Population Dynamics of Chesapeake Bay Virioplankton: Total-Community Analysis by Pulsed-Field Gel Electrophoresis

Recognition of viruses as the most abundant component of aquatic microbial communities has stimulated investigations of the impact of viruses on bacterio- and phytoplankton host communities. From results of field studies to date, it is concluded that in most aquatic environments, a reduction in the number of bacteria on a daily basis is caused by viral infection. However, the modest amount of in situ virus-mediated mortality may be less significant than viral infection serving to maintain clonal diversity in the host communities directly, through gene transmission (i.e., transduction), and indirectly, by elimination of numerically dominant host species. If the latter mechanism for controlling community diversity prevails, then the overall structure of aquatic viral communities would be expected to change as well over short seasonal and spatial scales. To determine whether this occurs, pulsed-field gel electrophoresis (PFGE) was used to monitor the population dynamics of Chesapeake Bay virioplankton for an annual cycle (1 year). Virioplankton in water samples collected at six stations along a transect running the length of the bay were concentrated 100-fold by ultrafiltration. Viruses were further concentrated by ultracentrifugation, and the concentrated samples were embedded in agarose. PFGE analysis of virus DNA in the agarose plugs yielded several distinct bands, ranging from 50 to 300 kb. Principal-component and cluster analyses of the virus PFGE fingerprints indicated that changes in virioplankton community structure were correlated with time, geographical location, and extent of water column stratification. From the results of this study, it is concluded that, based on the dynamic nature of the Chesapeake Bay virioplankton community structure, the clonal diversity of bacterio- and phytoplankton host communities is an important component of the virus community.     

Seasonal Depth-Related Gradients in Virioplankton: Standing Stock and Relationships with Microbial Communities in Lake Pavin (France)

This study presents a depth-related survey of virioplankton abundance in Lake Pavin (Massif Central, France), in relation to the abundances of heterotrophic prokaryotes, picocyanobacteria (Pcy), autotrophic picoeukaryotes (Peu), and of autotrophic (ANF) and heterotrophic (HNF) nanoflagellates. The sampling strategy was designed to be representative of the physico-chemical gradients of the whole water column of the lake, and the seasonal variability as well. In mixolimnic surface waters, all communities were present and viral abundance peaked in summer and autumn. Viral abundance was significantly correlated (p < 0.001) with Pcy, Peu, and ANF, indicating that cyanophages and perhaps other phytoplankton viruses represent a significant pool of viral standing stocks in the mixolimnion of Lake Pavin. Microautotrophs were absent in the deep monimolimnic water masses, where viruses and heterotrophic prokaryotes exhibited highest seasonal abundances in summer and/or autumn and were significantly correlated (p < 0.001) to each other. This indicates that the anoxic monimolimnion of Lake Pavin is an exclusive habitat for viruses and heterotrophic prokaryotes. We conclude that in this habitat, host availability is prevalent over other factors (temperature, oxygen, nutrients, grazers) in favoring viral proliferation.     

Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea

There are an estimated 10³⁰ virioplankton in the world oceans, the majority of which are phages (viruses that infect bacteria). Marine phages encompass enormous genetic diversity, affect biogeochemical cycling of elements, and partially control aspects of prokaryotic production and diversity. Despite their importance, there is a paucity of data describing virioplankton distributions over time and depth in oceanic systems. A decade of high-resolution time-series data collected from the upper 300 m in the northwestern Sargasso Sea revealed recurring temporal and vertical patterns of virioplankton abundance in unprecedented detail. An annual virioplankton maximum developed between 60 and 100 m during periods of summer stratification and eroded during winter convective mixing. The timing and vertical positioning of this seasonal pattern was related to variability in water column stability and the dynamics of specific picophytoplankton and heterotrophic bacterioplankton lineages. Between 60 and 100 m, virioplankton abundance was negatively correlated to the dominant heterotrophic bacterioplankton lineage SAR11, as well as the less abundant picophytoplankton, Synechococcus. In contrast, virioplankton abundance was positively correlated to the dominant picophytoplankton lineage Prochlorococcus, and the less abundant alpha-proteobacteria, Rhodobacteraceae. Seasonally, virioplankton abundances were highly synchronous with Prochlorococcus distributions and the virioplankton to Prochlorococcus ratio remained remarkably constant during periods of water column stratification. The data suggest that a significant fraction of viruses in the mid-euphotic zone of the subtropical gyres may be cyanophages and patterns in their abundance are largely determined by Prochlorococcus dynamics in response to water column stability. This high-resolution, decadal survey of virioplankton abundance provides insight into the possible controls of virioplankton dynamics in the open ocean.     

