河口细菌群落多样性及其控制因素:以切萨皮克湾为例

咸淡水的混合和重要营养盐与有机物的再循环,使得河口成为地球上生产力较高而动态变化明显的水生生态系统.一个典型的河口区断面中,细菌群落包含了一些从淡水到海洋的过渡类型:例如α-变形菌(Alphaproteobacteria)、p-变形菌(Betaproteobacteria)、γ-变形菌(Gammaproteobacteria)、蓝细菌(Cyanobactenia)[聚球藻(Synechococcus)]、拟杆菌(Bacteroidetes)、放线细菌(Actinobacteria)和疣微菌(Verrucomicrobia)等.此外,河口也包含其独特的细菌群落:SAR11组、玫瑰杆菌属(Roseobacter)、SAR86和放线细菌(Actinobacteria)的一些进化亚枝(subclades),表明海湾或者大型温带河口区细菌类群具有区域生态适应性.以研究较多的美国切萨皮克湾(Chesapeake Bay)为例,其细菌群落呈现出显著的季节性变化和周期性的年际变化特征;这些变化除了受水的滞留时间和细菌生长速度影响外,还可能受其他许多环境因子的影响.其中叶绿素a和水温变化的影响最大,其他环境因子如溶解氧、铵态氮、亚硝酸盐和硝酸盐以及病毒的丰度也有影响.近年来,基于群落水平的基因组学(genomics)和后基因组学(postgenomics)(转录组学和蛋白质组学)技术应用于研究自然条件下微生物群落错综复杂的基因多样性和表达,提供了揭示水环境中微生物群落组成和新功能基因的途径.     

Monoclonal antibody analysis of Perkinsus marinus extracellular products

The protozoan oyster parasite Perkinsus marinus releases a complex set of extracellular products (ECP) during in vitro culture. These products have been previously implicated in parasite virulence, and their expression can be altered by medium supplementation with oyster tissue homogenate. Little is known regarding ECP function, regulation, or mechanism of storage and release. Perkinsus marinus ECP were purified from a protein-free medium and used to produce a panel of five monoclonal antibodies. Several of the antibodies recognised series of proteins implying that the ECP may originate from comparatively few parental molecules. The ECP are secreted by several pathways, including the release of one product from an external cell layer, and two other products from two morphologically distinct intracellular compartments. Antibodies against separate epitopes on one protein provided information about possible protein structure. A sandwich ELISA format allowed sensitive quantification of that protein and showed significantly reduced protein expression in oyster tissue homogenate supplemented cultures. Immunopurification allowed tandem mass spectroscopic amino acid sequencing of that protein. Another antibody was used to characterise the P. marinus cell wall. This antibody specifically bound to trophozoite and tomont walls, and was used to investigate the morphological and antigenic changes in these walls during Ray's fluid thioglycollate medium-induced formation of hypnospores. It was also used to confirm that oyster tissue homogenate supplementation could induce formation of hypnospores. This antibody labeled P. marinus cells in fixed oyster tissue in a species-specific manner.     

Comparison of in vitro-cultured and wild-type Perkinsus marinus. III. Fecal elimination and its role in transmission

Perkinsus marinus, a pathogen of the eastern oyster Crassostrea virginica, is transmitted directly among oysters. Previous studies found viable P. marinus parasites in the feces and pseudofeces of oysters within hours of injection with parasites, suggesting that the parasite may be voided from live oysters and subsequently dispersed in the water column. The experiments described here were designed to quantify P. marinus shed in the feces and pseudofeces of experimentally infected oysters. The results indicated that parasites were shed in 2 phases. A 'decreasing' phase occurred within 2 wk of challenge and before net parasite proliferation began in the host. An 'increasing' phase occurred after P. marinus had begun replicating. The quantity of P. marinus recovered in the feces and pseudofeces of exposed oysters was only about 5 % of the dose administered. In vitro-cultured P. marinus were eliminated at a greater rate than wild-type P. marinus and the fraction discharged was not associated with culture phase. Oysters that were continuously dosed with P. marinus in their food gradually lost the ability to discard the parasite in pseudofeces. The quantity of P. marinus shed in feces of infected oysters was correlated with both the P. marinus body burden and subsequent survival time, suggesting that noninvasive fecal counts could predict infection intensity and survival. The results indicate that in an epizootic, shedding of P. marinus via feces is relatively small compared to the potential number released by cadavers of heavily infected oysters, but that fecal discharge may be important in transmission before infections become lethal.     

