 7-55% of the dissolved mineral phosphate suggesting that a considerable part of the chemically measured nanomolar phosphate was in a form unavailable for direct microbial uptake. A 1:1 relationship (r(2) = 0.96, P < 0.0001) was observed between the bioavailable total phosphate uptake and the phosphate uptake of all the flow sorted bacterioplankton cells, demonstrating that bacterioplankton were the main consumers of phosphate. Within the bacterioplankton a group of heterotrophic bacteria and Prochlorococcus phototrophic cyanobacteria, were the two major competing groups for bioavailable phosphate. These heterotrophic bacteria had low nucleic acid content and 60% of them comprised of SAR11 clade cells based on the results of fluorescence in situ hybridization. Each of the two competing bacterial groups was responsible for an average of 45% of the phosphate uptake, while Synechococcus cyanobacteria (7%) and picoplanktonic algae (0.3%) played minor roles in direct phosphate uptake. We have demonstrated that phosphate uptake in the oligotrophic gyre is rapid and dominated by two bacterial groups rather than by algae.

(35)S-Methionine and (3)H-leucine bioassay tracer experiments were conducted on two meridional transatlantic cruises to assess whether dominant planktonic microorganisms use visible sunlight to enhance uptake of these organic molecules at ambient concentrations. The two numerically dominant groups of oceanic bacterioplankton were Prochlorococcus cyanobacteria and bacteria with low nucleic acid (LNA) content, comprising 60% SAR11-related cells. The results of flow cytometric sorting of labelled bacterioplankton cells showed that when incubated in the light, Prochlorococcus and LNA bacteria increased their uptake of amino acids on average by 50% and 23%, respectively, compared with those incubated in the dark. Amino acid uptake of Synechococcus cyanobacteria was also enhanced by visible light, but bacteria with high nucleic acid content showed no light stimulation. Additionally, differential uptake of the two amino acids by the Prochlorococcus and LNA cells was observed. The populations of these two types of cells on average completely accounted for the determined 22% light enhancement of amino acid uptake by the total bacterioplankton community, suggesting a plausible way of harnessing light energy for selectively transporting scarce nutrients that could explain the numerical dominance of these groups in situ.

Low nucleic acid (LNA) bacterioplankton (sorted by flow cytometry) were characterised in surface water samples along a meridional transect from 48°N to 40°S across the Atlantic Ocean. The LNA bacterioplankton abundance and metabolic activity, assessed by their 35 S-methionine uptake rate, were similar along the transect, representing 36 ± 6 and 36 ± 11% of total bacterioplankton, respectively. Fluorescence in situ hybridisation analysis of the flow-sorted cells revealed that the LNA bacterioplankton population was dominated (59 ± 4%) by and contained virtually all the identifiable SAR11 clade cells throughout the Atlantic Ocean. Therefore, the present study provides ecological characterisation of this flow-sorted group and suggests both phylogenetic and functional constancy of the LNA bacterioplankton at the basin-scale. KEY WORDS: Flow cytometry sorting · Cell metabolic activity · SAR11 clade · CARD-FISH · Radioactive tracer labelling · Atlantic Ocean Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 45: [107][108][109][110][111][112][113] 2006 into the South Subtropical Frontal Zone (SSFZ, Belkin & Gordon 1996). As it was not possible to work on every sample collected along the transect, we selected representative samples for a basin-scale study. MATERIALS AND METHODSSampling area. The material was collected and measurements were made primarily on one Atlantic Meridional Transect (AMT) cruise on board the RRS 'James Clark Ross', cruise no. JR91, transect no. AMT-13, in September and October 2003 (Fig. 1). Up to 24 seawater samples were collected approximately every 12 h from a range of depths in the top 300 m using a rosette of 24 × 20 l Niskin bottles mounted on a conductivity-temperature-density (CTD) profiler. The Bpl cells were routinely fixed with 1% paraformaldehyde (PFA) final concentration.The abundance of Bpl was determined at every station , and for the present study 9 stations were chosen along the transect to represent the basin-scale range of surface waters (Fig. 1). The samples for the study of turnover rates of methionine (Met) by total bacterioplankton and by the LNA group sorted by flow cytometry were collected from depths of 3 to 7 m. Methionine uptake was chosen because of the high specific activity of the 35 S-methionine precursor and because previous studies have shown that microbial uptake of this amino acid are strongly correlated with the uptake of other amino acids such as leucine (Zubkov et al. 2004). The analyses also included the phylogenetic affiliation of the flow-sorted LNA cells using fluorescence in situ hybridisation (FISH). To test that the results obtained from the selected stations were representative of the Atlantic surface waters, an additional 15 stations ( Fig. 1) were included for comparison of the relative LNA abundance and Met uptake rates.Additional samples for phylogenetic analyses of bacterioplankton were collected from the Northern Atlantic at 5 stations on a later cruise on the RRS 'Discovery', cruise...