Drivers of interannual variability in virioplankton abundance at the coastal western Antarctic peninsula and the potential effects of climate change

An 8‐year time‐series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive interannual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Their findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus, the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling.     

模拟水流扰动对香溪河库湾浮游病毒-宿主动态的影响

【背景】浮游病毒是淡水生态系统的重要组成部分,在调节浮游细菌和藻类群落结构及调控系统物质循环过程中起着重要的作用。水库具有不同于湖泊的水动力过程,产生的扰动可能影响浮游病毒的调控功能。【目的】研究水力扰动对浮游病毒-宿主动态的影响,为阐释水库生境下浮游病毒生态功能提供理论依据。【方法】以香溪河库湾原水为材料,模拟不同流速扰动对病毒-宿主动态的影响;通过病毒丰度、宿主丰度、宿主裂解率、宿主溶源诱导率等参数的变化反映这种动态变化过程,并分析其与环境因子间的关系。【结果】0.05 m/s和0.10 m/s的流速扰动强度对浮游植物和浮游细菌生长有显著促进作用,但扰动对浮游病毒丰度的影响不显著;扰动能促进病毒介导的浮游植物和细菌裂解率上升,而且0.05 m/s扰动强度的促进作用大于0.10 m/s;同时,扰动显著降低了浮游植物溶源诱导率,但引起浮游细菌溶源诱导率的显著上升(P<0.05)。【结论】模拟扰动对浮游病毒-宿主动态过程产生了显著的影响,表明水库浮游病毒维持种群延续的生态策略可能与湖泊浮游病毒存在差异。     

Virioplankton: Viruses in Aquatic Ecosystems

The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest in viruses in the aquatic environment. Surprisingly little was known of the interaction of viruses and their hosts in nature. In the decade since the reports of extraordinarily large virus populations were published, enumeration of viruses in aquatic environments has demonstrated that the virioplankton are dynamic components of the plankton, changing dramatically in number with geographical location and season. The evidence to date suggests that virioplankton communities are composed principally of bacteriophages and, to a lesser extent, eukaryotic algal viruses. The influence of viral infection and lysis on bacterial and phytoplankton host communities was measurable after new methods were developed and prior knowledge of bacteriophage biology was incorporated into concepts of parasite and host community interactions. The new methods have yielded data showing that viral infection can have a significant impact on bacteria and unicellular algae populations and supporting the hypothesis that viruses play a significant role in microbial food webs. Besides predation limiting bacteria and phytoplankton populations, the specific nature of virus-host interaction raises the intriguing possibility that viral infection influences the structure and diversity of aquatic microbial communities. Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities.     

流式细胞仪检测纳帕海高原湿地浮游病毒和浮游细菌丰度

【背景】浮游病毒是水体微生物群落中重要的组成成分,深入研究浮游病毒的时空分布有助于更好地保护和开发当地的微生物资源。【目的】对采集到的纳帕海高原湿地水样中的浮游病毒和浮游细菌进行计数,揭示纳帕海高原湿地浮游病毒的分布规律。【方法】采用流式细胞仪检测2013年12月和2014年9月纳帕海高原湿地7个水样的浮游病毒与浮游细菌丰度,并对影响浮游病毒丰度的因素,如细菌丰度、叶绿素a含量以及其他环境因子进行了相关性分析。【结果】季节分布上,雨季浮游病毒和浮游细菌丰度高于旱季;水平分布上,原水样品的浮游病毒高于湿地水和淤泥水。旱季水样的浮游病毒丰度受到细菌丰度及叶绿素a浓度的影响较大;雨季水样的浮游病毒丰度受到水体的p H值和温度的影响较大。【结论】纳帕海高原湿地的浮游病毒和浮游细菌是比较活跃的。浮游病毒丰度在不同季节、不同采样点受到细菌丰度和叶绿素a浓度等因素的不同影响。在旱季噬菌体而非噬藻体或浮游植物病毒是纳帕海高原湿地中浮游病毒的优势种群。     