Zooplankton-associated and free-living bacteria in the York River, Chesapeake Bay: comparison of seasonal variations and controlling factors

Zooplankton provide microhabitats for bacteria, but factors which influence zooplankton-associated bacterial abundance are not well known. Through a year-long field study, we measured the concentration of free-living bacteria and bacteria associated with the dominant mesozooplankters Acartia tonsa and Balanus sp. Free-living bacteria peaked in the summer, while zooplankton-associated bacteria peaked in summer and winter. No relationships were found between bacterial abundance per individual and zooplankter width, length, surface area or body volume. Multiple regression analyses indicated that free-living and Acartia-associated bacterial concentrations were explained by temperature, salinity, ammonium, chl a, and all term interactions. Balanus-associated bacterial concentration was explained by ammonium and phosphate. Ammonium significantly influenced all sampled bacterial communities. In laboratory experiments, copepods raised under high ammonium concentration had higher bacterial concentrations than those raised under low ammonium condition. Transplant experiments showed that high ammonium favored loosely attached bacteria, whereas low ammonium selected for firmly attached bacteria, suggesting greater exchange between free-living and zooplankton-associated bacterial communities in nutrient-rich systems. Additional sampling of other zooplankton taxa all showed high bacterial concentrations, supporting the notion that zooplankton function as microbial hotspots and may play an important, yet overlooked, role in marine biogeochemical cycles.     

In vivo dynamics of the microparasite Perkinsus marinus during progression and regression of infections in eastern oysters

We used a total body parasite burden assay for the oyster pathogen Perkinsus marinus to investigate quantitative changes in microparasite burdens and frequency distributions. Heretofore, this type of study was limited mainly to macroparasites. The apparent in vivo growth pattern of P. marinus was characterized by a "lag" phase (< 10 cells/g wet weight [g wwt], a "log" phase (10-10,000 cells/g wwt), and a "stationary" phase (> 10,000 cells/g wwt). Infections declined exponentially under conditions unfavorable to the parasite but with a lengthening half-life, suggesting that elimination of parasites became increasingly difficult at low densities. Oysters held for 11 wk at 15 C, a temperature considered more favorable for oyster hemocytes than for P. marinus, were not able to eliminate infections. Parasite distributions within host populations were aggregated; in each sample, 1 or 2 oysters contained more parasites than all other oysters in the sample combined and the variance-to-mean ratio exceeded 1:1. The few hosts with large parasite burdens may be the most important individuals for survival and transmission of parasites. They are likely to play a key role in initiating and maintaining epizootics either in situ or after introduction of infected animals into a naive population.     

Interannual dynamics of viriobenthos abundance and morphological diversity in Chesapeake Bay sediments

Despite significant implications of viral activity in sediment ecosystems, there are limited data describing how sediment viral assemblages respond to broader ecosystem changes. To document this, the spatial and temporal dynamics of viral and bacterial abundance (BA) and changes in the morphological distribution of viruses were examined within three salinity regions over 2 years. Viral abundances (VA) ranged from 0.2 to 17 × 10(10) viruses mL(-1) sediment while direct bacterial counts ranged from 3.8 to 37 × 10(8) cells mL(-1) sediment. Peaks and valleys in the abundance of extracted viruses and bacteria from surface sediments occurred simultaneously, with lows in February 2004 and highs in April 2003. Across all samples, viral and BA were positively correlated (P < 0.001). Vertical profiles showed a decrease in viral and BA with depth in sediments. Based on transmission electron microscopy results, viruses with diminutive capsids (20-50 nm) and from the Myoviridae and Podoviridae viral family types were dominant within surface sediments. The most morphologically diverse viral assemblages occurred in autumn samples from the sandy, polyhaline station and spring samples from the mesohaline station. Seasonal changes showed an average 72% decrease in VA from spring to winter. These observations support the view that viriobenthos assemblages are responsive to seasonal environmental changes and that viral processes have significant implications for the biogeochemical processes mediated by bacterial communities within Bay sediments.     

