Ubiquity and Diversity of Heterotrophic Bacterial nasA Genes in Diverse Marine Environments

Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be active participants contributing to the bloom dynamics. Our statistical results suggested that salinity, temperature and nitrate may be some of the key environmental factors controlling the composition and dynamics of the marine NAB communities.     

Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity

Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Flavobacteria largely at the expense of Epsilonproteobacteria. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure.     

Bacterial Diversity in Shallow Oligotrophic Marine Benthos and Overlying Waters: Effects of Virus Infection,Containment, and Nutrient Enrichment

Little is known of the factors shaping sediment bacterial communities, despite their high abundance and reports of high diversity. Two factors hypothesized to shape bacterial communities in the water column are nutrient (resource) availability and virus infection. The role these factors play in benthic bacterial diversity was assessed in oligotrophic carbonate–based sediments of Florida Bay (USA). Sediment–water mesocosm enclosures were made from 1-m diameter clear polycarbonate cylinders which were pushed into sediments to 201 cm sediment depth enclosing 80 L of water. Mesocosms were amended each day for 14 d with 10 µM NH ₄ ⁺ and 1 µM PO ₄ ^3– . In a second experiment, viruses from a benthic flocculent layer were concentrated and added back to flocculent layer samples which were collected near the mesocosm enclosures. Photosynthesis by microalgae in virus-amended incubations was monitored by pulse-amplitude modulated (PAM) fluorescence. In both experiments, bacterial diversity was estimated using automated rRNA intergenic spacer analysis (ARISA), a high-resolution fingerprinting approach. Initial sediment bacterial operational taxonomic unit (OTU) richness (236 ± 3) was higher than in the water column (148 ± 9), where an OTU was detectable when its amplified DNA represented >0.09% of the total amplified DNA. Effects on bacterial diversity and operational taxonomic unit (OTU) richness in nutrient-amended mesocosms may have been masked by the effects of containment, which stimulated OTU richness in the water column, but depressed OTU richness and diversity in sediments. Nutrient addition significantly elevated virus abundance and the ratio of viruses to bacteria (p < 0.05 for both) in the sediments, concomitant with elevated bacterial diversity. However, water column bacterial diversity (in unamended controls) was not affected by nutrient amendments, which may be due to rapid nutrient uptake by sediment organisms or adsorption of P to carbonate sediments. Addition of live viruses to benthic flocculent layer samples increased bacterial OTU diversity and richness compared with heat-killed controls; however, cluster analyses showed that the community structure in the virus-amended mesocosms varied greatly between replicates. Despite the strong effects upon eubacterial communities, photosynthesis of co-occurring protists and cyanobacteria was not significantly altered by the presence of virus concentrates. This study supports the hypothesis that nutrient availability plays a key role in shaping sediment bacterial communities, and also that viruses may regulate the abundance of the dominant competitors and allow less dominant organisms to maintain or increase their abundance in a community due to decreased competition for resources.     

Screening of Marine Bacterial Producers of Polyunsaturated Fatty Acids and Optimisation of Production

Water samples from three different environments including Mid Atlantic Ridge, Red Sea and Mediterranean Sea were screened in order to isolate new polyunsaturated fatty acids (PUFAs) bacterial producers especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Two hundred and fifty-one isolates were screened for PUFA production and among them the highest number of producers was isolated from the Mid-Atlantic Ridge followed by the Red Sea while no producers were found in the Mediterranean Sea samples. The screening strategy included a simple colourimetric method followed by a confirmation via GC/MS. Among the tested producers, an isolate named 66 was found to be a potentially high PUFA producer producing relatively high levels of EPA in particular. A Plackett–Burman statistical design of experiments was applied to screen a wide number of media components identifying glycerol and whey as components of a production medium. The potential low-cost production medium was optimised by applying a response surface methodology to obtain the highest productivity converting industrial by-products into value-added products. The maximum achieved productivity of EPA was 20 mg/g, 45 mg/l, representing 11 % of the total fatty acids, which is approximately five times more than the amount produced prior to optimisation. The production medium composition was 10.79 g/l whey and 6.87 g/l glycerol. To our knowledge, this is the first investigation of potential bacteria PUFA producers from Mediterranean and Red Seas providing an evaluation of a colourimetric screening method as means of rapid screening of a large number of isolates.     