Viral impacts on total abundance and clonal composition of the harmful bloom-forming phytoplankton Heterosigma akashiwo

Recent observations that viruses are very abundant and biologically active components in marine ecosystems suggest that they probably influence various biogeochemical and ecological processes. In this study, the population dynamics of the harmful bloom-forming phytoplankton Heterosigma akashiwo (Raphidophyceae) and the infectious H. akashiwo viruses (HaV) were monitored in Hiroshima Bay, Japan, from May to July 1998. Concurrently, a number of H. akashiwo and HaV clones were isolated, and their virus susceptibilities and host ranges were determined through laboratory cross-reactivity tests. A sudden decrease in cell density of H. akashiwo was accompanied by a drastic increase in the abundance of HaV, suggesting that viruses contributed greatly to the disintegration of the H. akashiwo bloom as mortality agents. Despite the large quantity of infectious HaV, however, a significant proportion of H. akashiwo cells survived after the bloom disintegration. The viral susceptibility of H. akashiwo isolates demonstrated that the majority of these surviving cells were resistant to most of the HaV clones, whereas resistant cells were a minor component during the bloom period. Moreover, these resistant cells were displaced by susceptible cells, presumably due to viral infection. These results demonstrated that the properties of dominant cells within the H. akashiwo population change during the period when a bloom is terminated by viral infection, suggesting that viruses also play an important role in determining the clonal composition and maintaining the clonal diversity of H. akashiwo populations. Therefore, our data indicate that viral infection influences the total abundance and the clonal composition of one host algal species, suggesting that viruses are an important component in quantitatively and qualitatively controlling phytoplankton populations in natural marine environments.     

Efficient method to isolate and purify viruses of bacteria from marine environments

Aim:  To isolate viruses of specific heterotrophic bacterial strains from marine environments using a host addition/virus amplification protocol (HAVAP) for use in phage/host systems.
Methods and Results:  Bacteria-free seawater samples containing natural viruses assemblages were inoculated with a single laboratory grown bacterial host of interest in a nutrient-enriched [peptone, Fe(III) and yeast extract] seawater suspension. These conditions enhanced the replication of only those virus(s) capable of infecting the host bacterium. After incubation, free viruses were recovered at concentrations ranging 10⁵–10¹⁰ infectious virus particles per ml of seawater. Using this approach, 15 viruses were isolated and represented 12 unique phage/host systems. Two of the hosts tested were infected by more than one virus.
Conclusions:  Isolation of high concentrations of specific viruses is possible even if their initial concentrations in native waters are low. This approach allows the recovery of phage/host systems that may not be numerically dominant.
Significance and Impact of the Study:  This host enrichment protocol for virus detection and isolation is well-suited for aquatic viral ecology studies that require phage/host systems.     

A persistent, productive, and seasonally dynamic vibriophage population within Pacific oysters (Crassostrea gigas)

In an effort to understand the relationship between Vibrio and vibriophage populations, abundances of Vibrio spp. and viruses infecting Vibrio parahaemolyticus (VpVs) were monitored for a year in Pacific oysters and water collected from Ladysmith Harbor, British Columbia, Canada. Bacterial abundances were highly seasonal, whereas high titers of VpVs (0.5 x 10(4) to 11 x 10(4) viruses cm(-3)) occurred year round in oysters, even when V. parahaemolyticus was undetectable (< 3 cells cm(-3)). Viruses were not detected (<10 ml(-1)) in the water column. Host-range studies demonstrated that 13 VpV strains could infect 62% of the V. parahaemolyticus strains from oysters (91 pairings) and 74% of the strains from sediments (65 pairings) but only 30% of the water-column strains (91 pairings). Ten viruses also infected more than one species among V. alginolyticus, V. natriegens, and V. vulnificus. As winter approached and potential hosts disappeared, the proportion of host strains that the viruses could infect decreased by approximately 50% and, in the middle of winter, only 14% of the VpV community could be plated on summer host strains. Estimates of virus-induced mortality on V. parahaemolyticus indicated that other host species were required to sustain viral production during winter when the putative host species was undetectable. The present study shows that oysters are likely one of the major sources of viruses infecting V. parahaemolyticus in oysters and in the water column. Furthermore, seasonal shifts in patterns of host range provide strong evidence that the composition of the virus community changes during winter.     