Diel abundance and productivity patterns of autotrophic picoplankton in the lower Chesapeake Bay

Diet studies associating phototrophic picoplankton abundanceand productivity to tidal flow and pycnocline formation wereconducted during summer and winter. Higher picoplankton concentrationsand productivity were associated with waters above the pycnoclinein summer, with picoplankton abundance highest during ebb tidewhen phycocyanin enriched Synechococcus sp. were dominant. Inwinter, greater concentrations and productivity occurred inbottom waters and during flood tide, when phycoerythrin enrichedSynechococcus sp. were dominant.     

Sediment bacterial indicators in an urban shellfishing subestuary of the lower Chesapeake Bay.

The objectives of this study were to document the spatial and temporal distributions and compositions of bacteria in the sediments and overlying waters of an important urban shellfishing area in the lower Chesapeake Bay region, the Lynnhaven Estuary. Marked fluctuations were observed in the date of many of the physicochemical parameters and the indicator bacteria. The higher-salinity water and coarser sediment of the inlet site showed lower overall bacterial densities than did the headwater sites, where freshwater runoff and decreased tidal action were characteristic. Densities of benthic indicator bacteria, when expressed on a volumetric basis, were significantly greater than counts in the overlying waters. These counts were indicative of a fecally polluted system and were well above the safe maximum limits for shellfish-growing waters. Significantly fewer total and fecal bacteria were observed in both the water and the sediment during the warm months of May, July, and August. The primary sources of the Lynnhaven's bacterial pollution appeared to be typical of urban and agricultural runoff, although failure of septic tank systems was suspected as a problem in the Lynnhaven's western branch. These results illustrated that sediments in shellfishing areas could serve as a reservoir for high densities of indicator bacteria and that, potentially, pathogens could pose a health hazard.     

Perkinsus marinus in coastal Georgia, USA, following a prolonged drought

Oysters Crassostrea virginica are 'keystone' estuarine species in the southeastern USA, providing essential fish habitat, food for human consumption, filtration of water bodies, and protection against shoreline erosion. Relatively few oyster pathology studies have been conducted in Georgia. The parasitic protozoan Perkinsus marinus was first observed here in the 1960s, but has not been investigated since the late 1990s, when increasing oyster infection levels were apparent. In the late 1990s and early 2000s, the region suffered a prolonged drought, resulting in elevated salinities and the proliferation of various diseases in the marine environment. By 2003, salinities had returned to normal levels, but the effect of the drought on oysters was unknown. In June 2003, oyster reefs throughout Chatham County were sampled to evaluate the prevalence and intensity of P. marinus. The disease appears to have remained prevalent in the coastal waters of Georgia (100% prevalence at some sites), but the intensity was low, ranging from 0 to 1.83 on a scale where heavy infections rated a score of 5. While the disease did not occur at levels high enough to cause oyster mortalities, further monitoring, particularly on a temporal scale, is warranted.     

Comparison of in vitro-cultured and wild-type Perkinsus marinus. I. Pathogen virulence

Perkinsus marinus is a highly contagious pathogen of the eastern oyster Crassostrea virginica. Until recently, transmission studies have employed wild-type parasites isolated directly from infected oysters. Newly developed methods to propagate P. marinus in vitro have led to using cultured parasites for infection studies, but results suggest that cultured parasites are less virulent than wild-type parasites In this paper, we report results of experiments designed to quantify differences between wild-type and cultured P. marinus virulence and to test the following hypotheses: (1) in vitro-cultured parasites are less virulent than wild-type parasites; (2) virulence decreases gradually during in vitro culture; (3) virulence of in vitro cultures can be restored by in vivo passage; (4) virulence changes with culture phase. Our results demonstrate that parasites freshly isolated from infected hosts are much more virulent than those propagated in culture, indicating a potential deficiency in the culture medium used. Virulence was lost immediately in culture and, for that reason, the practice of repassing cultured cells through the host to restore virulence does not work for P. marinus. Virulence was also associated with culture phase: log-phase parasites were significantly more virulent than those obtained from lag- or stationary-phase cultures.     

