Abundance and Distribution of Ostreococcus sp. in the San Pedro Channel, California, as Revealed by Quantitative PCR

Ostreococcus is a genus of widely distributed marine phytoplankton which are picoplanktonic in size (<2 μm) and capable of rapid growth. Although Ostreococcus has been detected around the world, little quantitative information exists on its contribution to planktonic communities. We designed and implemented a genus-specific TaqMan-based quantitative PCR (qPCR) assay to investigate the dynamics and ecology of Ostreococcus at the USC Microbial Observatory (eastern North Pacific). Samples were collected from 5 m and the deep chlorophyll maximum (DCM) between September 2000 and August 2002. Ostreococcus abundance at 5 m was generally <5.0 × 10³ cells ml⁻¹, with a maximum of 8.2 × 10⁴ cells ml⁻¹. Ostreococcus abundance was typically higher at the DCM, with a maximum of 3.2 × 10⁵ cells ml⁻¹. The vertical distribution of Ostreococcus was examined in March 2005 and compared to the distribution of phototrophic picoeukaryotes (PPE) measured by flow cytometry. The largest contribution to PPE abundance by Ostreococcus was ~70% and occurred at 30 m, near the DCM. Despite its relatively low abundance, the depth-integrated standing stock of Ostreococcus in March 2005 was ~30 mg C m⁻². Our work provides a new technique for quantifying the abundance of Ostreococcus and demonstrates the seasonal dynamics of this genus and its contribution to picoeukaryote biomass at our coastal sampling station.     

Relationship of Geographic Distance,Depth, Temperature,and Viruses with Prokaryotic Communities in the Eastern Tropical Atlantic Ocean

The richness and biogeographical distribution pattern of bacterial and archaeal communities was assessed by terminal restriction fragment length polymorphism analysis of polymerase chain reaction-amplified fragments of the 16S rRNA gene at the surface (15-25 m depth), in the deep chlorophyll maximum layer (DCM; 50 m depth), and deep waters (75-1000 m depth) of the eastern tropical Atlantic Ocean. Additionally, prokaryotic and viral abundance and the frequency of infected prokaryotic cells (FIC) were determined along with physico-chemical parameters to identify factors influencing prokaryotic richness and biogeography. Viral abundance was highest in the DCM layer averaging 45.5 x 10(6) ml(-1), whereas in the mixed surface layer and in the waters below the DCM, average viral abundance was 11.3 x 10(6) and 4.3 x 10(6) ml(-1), respectively. The average estimate of FIC was 8.3% in the mixed surface layer and the DCM and 2.4% in deeper waters. FIC was positively related to prokaryotic and viral abundance and negatively to archaeal richness. There was no detectable effect of geographic distance (maximum distance between stations approximately 4600 km) or differences between water masses on bacterial and archaeal community composition. Bacterial communities showed a clear depth zonation, whereas changes in archaeal community composition were related to temperature and FIC. The results indicate that planktonic archaeal virus host systems are a dynamic component of marine ecosystems under natural conditions.     

Phototrophic picoeukaryotes of Onega Bay,the White Sea: Abundance and species composition

The abundance, biomass, and composition of phototrophic picoeukaryotes (PPE, cell size less than 3 μm) were studied in Onega Bay of the White Sea in June 2015. The highest PPE abundance and biomass were registered in the 0–5-m water layer. In the bay, in the 0–5-m water layer, the average abundance and biomass varied from 0 to 36.8 × 10⁴ cell/L and from 0 to 117 μg С/m³, respectively. The Illumina sequencing of V4 region of 18S rRNA gene revealed eight classes of PPE. Mamiellophyceae dominated both by number of reads and by operational taxonomic units. The green algae Bathycoccus prasinos, Ostreococcus tauri, and Micromonas pusila, as well as diatoms Skeletonema marinoi and Minidiscus trioculatus, were identified to the species level.     