南海北部海域春季浮游细菌和病毒空间分布及其影响因素

应用流式细胞检测技术测定了2014年春季南海北部海域浮游细菌和病毒丰度,研究了其水平和垂直分布特征并对其与环境因子的相关性进行了分析。结果表明,调查海区浮游细菌和病毒丰度分别介于1.28×10~4—9.96×10~5个/m L和4.69×10~5—5.39×10~7个/m L之间,二者丰度随水深的增加基本呈现逐渐下降的趋势,而水平分布趋势不明显。浮游细菌和病毒丰度与温度、p H和溶解氧显著正相关,与水深、盐度、活性磷酸盐、硅酸盐、硝酸盐和总氮则呈显著负相关关系(P0.01),说明该海域细菌和病毒数量受到上述环境因子的共同调控。分析浮游细菌和病毒的相互关系发现,VBR(Virus to bacteria ratio)平均32.23,最小值位于S11站位25m层,最大值则位于S7站位75m层,分别为4.80和264.63,VBR值小于100的站位占到调查站位总数的95.6%。VBR值除与细菌呈显著负相关关系外(P0.01),与其它环境因子相关性不明显(P0.05),说明该海区细菌是病毒的主要寄主,病毒可能主要是以噬菌体的状态存在。     

CHARACTERIZATION OF HaRNAV,A SINGLE‐STRANDED RNA VIRUS CAUSING LYSIS OF HETEROSIGMA AKASHIWO (RAPHIDOPHYCEAE)1

HaRNAV, a novel virus that infects the toxic bloom‐forming alga Heterosigma akashiwo (Hada) Hada ex Hada et Chihara, was characterized based on morphology, pathology, nucleic acid type, structural proteins, and the range of host strains that it infects. HaRNAV is a 25‐nm single‐stranded RNA (ssRNA) virus with a genome size of approximately 9100 nucleotides. This is the first report of an ssRNA virus that causes lysis of a phytoplankton species. The virus particle is sensitive to chloroform and contains at least five structural proteins ranging in apparent size from 24 to 34 kDa. HaRNAV infection causes swelling of the endoplasmic reticulum and progeny virus particles assemble in the cytoplasm of the host, frequently in crystalline arrays. The infectivity of HaRNAV was tested against 15 strains of H. akashiwo isolated from Japanese waters, the Northeast Pacific, and the Northwest Atlantic. HaRNAV caused lysis of three strains from the Northeast Pacific and two strains from Japan but none from the Northwest Atlantic. The characterization of HaRNAV demonstrates that HaRNAV is a novel type of phytoplankton virus but has some similarities with plant viruses belonging to the Sequiviridae and to other known ssRNA viruses. Further genomic analysis, however, is necessary to determine any phylogenetic relationships. The discovery of HaRNAV emphasizes the diversity of H. akashiwo viral pathogens and, more importantly, algal–virus pathogens and the complexity of virus–host interactions in the environment.     

Viral control of phytoplankton populations--a review

Phytoplankton population dynamics are the result of imbalances between reproduction and losses. Losses include grazing, sinking, and natural mortality. As the importance of microbes in aquatic ecology has been recognized, so has the potential significance of viruses as mortality agents for phytoplankton. The field of algal virus ecology is steadily changing and advancing as new viruses are isolated and new methods are developed for quantifying the impact of viruses on phytoplankton dynamics and diversity. With this development, evidence is accumulating that viruses can control phytoplankton dynamics through reduction of host populations, or by preventing algal host populations from reaching high levels. The identification of highly specific host ranges of viruses is changing our understanding of population dynamics. Viral-mediated mortality may not only affect algal species succession, but may also affect intraspecies succession. Through cellular lysis, viruses indirectly affect the fluxes of energy, nutrients, and organic matter, especially during algal bloom events when biomass is high. Although the importance of viruses is presently recognized, it is apparent that many aspects of viral-mediated mortality of phytoplankton are still poorly understood. It is imperative that future research addresses the mechanisms that regulate virus infectivity, host resistance, genotype richness, abundance, and the fate of viruses over time and space.     