Flow cytometric analysis of lectin binding to in vitro-cultured Perkinsus marinus surface carbohydrates

Parasite surface glycoconjugates are frequently involved in cellular recognition and colonization of the host. This study reports on the identification of Perkinsus marinus surface carbohydrates by flow cytometric analyses of fluorescein isothiocyanate-conjugated lectin binding. Lectin-binding specificity was confirmed by sugar inhibition and Kolmogorov-Smirnov statistics. Clear, measurable fluorescence peaks were discriminated, and no parasite autofluorescence was observed. Parasites (GTLA-5 and Perkinsus-1 strains) harvested during log and stationary phases of growth in a protein-free medium reacted strongly with concanavalin A and wheat germ agglutinin, which bind to glucose-mannose and N-acetyl-D-glucosamine (GlcNAc) moieties, respectively. Both P. marinus strains bound with lower intensity to Maclura pomifera agglutinin, Bauhinia purpurea agglutinin, soybean agglutinin (N-acetyl-D-galactosamine-specific lectins), peanut agglutinin (PNA) (terminal galactose specific), and Griffonia simplicifolia II (GlcNAc specific). Only background fluorescence levels were detected with Ulex europaeus agglutinin I (L-fucose specific) and Limulus polyphemus agglutinin (sialic acid specific). The lectin-binding profiles were similar for the 2 strains except for a greater relative binding intensity of PNA for Perkinsus-1 and an overall greater lectin-binding capacity of Perkinsus-1 compared with GTLA-5. Growth stage comparisons revealed increased lectin-binding intensities during stationary phase compared with log phase of growth. This is the first report of the identification of surface glycoconjugates on a Perkinsus spp. by flow cytometry and the first to demonstrate that differential surface sugar expression is growth phase and strain dependent.     

Predictability of Vibrio cholerae in Chesapeake Bay

Vibrio cholerae is autochthonous to natural waters and can pose a health risk when it is consumed via untreated water or contaminated shellfish. The correlation between the occurrence of V. cholerae in Chesapeake Bay and environmental factors was investigated over a 3-year period. Water and plankton samples were collected monthly from five shore sampling sites in northern Chesapeake Bay (January 1998 to February 2000) and from research cruise stations on a north-south transect (summers of 1999 and 2000). Enrichment was used to detect culturable V. cholerae, and 21.1% (n = 427) of the samples were positive. As determined by serology tests, the isolates, did not belong to serogroup O1 or O139 associated with cholera epidemics. A direct fluorescent-antibody assay was used to detect V. cholerae O1, and 23.8% (n = 412) of the samples were positive. V. cholerae was more frequently detected during the warmer months and in northern Chesapeake Bay, where the salinity is lower. Statistical models successfully predicted the presence of V. cholerae as a function of water temperature and salinity. Temperatures above 19°C and salinities between 2 and 14 ppt yielded at least a fourfold increase in the number of detectable V. cholerae. The results suggest that salinity variation in Chesapeake Bay or other parameters associated with Susquehanna River inflow contribute to the variability in the occurrence of V. cholerae and that salinity is a useful indicator. Under scenarios of global climate change, increased climate variability, accompanied by higher stream flow rates and warmer temperatures, could favor conditions that increase the occurrence of V. cholerae in Chesapeake Bay.     