Abundance, frequency of dividing cells and growth rates of Synechococcus sp. (cyanobacteria) in the stratified Northwest Mediterranean Sea

The abundance, frequency of dividing cells and growth ratesof the planktonic cyano bacteria Synechococcus sp. during thesummer of 1995 and 1996 were estimated in the Northwest MediterraneanSea to test whether depth-dependent growth rates of this speciesexplain its dominance in the deep chlorophyll maximum (DCM)layer formed during summer thermal stratification in the NWMediterranean, compared to the surface layer. Abundance at theDCM layer (50–70 m) was up to two orders of magnitudegreater than that at the surface, with values ranging from 1.7to 13x10⁶ cells I-¹ and from 4 to 175 x 10⁶ cells I-¹ at thesurface and in DCM waters, respectively. Gross growth rates,however, were much higher at the surface than in the DCM layer(surface: 0.76–1.07 day DCM: 0.30–0.47 day-¹ Thehigher gross growth rates at the surface layer were supportedby a higher frequency of dividing cells (surface: 0.09–0.24;DCM: 0.01–0.12). The negative correlation between theabundance or standing stock and growth rates of these planktonicpicocyanobacteria points to losses, and not growth rate, asthe main control on the abundance of Synechococcus. Althoughwe provide some evidence that grazing alone may be able to accountfor these losses, further, direct determinations are clearlyneeded to elucidate the regulation of the abundance of Synechococcusin the NW Mediterranean.     

Grazing impact of different heterotrophic nanoflagellates on eukaryotic (Ostreococcus tauri) and prokaryotic picoautotrophs (Prochlorococcus and Synechococcus)

Autotrophic picoplankton (<3 microm) composed of both prokaryotes and eukaryotes are the most abundant primary producers on Earth. In this study we examined the ingestion of the picoeukaryote Ostreococcus tauri by different marine heterotrophic nanoflagellates (HNF) with various morphologies, swimming and feeding behaviours. Cultures of specific bacterivorous nanoflagellates (Rhynchomonas nasuta, Jakoba libera, and a culture of Cafeteria sp./Monosiga sp.) and natural nanoflagellate populations were used as grazers. For comparison with Ostreococcus, we used similar-sized prokaryotes as prey, Prochlorococcus and Synechococcus. We observed large species-specific differences in terms of: use of picoautotrophs among nanoflagellates, time lag between prey addition and prey consumption (0-196 h), grazing rate (0-0.12 h(-1)), growth rate (0-0.3 h(-1)) and maximum abundance of HNF reached in experimental bottles (e.g. from 10(4) to 10(5) cells ml(-1), for a natural coastal population and a Cafeteria sp./Monosiga sp. culture feeding Ostreococcus respectively). Overall, this study shows that the nanoflagellate community composition is conclusive for picoautotrophic community structure and, vice versa, the picoautotrophic community structure favours or inhibits the growth of some nanoflagellate groups.     

长江口及其邻近水域冬季浮游植物群集

应用Uterm hl方法分析了2005年2月28日至3月10日在长江口及其邻近水域进行的大面调查所获浮游植物采水样品,报道了该水域浮游植物的群落特征.初步鉴定浮游植物5门67属130种(含未定名25种).调查水域浮游植物群落主要由硅藻组成,其次为甲藻,此外还有少量的金藻、蓝藻和绿藻.主要优势种为具槽帕拉藻(Paralia sulcata)、中肋骨条藻(Skeletonema costatum)、圆海链藻(Thalassiosira rotula)、标志布莱克里亚藻(Bleakeleya nota-ta)、辐射圆筛藻(Coscinodiscus radiatus)和离心列海链藻(Thalassiosira excentrica).调查区浮游植物的细胞丰度介于0.1~90.0cells.ml-1,平均值为10.1cells.ml-1.浮游植物的水平分布特征是近岸处浮游植物丰度高,远岸处丰度低.水体表层的浮游植物细胞丰度最高,表层之下细胞丰度略有降低,但变化不大.浮游植物的细胞丰度和叶绿素a与硝酸盐、亚硝酸盐、铵盐、磷酸盐和硅酸盐浓度呈显著正相关,而与盐度呈负相关.调查区中部香农-威纳多样性指数和Pielou均匀度指数较高,而东北部和近岸水域较低.     