Planktonic viruses,heterotrophic bacteria,and nanoflagellates in fresh and coastal marine waters of the Kara Sea Basin (the Arctic)

In August–September 2009, the concentration of dissolved organic matter and quantitative distribution of virioplankton, bacterioplankton, and heterotrophic nanoflagellates were studied in the coastal waters of the Kara Sea, the fresh waters of the islands and the coasts of the sea, and the estuaries of the Ob’ and Yenisei rivers. A high positive correlation was observed between the abundances of viruses and bacteria. The frequency of visibly infected bacteria in marine waters ranged from 0.6 to 4.3% (an average of 1.6%); in the fresh waters of islands and coastline and in estuaries, it ranged from 0.3 to 3.9% (an average of 1.5%) and from 0.5 to 1.6% (an average of 1.1%) respectively. In most surveyed water bodies, the role of viruses in bacterioplankton mortality was considerably higher than that of heterotrophic flagellates.     

Nucleic Acid Homology of Murine Type-C Viral Genes

The nucleic acid sequence homology between various murine, endogenous type-C viruses (three host range classes of BALB/c virus, the AT-124 virus, and the CCL 52 virus) and two laboratory strains of murine leukemia virus (Rauscher and Kirsten) was determined by DNA:RNA hybridization. The viral sequences exhibit varying degrees of partial homology. DNA:DNA hybridizations were performed between [³H]DNA probes prepared from N- and X-tropic BALB/c endogenous viruses and cellular DNAs from BALB/c, NIH Swiss, and AKR inbred mouse strains as well as from California feral mice and the Asian mouse subspecies Mus musculus molossinus and M. musculus castaneus. All of these strains of mice are shown to possess multiple (six to seven per haploid genome), partially related copies of type-C virogenes in their DNAs. Thermal melting profiles of the DNA:RNA and DNA:DNA hybrids suggest that the partial homology of the viral nucleic acid sequences is the result of base alterations throughout the viral genomes, rather than the loss of discrete segments of viral sequences.     

Viral Impacts on Total Abundance and Clonal Composition of the Harmful Bloom-Forming Phytoplankton Heterosigma akashiwo

Recent observations that viruses are very abundant and biologically active components in marine ecosystems suggest that they probably influence various biogeochemical and ecological processes. In this study, the population dynamics of the harmful bloom-forming phytoplankton Heterosigma akashiwo (Raphidophyceae) and the infectious H. akashiwo viruses (HaV) were monitored in Hiroshima Bay, Japan, from May to July 1998. Concurrently, a number of H. akashiwo and HaV clones were isolated, and their virus susceptibilities and host ranges were determined through laboratory cross-reactivity tests. A sudden decrease in cell density of H. akashiwo was accompanied by a drastic increase in the abundance of HaV, suggesting that viruses contributed greatly to the disintegration of the H. akashiwo bloom as mortality agents. Despite the large quantity of infectious HaV, however, a significant proportion of H. akashiwo cells survived after the bloom disintegration. The viral susceptibility of H. akashiwo isolates demonstrated that the majority of these surviving cells were resistant to most of the HaV clones, whereas resistant cells were a minor component during the bloom period. Moreover, these resistant cells were displaced by susceptible cells, presumably due to viral infection. These results demonstrated that the properties of dominant cells within the H. akashiwo population change during the period when a bloom is terminated by viral infection, suggesting that viruses also play an important role in determining the clonal composition and maintaining the clonal diversity of H. akashiwo populations. Therefore, our data indicate that viral infection influences the total abundance and the clonal composition of one host algal species, suggesting that viruses are an important component in quantitatively and qualitatively controlling phytoplankton populations in natural marine environments.     