Predictability of Vibrio cholerae in Chesapeake Bay

Vibrio cholerae is autochthonous to natural waters and can pose a health risk when it is consumed via untreated water or contaminated shellfish. The correlation between the occurrence of V. cholerae in Chesapeake Bay and environmental factors was investigated over a 3-year period. Water and plankton samples were collected monthly from five shore sampling sites in northern Chesapeake Bay (January 1998 to February 2000) and from research cruise stations on a north-south transect (summers of 1999 and 2000). Enrichment was used to detect culturable V. cholerae, and 21.1% (n = 427) of the samples were positive. As determined by serology tests, the isolates, did not belong to serogroup O1 or O139 associated with cholera epidemics. A direct fluorescent-antibody assay was used to detect V. cholerae O1, and 23.8% (n = 412) of the samples were positive. V. cholerae was more frequently detected during the warmer months and in northern Chesapeake Bay, where the salinity is lower. Statistical models successfully predicted the presence of V. cholerae as a function of water temperature and salinity. Temperatures above 19 degrees C and salinities between 2 and 14 ppt yielded at least a fourfold increase in the number of detectable V. cholerae. The results suggest that salinity variation in Chesapeake Bay or other parameters associated with Susquehanna River inflow contribute to the variability in the occurrence of V. cholerae and that salinity is a useful indicator. Under scenarios of global climate change, increased climate variability, accompanied by higher stream flow rates and warmer temperatures, could favor conditions that increase the occurrence of V. cholerae in Chesapeake Bay.     

Incidence of Vibrio parahaemolyticus in Chesapeake Bay

A Bay-wide survey of the distribution of Vibrio parahaemolyticus was carried out in Chesapeake Bay during May 1972, to determine whether the annual cycle of V. parahaemolyticus which was observed to occur in the Rhode River subestuary of Chesapeake Bay took place in other parts of Chesapeake Bay. In an earlier study, April to early June, when the water temperature rises from 14 to 19 C, was found to be a critical period in the annual cycle of the organism in the Rhode River, since this is the time period when the annual cycle is initiated. Results of this study, however, revealed that V. parahaemolyticus could not be found in the water column during May 1972. Nevertheless, several samples of sediment and plankton yielded V. parahaemolyticus isolates. Comparison of data with those for the Rhode River area examined in the earlier studies of the annual cycle of V. parahaemolyticus suggests that the time of initiation of the annual cycle of V. parahaemolyticus in the open Bay proper may be influenced by various factors such as temperature and salinity, i.e., deeper water locations may show initiation of the V. parahaemolyticus annual cycle later than shallow areas. Confirmation of the presence of the organisms in the samples studied was accomplished using numerical taxonomy with 19 reference strains also included in the analyses.     

Ecology of Vibrio parahaemolyticus in Chesapeake Bay

A study of the ecology of Vibrio parahaemolyticus and related vibrios in the Rhode River area of Chesapeake Bay was carried out over the period December 1970 through August 1971. The incidence of V. parahaemolyticus and related vibrios was found to be correlated with water temperature. The vibrios could not be detected in the water column during the winter months, although they were present in sediment. From late spring to early summer, when water temperatures were 14 +/- 1 C, vibrios over-wintering in sediment were released from the bottom communities and attached to zooplankton, proliferating as the temperature rose. The number of vibrios in and on plankton was reflected in the water column bacterial population densities at water temperatures of ca. 19 C. Thus, temperature of the water column in the range of 14 to 19 C was found to be critical in the annual cycle of the vibrios. Interaction between sediment, water, and zooplankton was found to be essential in the natural estuarine ecosystem. Bacterial counts of zooplankton were found to be temperature dependent. The bacterial population associated with zooplankton was found to be predominantly on external surfaces and was specific, differing from that of the sediment. Vibrio spp. and related organisms comprised the total bacterial population associated with zooplankton in summer months. The ecological role of Vibrio spp., including V. parahaemolyticus, was found to be significant, with respect to their property of chitin digestion and in relation to the population dynamics of zooplankton in Chesapeake Bay.     