Effects of Photosynthesis on Bacterial Phosphatase Production in Biofilms

The fraction of bacteria displaying phosphatase activity within natural photosynthetic biofilms was examined in relation to phosphorus limitation and algal photosynthesis. An artificial substrate that forms a fluorescent precipitate was used in conjunction with the nucleic acid stain DAPI to enumerate extracellular phosphatase expression by biofilm bacteria exposed to different photosynthetic activities and phosphorus supplies. The proportion of bacteria displaying phosphatase activity changed in response to the presence or absence of algal photosynthesis. In general, phosphate-deprived biofilms had positive linear trends in bacterial phosphatase activity (p <0.001), with greater proportions of bacteria displaying phosphatase under photosynthetic inhibition compared to active photosynthesis. Under sufficient phosphate supplies, biofilms had negative linear trends (p <0.05) or were lower in the proportion of bacteria displaying phosphatase activity in the presence of algal photosynthesis, whereas bacterial phosphatase activity was generally maintained when photosynthesis was inhibited. it is suggested that the amount of extracellular organic carbon released within the biofilm matrix during photosynthesis indirectly affected bacterial phosphatase synthesis.     

Comparison of Rates of Flagellate Bacterivory and Bacterial Production in a Marine Coastal System

Protozoan predation on bacteria and bacterioplankton secondary production were simultaneously determined in La Salvaje Beach water during 1990. Protozoan grazing on bacterioplankton was measured from fluorescently labeled bacterium uptake rates; estimates of bacterial secondary production were obtained from [³H]thymidine incorporation rates. Two different conversion factors were used to transform thymidine incorporation rates into bacterial production rates; both of them were specific for La Salvaje Beach and were calculated by using empirical and semitheoretical approaches. The average flagellate predation rate was 14.0 bacteria flagellate^-1 h^-1; the average population predation rate was 7.35 x 10⁶ bacteria liter^-1 h^-1. The estimates of bacterial production differed greatly depending on the conversion factor used, and so did the percentages of bacterial production consumed by flagellated protozoa (4.6% when the empirical conversion factor for La Salvaje Beach was used and 113% when the semitheoretical conversion factor specific for this system was used). The ecological implications of each of these values are discussed.     

Estimating Bacterial Production in Marine Waters from the Simultaneous Incorporation of Thymidine and Leucine

We examined the simultaneous incorporation of [³H]thymidine and [¹⁴C]leucine to obtain two independent indices of bacterial production (DNA and protein syntheses) in a single incubation. Incorporation rates of leucine estimated by the dual-label method were generally higher than those obtained by the single-label method, but the differences were small (dual/single = 1.1 ± 0.2 [mean ± standard deviation]) and were probably due to the presence of labeled leucyl-tRNA in the cold trichloroacetic acid-insoluble fraction. There were no significant differences in thymidine incorporation between dual- and single-label incubations (dual/ single = 1.03 ± 0.13). Addition of the two substrates in relatively large amounts (25 nM) did not apparently increase bacterial activity during short incubations (<5 h). With the dual-label method we found that thymidine and leucine incorporation rates covaried over depth profiles of the Chesapeake Bay. Estimates of bacterial production based on thymidine and leucine differed by less than 25%. Although the need for appropriate conversion factors has not been eliminated, the dual-label approach can be used to examine the variation in bacterial production while ensuring that the observed variation in incorporation rates is due to real changes in bacterial production rather than changes in conversion factors or introduction of other artifacts.     