Microbiological analysis of cryopegs from the Varandei Peninsula, Barents Sea

The paper deals with the microbiological characterization of water-saturated horizons in permafrost soils (cryopegs) found on the Varandei Peninsula (Barents Sea coast), 4-20 m deep. The total quantity of bacteria in the water of cryopegs was 3.5 x 10(8) cells/ml. The population of cultivated aerobic heterotrophic bacteria was 3-4 x 10(7) cells/ml and the number of anaerobic heterotrophic bacteria varied from 10(2) to 10(5) cells/ml depending on cultivation temperature and salinity. Sulfate-reducing bacteria and methanogenic archaea were found as hundreds and tens of cells per ml of water, respectively. A pure culture of a sulfate-reducing strain B15 was isolated from borehole 21 and characterized. Phylogenetic analysis has shown that the new bacterium is a member of the genus Desulfovibrio with Desulfovibrio mexicanus as its closest relative (96.5% similarity). However, the significant phenotypic differences suggest that strain B15 is a new species of sulfate-reducing bacteria.     

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic

The contribution of Chloroflexi-type SAR202 cells to total picoplankton and bacterial abundance and uptake of D- and L-aspartic acids (Asp) was determined in the different meso- and bathypelagic water masses of the (sub)tropical Atlantic (from 35 degrees N to 5 degrees S). Fluorescence in situ hybridization (FISH) revealed that the overall abundance of SAR202 was < or = 1 x 10(3) cells ml(-1) in subsurface waters (100 m layer), increasing in the mesopelagic zone to 3 x 10(3) cells ml(-1) and remaining fairly constant down to 4000 m depth. Overall, the percentage of total picoplankton identified as SAR202 increased from < 1% in subsurface waters to 10-20% in the bathypelagic waters. On average, members of the SAR202 cluster accounted for about 30% of the Bacteria in the bathypelagic waters, whereas in the mesopelagic and subsurface waters, SAR202 cells contributed < 5% to total bacterial abundance. The ratio of D-Asp : L-Asp uptake by the bulk picoplankton community increased from the subsurface layer (D-Asp : L-Asp uptake ratio approximately 0.03) to the deeper layers reaching a ratio of approximately 1 at 4000 m depth. Combining FISH with microautoradiography to determine the proportion of SAR202 cells taking up D-Asp versus L-Asp, we found that approximately 30% of the SAR202 cells were taking up L-Asp throughout the water column while D-Asp was essentially not taken up by SAR202. This D-Asp : L-Asp uptake pattern of SAR202 cells is in contrast to that of the bulk bacterial and crenarchaeal community in the bathypelagic ocean, both sustaining a higher fraction of D-Asp-positive cells than L-Asp-positive cells. Thus, although the Chloroflexi-type SAR202 constitutes a major bathypelagic bacterial cluster, it does not contribute to the large fraction of d-Asp utilizing prokaryotic community in the meso- and bathypelagic waters of the North Atlantic, but rather utilizes preferentially L-amino acids.     

Viral abundance, decay, and diversity in the meso- and bathypelagic waters of the north atlantic

To elucidate the potential importance of deep-water viruses in controlling the meso- and bathypelagic picoplankton community, the abundance, decay rate, and diversity of the virioplankton community were determined in the meso- and bathypelagic water masses of the eastern part of the subtropical North Atlantic. Viral abundance averaged 1.4 x 10(6) ml(-1) at around 100 m of depth and decreased only by a factor of 2 at 3,000 to 4,000 m of depth. In contrast, picoplankton abundance decreased by 1 order of magnitude to the Lower Deep Water (LDW; 3,500- to 5,000-m depth). The virus-to-picoplankton ratio increased from 9 at about 100 m of depth to 110 in the LDW. Mean viral decay rates were 3.5 x 10(-3) h(-1) between 900 m and 2,750 m and 1.1 x 10(-3) h(-1) at 4,000 m of depth, corresponding to viral turnover times of 11 and 39 days, respectively. Pulsed-field gel electrophoresis fingerprints obtained from the viral community between 2,400 m and 4,000 m of depth revealed a maximum of only four bands from 4,000 m of depth. Based on the high viral abundance and the low picoplankton production determined via leucine incorporation, we conclude that the viral production calculated from the viral decay is insufficient to maintain the high viral abundance in the deep North Atlantic. Rather, we propose that substantial allochthonous viral input or lysogenic or pseudolysogenic production is required to maintain the high viral abundance detected in the meso- and bathypelagic North Atlantic. Consequently, deep-water prokaryotes are apparently far less controlled in their abundance and taxon richness by lytic prokaryotic phages than the high viral abundance and the virus-to-picoplankton ratio would suggest.     