Linking seasonal inorganic nitrogen shift to the dynamics of microbial communities in the Chesapeake Bay

Seasonal shifts of dissolved inorganic nitrogen (DIN) and the dynamics of microbial communities for nitrogen transformation were investigated in the water column of Chesapeake Bay. The relative abundance of nitrogen over phosphorus (N*) showed a strong seasonal and spatial pattern: gradually decreased from upstream to downstream; high in winter and low in summer. Because the phosphorus concentration remained relatively stable, the spatiotemporal pattern of N* implied that a substantial fraction of DIN was removed in the bay, especially in summer. Correlation analyses indicated the functional microbial communities and environmental variables, such as temperature, dissolved oxygen, salinity, played important roles for connecting the seasonal variation of N*. Among them, temperature was the trigger factor. High temperature in the summer induced the growth of functional microbes, which subsequently consumed a large portion of DIN inputted from the tributaries and reduced the N*. The current study provided the relative importance of microbial communities and environmental variables in driving the DIN loss in the bay.     

Metagenomic Characterization of Chesapeake Bay Virioplankton

Viruses are ubiquitous and abundant throughout the biosphere. In marine systems, virus-mediated processes can have significant impacts on microbial diversity and on global biogeocehmical cycling. However, viral genetic diversity remains poorly characterized. To address this shortcoming, a metagenomic library was constructed from Chesapeake Bay virioplankton. The resulting sequences constitute the largest collection of long-read double-stranded DNA (dsDNA) viral metagenome data reported to date. BLAST homology comparisons showed that Chesapeake Bay virioplankton contained a high proportion of unknown (homologous only to environmental sequences) and novel (no significant homolog) sequences. This analysis suggests that dsDNA viruses are likely one of the largest reservoirs of unknown genetic diversity in the biosphere. The taxonomic origin of BLAST homologs to viral library sequences agreed well with reported abundances of cooccurring bacterial subphyla within the estuary and indicated that cyanophages were abundant. However, the low proportion of Siphophage homologs contradicts a previous assertion that this family comprises most bacteriophage diversity. Identification and analyses of cyanobacterial homologs of the psbA gene illustrated the value of metagenomic studies of virioplankton. The phylogeny of inferred PsbA protein sequences suggested that Chesapeake Bay cyanophage strains are endemic in that environment. The ratio of psbA homologous sequences to total cyanophage sequences in the metagenome indicated that the psbA gene may be nearly universal in Chesapeake Bay cyanophage genomes. Furthermore, the low frequency of psbD homologs in the library supports the prediction that Chesapeake Bay cyanophage populations are dominated by Podoviridae.     

Hybridization Analysis of Chesapeake Bay Virioplankton

It has been hypothesized that, by specifically lysing numerically dominant host strains, the virioplankton may play a role in maintaining clonal diversity of heterotrophic bacteria and phytoplankton populations. If viruses selectively lyse only those host species that are numerically dominant, then the number of a specific virus within the virioplankton would be expected to change dramatically over time and space, in coordination with changes in abundance of the host. In this study, the abundances of specific viruses in Chesapeake Bay water samples were monitored, using nucleic acid probes and hybridization analysis. Total virioplankton in a water sample was separated by pulsed-field gel electrophoresis and hybridized with nucleic acid probes specific to either single viral strains or a group of viruses with similar genome sizes. The abundances of specific viruses were inferred from the intensity of the hybridization signal. By using this technique, a virus comprising 1/1,000 of the total virioplankton abundance (ca. 10⁴ PFU/ml) could be detected. Titers of either a single virus species or a group of viruses changed over time, increasing to peak abundance and then declining to low or undetectable levels, and were geographically localized in the bay. Peak signal intensities, i.e., peak abundances of virus strains, were 10-fold greater than the low background level. Furthermore, virus species were found to be restricted to a particular depth, since probes specific to viruses from bottom water did not hybridize with virus genomes from surface water at the same geographical location. Overall, changes in abundances of specific viruses within the virioplankton were episodic, supporting the hypothesis that viral infection influences, if not controls, clonal diversity within heterotrophic bacteria and phytoplankton communities.