Plasmids in Clostridium botulinum and related Clostridium species.

Toxigenic Clostridium botulinum and nontoxigenic C. sporogenes, C. subterminale, and C. botulinum-like organisms from a variety of sources were screened for plasmids. Of the 68 toxigenic C. botulinum isolates, 56% carried one or more plasmids, ranging in mass from 2.1 to 81 megadaltons. Within individual groups (based on the type of neurotoxin produced), many strains showed identical plasmid banding patterns on agarose gels. Of the 15 nontoxigenic strains tested, 40% also carried one or more plasmids ranging from 1.7 to 25.0 megadaltons, with both unique and common banding patterns represented. A total of 67 plasmids from both toxigenic and nontoxigenic strains were detected. At this time, no phenotypic functions have been assessed for these plasmids, and they must therefore be considered cryptic. A variety of lysing and extraction techniques were necessary to detect plasmids in the different C. botulinum groups.     

Plasmids in Listeria monocytogenes and other Listeria species.

One hundred and twenty-two food, clinical, and veterinary strains of Listeria monocytogenes were examined for the presence of plasmids. Twenty-five (20%) contained plasmids, which varied from 1.3 to 66 MDa in size. Of 10 strains of other Listeria species (L. innocua, L. ivanovii, L. welshimeri, L. seeligeri, L. grayi, and L. murrayi) examined, seven (70%) contained plasmids, varying from 38 to 53 MDa. No strains with multiple plasmids were found. Plasmids of identical size were isolated from related strains in some, although not all, cases. The presence of a plasmid in a strain was not related to phenotypic characters of known extrachromosomal inheritance.     

Lake warming favours small-sized planktonic diatom species

Diatoms contribute to a substantial portion of primary production in the oceans and many lakes. Owing to their relatively heavy cell walls and high nutrient requirements, planktonic diatoms are expected to decrease with climate warming because of reduced nutrient redistribution and increasing sinking velocities. Using a historical dataset, this study shows that diatoms were able to maintain their biovolume with increasing stratification in Lake Tahoe over the last decades; however, the diatom community structure changed. Increased stratification and reduced nitrogen to phosphorus ratios selected for small-celled diatoms, particularly within the Cyclotella genus. An empirical model showed that a shift in phytoplankton species composition and cell size was consistent within different depth strata, indicating that altered nutrient concentrations were not responsible for the change. The increase in small-celled species was sufficient to decrease the average diatom size and thus sinking velocity, which strongly influences energy transfer through the food web and carbon cycling. Our results show that within the diverse group of diatoms, small-sized species with a high surface area to volume ratio were able to adapt to a decrease in mixing intensity, supporting the hypotheses that abiotic drivers affect the size structure of planktonic communities and that warmer climate favours small-sized diatom cells.     

Marine diatom species harbour distinct bacterial communities

We examined bacterial dynamics in batch cultures of two axenic marine diatoms (Thalassiosira rotula and Skeletonema costatum). The axenic diatoms were inoculated with natural bacterial assemblages and monitored by 4,6-diamidino-2-phenolindole (DAPI) counts, denaturing gradient gel electrophoresis (DGGE) with subsequent analysis of excised, sequenced 16S rRNA gene fragments, and fluorescence in situ hybridization (FISH) with group-specific 16S rRNA oligonucleotide probes. Our results show that algal growth exhibited pronounced differences in axenic treatments and when bacteria were present. Bacterial abundance and community structure greatly depended on species, growth and physiological status of even closely related algae. Free-living and phytoplankton-associated bacteria were very different from each other and were dominated by distinct phylogenetic groups. The diatom-associated bacteria mainly belonged to the Flavobacteria-Sphingobacteria group of the Bacteroidetes phylum whereas free-living bacteria, which were rather similar in both cultures, comprised mainly of members of the Roseobacter group of alpha-Proteobacteria. Presence and disappearance of specific bacteria during algal growth indicated pronounced differences in environmental conditions over time and selection of bacteria highly adapted to the changing conditions. Tight interactions between marine bacteria and diatoms appear to be important for the decomposition of organic matter and nutrient cycling in the sea.     

Plasmids in Frankia sp.

A method to achieve cell lysis and isolate Frankia sp. plasmid DNA was developed. A screening of Frankia sp. strains belonging to different host compatibility groups (Alnus sp., Elaeagnus sp., Ceanothus sp.) showed that, of 39 strains tested, 4 (strains Cp11, ARgN22d, ArI3, and EUN1f) possessed plasmids ranging in size from 7.1 to 32.2 kilobase pairs as estimated from agarose gel electrophoresis and electron microscopy. A total of 11 plasmids were detected.     