Modelling viral impact on bacterioplankton in the North Sea using artificial neural networks

The temporal variability of the viral impact on bacterioplankton during the summer-winter transition in the North Sea was determined and artificial neural networks (ANNs) were developed to predict viral production and the frequency of infected bacterial cells (FIC). Viral production and FIC were estimated using a virus-dilution approach during four cruises in the southern North Sea between July and December 2000 and an additional cruise in June 2001. Supplementary data such as bacterial production, and bacterial and viral abundance were collected to relate changes in FIC and viral production to the dynamics of other biotic parameters. Average viral abundance varied between 4.4 x 10(6) ml(-1) in December and 29.8 x 10(6) ml(-1) in July. Over the seasonal cycle, viral abundance correlated best with bacterial production. Average bacterial abundance varied between 0.5 x 10(6) ml(-1) in December and 1.3 x 10(6) ml(-1) in July. Monthly average values of FIC ranged from 9% in September to 39% in June and the average viral production from 11 x 10(4) ml(-1) h(-1) in December to 35 x 10(4) ml(-1) h(-1) in July. The data set was used to develop ANN-based models of viral production and FIC. Viral production was modelled best using sampling time, and bacterial and viral abundance as input parameters to an ANN with two hidden neurons. Modelling of FIC was performed using bacterial production as an additional input parameter for an ANN with three hidden neurons. The models can be used to simulate viral production and FIC based on regularly recorded and easily obtainable parameters such as bacterial production, bacterial and viral abundance.     

Seasonal succession of tintinnids in the Nervion River estuary, Basque Country, Spain

The seasonal succession of tintinnids was examined in the outerpart of the Nervión River estuary. Sampling was carriedout at monthly intervals from March 2000 to March 2002. In thisperiod, 21 species, belonging to 12 genera, were recorded, amongwhich Tintinnopsis was the most abundant genus, contributingup to 86% of the total ciliate abundance. The maximum abundancewas recorded in summer, with 7.4 x 10³ individuals L^-1 in July2001, while the lowest value occurred in winter. A significantand positive correlation was found between temperature and tintinnidabundance. Most of the species showed a distinct seasonal occurrenceand on this basis five different groups were differentiated.Two main changes in the species composition were recorded, onein March–April and the second in October–November.In this paper, the seasonal dynamics and the spatial distribution,as well as remarks on the morphology and ecology, of the mostimportant tintinnid species in the estuary are given.     

Abundance and Biomass of Heterotrophic Flagellates, and Factors Controlling Their Abundance and Distribution in Sediments of Botany Bay

The abundance and biomass of heterotrophic flagellates were estimated monthly in sediments of Botany Bay during March 1999-February 2000. The annual abundance and biomass were in the ranges of 0.46-4.70 x 10(5) cells/cm(3) and of 0.30-8.61 micro g C/cm(3), respectively. The majority of heterotrophic flagellates (93-100%) were less than 10 mm in length and few flagellates were larger than 10 mm. Of the total microbial carbon biomass, heterotrophic flagellates made up about 5% (but at times up to 35%). The contribution of heterotrophic flagellates varied from month to month, and among the sites. The abundance of heterotrophic flagellates was negatively correlated with sediment grain size and positively correlated with the abundance of bacteria, algae (autotrophic flagellates and diatoms), and their probable grazers. A best subsets regression analysis showed that bacterial and algal abundance are the most important factors controlling the abundance of heterotrophic flagellates. When the previously reported grazing rates on bacteria were applied, heterotrophic flagellates would consume a maximum of 64% of bacterial standing stock daily in Botany Bay, suggesting that heterotrophic flagellates are important as bacterivores. However, the importance of heterotrophic flagellate grazing probably varies significantly among the sites and from month to month.     

Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies

Prochlorococcus is a marine cyanobacterium which is found at high abundances in world's tropical and subtropical oligotrophic oceans. The genus Prochlorococcus can be divided into two major groups based on light physiology. Both of these groups can be further subdivided into genetically distinct lineages, or ecotypes. Real-time polymerase chain reaction (PCR) assays based on sequence differences in the 16S-23S rDNA internal transcribed spacer or the 23S rDNA were developed to examine the distribution of each ecotype in the field. The real-time PCR assays enabled linear quantification of concentrations ranging from 10 to 4 x 10(5) cells ml(-1). These assays were applied to a stratified water column in the Sargasso Sea. The majority of Prochlorococcus cells above 110 m belonged to the one of the low chlorophyll b/a ratio (high-light adapted) ecotypes, while two types of high chlorophyll b/a ratio (low-light adapted) cells dominated below 110 m. The other three types were found at significantly lower numbers or not detected at all. Differences in the abundance of ecotypes within the major light physiology groupings suggest that other factors, such as nutrient utilization and differential mortality, are driving their relative distributions. Real-time PCR assays will enable further exploration of these factors and temporal and geographic variability in ecotype abundance.     

Occurrence,Dynamics and Production of Picoplankton in Hungarian Shallow Lakes

Phototrophic picoplankton were detected in 10⁵-10⁶ cells/ml concentrations in seven water bodies of differing chemistry and trophic level. Dominant picoplankters were, at all sites, coccoid cyanobacteria of 0.8-1.2 μm dimensions, exhibiting red or yellow autofluorescence. Apart from the effects of water temperature their quantitative dynamics were significantly influenced by the nitrogen supply and the herbivorous zooplankton (Cladocera). Their maximum contribution to the total planktonic primary production was about 50%, both in mesotrophic and hypereutrophic environments. However during the bloom of filamentous nitrogen-fixing blue-greens their role became negligible. In phytoplankton communities the significance of picoplankton is overestimated several times, when based on the cell count, while it is underestimated on the basis of biomass. The most useful characteristics of phytoplankton size groups was the total surface area of their cells.     

Bacterial quantity and microbial reactivity in Tugur bay of the Okhotsk Sea

The paper presents the results of investigation of the total abundance and the biomass of bacterioplankton, the abundance of heterotrophic bacteria, and the activity of microbiological processes involved in the carbon cycle in the water of the Bay of Tugur of the Sea of Okhotsk. In different regions of the bay, the total abundance of bacterioplankton was found to vary from 0.51 x 10(6) to 2.54 x 10(6) cells/ml; the bacterioplankton biomass, from 8.5 to 46.5 micrograms C/l; the abundance of heterotrophic bacteria, from 0.06 x 10(3) to 2.12 x 10(3) cells/ml; the bacterial assimilation of CO2, glucose, acetate, and protein hydrolysate, from 0.8 to 6.3, from 0.11 to 1.88, from 0.07 to 0.56, and from 0.01 to 0.22 mg C/(m3 day), respectively; the degradation of organic matter ranged from 28 to 221 mg C/(m3 day); and the intensity of methane oxidation, from 0.0005 to 0.17 microliter CH4/l. The spatial pattern and the functional characteristics of bacterioplankton in the Bay of Tugur were found to be dependent on the tidal dynamics.     

Seasonal variation of particulate organic carbon, dissolved organic carbon and the contribution of microbial communities to the live particulate organic carbon in a shallow near-bottom ecosystem at the Northwestern Mediterranean Sea