Bioprocess Intensification for Production of Novel Marine Bacterial Antibiotics Through Bioreactor Operation and Design

There is a lack of research into bioreactor engineering and fermentation protocol design in the field of marine bacterial antibiotic production. Most production strategies are carried out at the shake-flask level and lack a mechanistic understanding of the antibiotic production process, offering poor prospects for successful scale-up. This review shows that data need to be collated on media and physical optima differences between the trophophase and idiophase, along with investigations into the control mechanisms for biosynthesis, to allow implementation of novel fermentation protocols. Immobilization may play a part in bioprocess intensification of marine bacterial antibiotic production, through again this area is understudied. Similarly, mass transfer and shear stress data of fermentations are needed to provide the bioreactor design requirements to intensify antibiotic biosynthesis, with process scale-up in mind. The application of bioprocess intensification methods to the production of antibiotics (and other metabolites) from marine microbes will become an important strategy for improving supply of natural products, in order to assess their suitability as chemotherapeutic drugs. Received March 11, 1999; accepted May 4, 1999.     

Bacterial Diversity in a Marine Methanol-Fed Denitrification Reactor at the Montreal Biodome,Canada

The bacterial biota of a methanol-fed denitrification reactor used to treat seawater at the Montreal Biodome were investigated using culture-dependent and molecular biology methods. The microbiota extracted from the reactor carriers were cultivated on three media. Three isolate types were recovered and their 16S ribosomal DNA (rDNA) genes were determined. The analysis showed that the isolate types were related to -Proteobacteria. They are members of the Hyphomicrobium and Paracoccus genera and the Phyllobacteriaceae family. Uncultured bacteria were identified through a 16S rDNA library generated from total DNA extracted from the microbiota. Clones were screened for different restriction profiles and for different DGGE (denaturing gradient gel electrophoresis) migration profiles. More than 70% of clones have the same restriction profile, and the sequence of representative clones showed a relation with the Methylophaga members of the Piscirickettsia family (-Proteobacteria). Sequences from other profiles were related to bacterial species involved in denitrification. The number of species in the denitrification reactor was estimated at 15. Bacterial colonization on newly added carriers in the denitrification reactor was monitored by PCR-DGGE. The DGGE migration profiles evolved during the first 5 weeks and then remained essentially unchanged. PCR-DGGE was also used to monitor the microbial profiles in various aquarium locations. As expected, bacterial populations differed from one location to another, except for the sand and trickling filters which presented similar DGGE migration profiles.     

Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity

Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic fingerprinting by PCR-denaturing gradient gel electrophoresis revealed clear differences in the composition of Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Verrucomicrobia populations in soils without plants compared to that of populations in planted soils, whereas no influence of plant species composition on bacterial diversity could be discerned. These results indicate that the presence of higher plant species affects the species composition of bacterial groups in a reproducible manner and even outside of the rhizosphere. In contrast, the environmental factors tested did not affect the composition of Acidobacteria, Actinobacteria, Archaea, and Firmicutes populations. One-third (52 out of 160) of the sequence types were found to be specifically and reproducibly associated with the absence or presence of plants. Unexpectedly, this was also true for numerous minor constituents of the soil bacterial assemblage. Subsequently, one of the low-abundance phylotypes (beta10) was selected for studying the interdependence under particular experimental conditions and the underlying causes in more detail. This so-far-uncultured phylotype of the Betaproteobacteria species represented up to 0.18% of all bacterial cells in planted lysimeters compared to 0.017% in unplanted systems. A cultured representative of this phylotype exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. Our results suggest that the bacterial species composition in soil is determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.     

Different Decaying Wood Effects on Bacterial Diversity: Insights from Molecular Methods

Decaying wood is a novel key factor required for biodiversity and function of a forest, as it provides a good account of substrate and habitats for various organisms. Herein, the bacterial diversity in decaying wood of Betula platyphylla was discussed through high throughput sequencing. Our results showed that most of the obtained sequences belonged to the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria and Verrucomicrobia. Bacterial community compositions in samples with higher moisture content were obviously different than that with lower content, which could be reflected by richness estimators, diversity indices, and cluster and heatmap analysis. All three networks were non-random and possessed topological features of complex systems such as small-world and modularity features. However, these networks exhibited distinct topological features, indicating the potential ability of extensive cooperative and competitive interactions in the decayed wood microenvironments. Redundant analysis showed that most bacterial phyla were mainly distributed in higher-moisture trunks. The obtained data will increase the knowledge of the complex bacterial diversity associated with dead wood, and lay a foundation for the bioconversion technology of plant cell walls using bacteria.     