Seasonal and spatial variability of virio-, bacterio-, and picophytoplanktonic abundances in three peri-alpine lakes

Flow cytometry (FCM) was used to assess microbial community abundances and patterns in three natural, large and deep peri-alpine hydrosystems, i.e., lakes Annecy (oligotrophic), Bourget, and Geneva (mesotrophic). Picocyanobacteria, small eukaryotic autotrophs, heterotrophic prokaryotes, and viruses were studied in the 0–50 m surface layers to highlight the impact of both physical and chemical parameters as well as possible biotic interactions on the functioning of microbial communities. Some specificities were recorded according to the trophic status of each ecosystem such as the higher number of viruses and heterotrophic bacteria in mesotrophic environments (i.e., Lakes Geneva and Bourget) or the higher abundance of picocyanobacteria in the oligotrophic Lake Annecy. However, both seasonal (temperature) and spatial (depth) variations were comparatively more important than the trophic status in driving the microbial communities’ abundances in these three lakes, as revealed by principal component analysis (PCA). A strong viral termination of the heterotrophic bacterial blooms could be observed in autumn for each lake, in parallel to the mixing of the upper lit layers. As virus to bacteria ratio (VBR) was indeed very high at this period with values varying between 87 and 114, such important relationships between viruses and bacteria were likely. The magnitudes of seasonal variations in VBR, with the highest values ever reported so far, were largely greater than the magnitude of theoretical variations due to the trophic status, suggesting also a strong seasonality in virioplankton production associated to prokaryotic dynamics. FCM analyses allowed discriminating several viral groups. Virus-Like Particles group 1 (VLP1) and group 2 (VLP2) were always observed and significantly correlated to bacteria for the former and chlorophyll a and picocyanobacteria for the latter, suggesting that most of VLP1 and VLP2 could be bacteriophages and cyanophages, respectively. On the basis of these results, new ways of investigation emerge concerning the study of relationships between specific picoplanktonic groups; and overall these results provide new evidence of the necessity to consider further viruses for a better understanding of lake plankton ecology. Handling editor: Luigi Naselli-Flores     

仿刺参养殖池塘浮游病毒丰度与环境因子的相关性分析

为了揭示仿刺参养殖池塘生态系统中浮游病毒与环境因子的关系,于2008年3—11月对大连市谢屯地区的仿刺参养殖池塘中的浮游病毒丰度进行了定期检测,同时对水温、pH、溶解氧、盐度、叶绿素a含量、化学需氧量、无机氮、活性磷酸盐、异养细菌等因子进行了监测,对浮游病毒丰度与这些环境因子之间的相关性进行了分析。结果表明:仿刺参养殖池塘中浮游病毒的平均丰度为8.32×1010VLPs.L-1(最高值为4月的18.2×1010VLPs.L-1,最低值为11月的1.31×1010VLPs.L-1),外海水中浮游病毒平均丰度为6.45×1010VLPs.L-1(最高值为4月的12.6×1010VLPs.L-1,最低值为6月的2.02×1010VLPs.L-1),仿刺参养殖池塘中营养盐、水温、pH及盐度对浮游病毒丰度的影响较大,而外海水中叶绿素a和异养细菌对浮游病毒丰度的影响较大。     

Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology

Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high‐throughput and multiplexed hybridization‐based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End‐labelled PCR products are hybridized to taxon‐specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37‐day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate.     

Distribution of microbial populations and their relationship with environmental parameters in the coastal waters of Qingdao,China

In order to understand the large‐scale distribution of microbial populations simultaneously and their relationship with environmental parameters, flow cytometry was used to analyse samples collected from 46 stations in the coastal waters of Qingdao in spring, 2007. The distribution of virus was significantly and positively correlated with heterotrophic bacteria. Two groups of picophytoplankton (Synechococcus and picoeukaryotes) were detected; however, Prochlorococcus was not found. Picoeukaryotes and nanophytoplankton were abundant in the near‐shore waters, whereas Synechococcus was abundant in the off‐shore areas. No variation was found in vertical distribution of virus, heterotrophic bacteria, Synechococcus and nanophytoplankton abundances, except picoeukaryotes abundance in the bottom layer was dramatically lower than that in the upper layers. Correlation analyses indicated that the relationship between abiotic variables and heterotrophic bacteria, pico‐ and nanophytoplankton was closer than that between abiotic variables and virioplankton. Temperature and nutrients were the synchronous factors controlling the growth of heterotrophic bacteria, pico‐ and nanophytoplankton in the coastal waters of Qingdao in spring. The results suggested that synergistic and antagonistic effects existed among microbial groups.