Microbial planktonic communities (i.e. bacteria and protozoa), phytoplankton, dissolved organic carbon (DOC) and particulate organic carbon (POC) were seasonally examined at Medes Islands (Northwestern Mediterranean) to assess their variation in abundance and composition throughout the year in a near-bottom littoral ecosystem. From October 1995 to November 1996, samples were collected between two and six times per month at 0.5 m above the bottom. Mean DOC and POC values throughout the year were 2560 180 (SE) and 387 ± 35 g C l^-1, respectively. All year, detrital organic carbon (detrital=total POC - live carbon) represented the main POC fraction, and mean live carbon was 24 ± 9 g C l^-1. Winter and spring had maximum values of POC, and spring and summer had maximum values of DOC. Heterotrophic bacteria, with a mean abundance of 5.16 ± 0.08 x 10⁵ cells ml^-1, were the main contributor to live carbon (26 ± 7%). During winter, heterotrophic bacterial biomass decreased 40% due to a decrease in mean biovolume per cell. Synechococcus sp. and Prochlorococcus sp. abundance were 2.24 ± 0.09 x 10⁴ and 1.05 ± 0.07 x 10⁴ cells ml^-1, respectively. However, while Synechococcus sp. were present all year, Prochlorococcus sp. were not observed from April to July. Mean phytoplankton (i.e. diatoms and dinoflagellates) abundance was 2.06 ± 0.40 x 10⁴ cells l^-1 with biomass at a maximum during the winter months, the period with the lowest temperature and the highest nutrient concentration. The size composition of live carbon showed two clearly distinct periods: from December to March, live carbon was dominated in biomass by microplankton, while from April to November, pico- and nanoplankton cells were dominant. Overall, the dynamics of the near-bottom planktonic communities was characterized by a low biomass of heterotrophic and autotrophic bacteria, phytoplankton and ciliates in contrast to previous water column studies. This pattern and the high temporal heterogeneity of the different planktonic communities are discussed in relation to the physical and chemical characteristics of the environment, as well as to the potential role that benthic communities may be exerting in the control of the near-bottom planktonic communities.      

Dynamics and ecology of an Indo-Pacific conch, Conomurex persicus (Mollusca: Gastropoda) in southeastern Turkey

Conomurex persicus, one of the tropical conchs, has been introduced to one of the subtropical regions, the northeastern Mediterranean Sea, and invaded sandy bottoms between 1 and 10 m deep. Population dynamics were studied from specimens collected with a standard dredge (60 x 15 cm mouth opening, 0.5 x 0.5 cm eye opening of net). Samples of C persicus were collected monthly along the 5 and 10 m depth contours off Erdemli, Mersin, Turkey, in February and May 2000. Intra-annual density depended on salinity levels, while inter-annual density was correlated with bottom water temperature. Specimens underwent spring emergences and winter burial and sheltering (disappearance). Emergence took place in March when temperatures rose and the disappearance occurred in October-November when temperatures dropped. Adults live at 10 m, juveniles are recruited at a 5 m depth. Recruitment began in April and continued for the next 6 months. In contrast to shell width or shell lip thickness, shell length was not a convenient index for estimation of growth parameters. Annual production and mortality were calculated to be 7.86 g m(-2) and 3.80 g m(-2), respectively, in April-November.     

Flow cytometry assessment of bacterioplankton in tropical marine environments

Flow cytometry was used to characterize bacterioplankton from two tropical environments in Brazil: the eutrophic Guanabara Bay and the oligotrophic southwest Atlantic Ocean. Bacterial abundance was evaluated by flow cytometry, and cells were stained with SYTO 13, allowing demonstration of differences in nucleic acid content. Bacterial production was also evaluated by means of 3H-leucine incorporation. Bacterial numbers were different for both sites. In Atlantic Ocean samples, we found a maximum of 5.50 x 10(5) cells ml(-1), and low nucleic acid content organisms predominated. In Guanabara Bay, bacterial numbers were one order of magnitude higher than in the ocean, and they varied from outer bay (1.01 x 10(6) cells ml(-1)) to inner bay (6.90 x 10(6) cells ml(-1)). Bacterial activity in ocean samples varied from 4.6 to 126 ng C l(-1) h(-1), while in the bay, mean values ranged from 1.95 microg C l(-1) h(-1) (outer bay) to 7.35 microg C l(-1) h(-1) (inner bay). Values found for both parameters are characteristic of different trophic situations. These results illustrate the utility of cytometric analyses of bacterioplankton populations in characterizing their large spatial and temporal scales of distribution in aquatic ecosystems.