Production of Bacterial Substrate by Marine Copepods: Effect of Phytoplankton Biomass and Cell Size

Laboratory experiments were performed to evaluate the importanceof grazing activity of the marine copepod Acartia tonsa forproduction of substrate for bacteria. Acartia tonsa were feda range of concentrations of the nanoflagellate Rhodomonas baltica,the diatom Ditylum brightwelli and the dinoflagellate Ceratiumlineatum. Regardless of the concentration of R. baltica, nodetectable response in bacterial biomass was observed due tograzing. However, when A. tonsa grazed the larger phytoplanktoncells of D. brightwelli and C. lineatum, responses in bacterioplanktonwere observed. It was estimated that approximately 54–69%of the grazed carbon was lost to the surroundings when A. tonsawas feeding on these large phytoplankton species. The laboratoryresults were applied to a dataset from a coastal temperate ecosystem.This analysis showed that the copepod contribution to the DOCpool was as important as the leakage from the primary producers.It is concluded, that the DOM contribution from copepods willbe largest when grazing plankton communities are composed oflarge species.     

光动力疗法治疗细菌和病毒性疾病

目前控制细菌和病毒疾病的方法很多,但尚无良方,本文介绍了细菌和病毒的基本特性和常用的防治方法,着重对一种有希望的新疗法－－光动力疗法的研究现状,尚存问题和发展方向作一概述。     

Effects of Surface Area and Flow Rate on Marine Bacterial Growth in Activated Carbon Columns

The colonization of granular activated carbon columns by bacteria can have both beneficial and potentially detrimental consequences. Bacterial growth on the carbon surface can remove adsorbed organics and thus partially regenerate the carbon bed. However, growth can also increase the levels of bacteria in the column effluents, which can adversely affect downstream uses of the treated water. This study of a sand column and several activated carbon columns demonstrated that considerable marine bacterial growth occurred in both sand and carbon columns and that this growth increased the number of bacteria in column effluents. Activated carbon supported approximately 50% more bacteria than did sand. Bacterial growth on activated carbon was reduced by increasing the flow rate through a carbon column and increasing the carbon particle size. Scanning electron micrographs showed that bacteria preferred to attach in the protected crevices on both the sand and carbon surface. The results of this study indicated that the colonization of activated carbon by marine bacteria was enhanced because of carbon's high surface area, its rough surface texture, and its ability to absorb organic materials.     

Assessing the Diversity of Marine Bacterial β-Glucosidases by Capillary Electrophoresis Zymography

We propose a new method for the fast separation and detection of β-glucosidases in environmental samples. With this approach, β-glucosidases extracted from bacteria are evidenced by substrate-incorporated capillary electrophoresis (CE zymography) and their kinetic parameters can be determined by repeated injections using different substrate concentrations. Preliminary results obtained with natural bacterial communities from the coastal North Sea suggest that the diversity of β-glucosidases in the marine environment might be much higher than previously observed.     

Short-Term Effects of South Louisiana and Kuwait Crude Oils on Glucose Utilization by Marine Bacterial Populations

Two crude oils, South Louisiana and Kuwait, were examined for their impact on glucose utilization by bacterial populations from the Gulf of Mexico. The uptake and mineralization of [U-¹⁴C]glucose was assayed after a 4- to 23-h exposure to various concentrations of added crude oil (0, 0.001, 0.01, and 0.1% [vol/vol]). The effects of oil were determined in a total of 15 sediment and 13 water samples collected from offshore, open-bay, and salt marsh environments. The utilization of glucose by bacterial populations usually was not affected by added oil; in 10 sediment and 11 water samples, oil had no significant effect on either glucose uptake or mineralization. Stimulation by oil was recorded in four sediment samples. Oil inhibition occurred in one sediment and two water samples, but only in the presence of the highest concentration of added oil, i.e., 0.1%. Our data suggest that short-term exposure to either South Louisiana or Kuwait crude oil, even at 0.1%, usually has no toxic effect on glucose utilization by marine bacterial populations.