The search for a better understanding of why cyanobacteria often dominate phytoplankton communities in eutrophic freshwater ecosystems has led to a growing interest in the interactions between cyanobacteria and bacteria. Against this background, we studied the location of bacteria within Microcystis colonies, and compared the structural and phylogenetic diversity of Microcystis-attached and free-living bacterial communities living in the same French lake, the Villerest reservoir. Using transmission electron microscopy, we show that most of the bacteria inside the colonies were located close to detrital materials that probably resulted from lysis of Microcystis cells. The 16S rRNA sequencing approach revealed a clear distinction between the attached and free-living communities at the levels of both their general structure and their operational taxonomic unit (OTU) composition. In particular, Microcystis colonies appeared to be depleted of Actinobacteria, but conversely enriched in Gammaproteobacteria, in particular when the bloom was declining. At the OTU level, a clear distinction was also found between attached and free-living bacteria, and new clades were identified among our sequences. All these findings suggest that Microcystis colonies constitute a distinct habitat for bacteria living in freshwater ecosystems, and that direct and indirect interactions (cell lysis, nutrient recycling, etc.) may occur between them inside these colonies.

The cell cycle of the chlorophyll b-possessing marine cyanobacterium Prochlorococcus is highly synchronized under natural conditions. To understand the underlying molecular mechanisms we cloned and sequenced dnaA and ftsZ, two key cell cycle-associated genes, and studied their expression. An axenic culture of Prochlorococcus sp. strain PCC 9511 was grown in a turbidostat with a 12 h-12 h light-dark cycle for 2 weeks. During the light periods, a dynamic light regimen was used in order to simulate the natural conditions found in the upper layers of the world's oceans. This treatment resulted in strong cell cycle synchronization that was monitored by flow cytometry. The steady-state mRNA levels of dnaA and ftsZ were monitored at 4-h intervals during four consecutive division cycles. Both genes exhibited clear diel expression patterns with mRNA maxima during the replication (S) phase. Western blot experiments indicated that the peak of FtsZ concentration occurred at night, i.e., at the time of cell division. Thus, the transcript accumulation of genes involved in replication and division is coordinated in Prochlorococcus sp. strain PCC 9511 and might be crucial for determining the timing of DNA replication and cell division.Most knowledge about the regulation of bacterial cell division and replication of DNA stems from the analysis of only three species, Escherichia coli (43, 44), Caulobacter crescentus (35, 37), and Bacillus subtilis (25,34). In some cyanobacteria these processes are reported to be under the control of a circadian clock (1,5,15,18,24,39). However, studies directly concerning the diel expression of cell cycle-relevant genes in cyanobacteria are scarce (21).The cell cycle of the marine cyanobacterium Prochlorococcus is characterized by a well-defined and discrete DNA synthesis phase, S (42). In the field, the cell cycle is highly synchronized by the daily alternation of night and day. DNA replication occurs in late afternoon, and cell division occurs at night (15,20,41,42). It is not known at which stage or by which regulatory mechanism the linkage between cell cycle and environmental conditions is achieved. Experiments in which the time of light onset was changed suggested that the passage from darkness to light (equivalent to sunrise) might be involved in timing of DNA synthesis in Prochlorococcus (16a).To elucidate potential components involved in the synchronization and diel control of cell cycle progression in Prochlorococcus, the genes dnaA and ftsZ were cloned and analyzed. The GTP-binding protein FtsZ is widely distributed among eubacteria, archaea, and plastids and is usually considered the key factor in the initiation of cell division by the formation of a ring-shaped structure that recruits several other proteins (FtsA, FtsQ, and FtsW) to the division site (8). FtsZ has also recently been found in a mitochondrion (2), where it is normally replaced by Dynamin (reviewed in reference 9). DnaA is a ubiquitous bacterial protein that acts as a helicase to initiate DNA replication in eubacteria. I...

No abstract