Environmental controls of diatom species in northeast Pacific sediments

Non-linear, unimodal techniques are suitable for estimation of environmental properties in the northeast (NE) Pacific based on fossil diatom taxa (species and/or species groups) found in modern (core-top) sediments. Canonical Correspondence Analysis (CCA), a constrained ordination technique, discerned best-fit relationships among two multivariate datasets (the floral and the environmental) and thus yielded insight into the environmental variables that best explain the species variance within diatom populations. Based on these insights, we developed predictive functions for annual Primary Productivity (PP) and seasonal range of sea Sea-Surface Temperature using unimodal models and cross validation techniques. Estimates of annual PP (r²_jack = 0.92; RMSEP = 91.94 gC/m²/y) explained the highest percentage of variance in the core-top diatom record (22.1%).     

Observations on some species of the diatom genus Gomphonema C. A. Agardh

Gomphonema acuminatum var. coronatum Ehrenb., G. capitatum Ehrenb., G. constrictum Ehrenb., G. gracile Ehrenb., G. intricatum var. vibrio Ehrenb., G. subclavatum Grun. and G. ventricosum Greg. all conform to the basic features of the genus Gomphonema C. Ag. as exemplified by detailed electron microscopical studies of G. parvulum Kütz. This biraphidaceous diatom genus is characterised by heteropolar, asymmetrical cells which have a single isolated punctum, displaced somewhat from the centre of the valve. Electron microscopical observations reveal a reniform or horseshoe-shaped poroidal structure to the valve. It is suggested that this is found only in “true” members of the genus Gomphonema. Other “gomphonemoid” types with differing pore structure should be removed into related genera.     

Plasmids of Azotobacter vinelandii.

Four laboratory strains and two isolates of Azotobacter vinelandii were found to contain plasmids. Twenty-five laboratory strains which could fix nitrogen did not have free, covalently closed circular plasmid DNA. The plasmids varied in size from 9 to 52 megadaltons, and each strain yielded only one plasmid. No discernible differences in ability to fix nitrogen were found between plasmid-bearing and cured cultures.     

Environmental control of lipid and biomass production in two diatom species

Biomass and neutral lipid accumulation were examined in Chaetoceros muelleri var. subsalsum and Navicula saprophila using a multivariate, fractional factorial design. Variables included were conductivity, temperature, nitrogen concentration, silicon concentration, time (culture age), and alkalinity. Measured characteristics included nile red fluorescence (as a measure of neutral lipid content) and ash-free dry weight (AFDW). Nitrogen concentration was the variable with the greatest effect on neutral lipid and ash-free dry weight accumulation over the ranges tested. Increasing conductivity in the range examined had a significant, negative impact on neutral lipid accumulation in both of these strains, while increasing alkalinity had a positive effect on lipid and ash-free dry weight in both strains. Experimental designs such as those described here have great potential utility in biological systems with complex interactions.     

Plasmids for recombination-based screening.

To facilitate recombination-based screening, we constructed the ColE1-based plasmid, pi G4, that confers chloramphenicol resistance, contains a polylinker with multiple unique restriction enzyme recognition sequences, and contains the genetic marker, supF. To facilitate recombination-based screening followed by rapid DNA sequencing, we inserted the selectable marker, supF, into each of 20 high-copy-number (hcn) pUC-derived NoC plasmids that were designed for multiplex DNA sequencing. To facilitate recombination-based screening of common cDNA libraries that often contain ColE1 sequences, we constructed a supF-carrying plasmid whose replication was driven from an R6K replicon that does not share sequence homology with ColE1. Furthermore, we incorporated a useful polylinker and increased the copy number of this plasmid to create the 4.4-kb hcn plasmid, pMAD1. Thus, these plasmids allow: (1) background-free transformation of cells by a supF plasmid carrying an antibiotic-resistance marker; (2) simultaneous performance of the recombination-based assay and DNA sequencing; and (3) screening bacteriophage cDNA libraries that contain ColE1 sequences by recombination with a supF plasmid that is not homologous to ColE1 derivatives.     

Plasmids in avirulent strains of Agrobacterium.

Twelve strains of Agrobacterium radiobacter isolated from naturally occurring crown galls or soil were found to be avirulent on sunflower, tomato, Kalanchoe, and carrot. Eleven strains contained plasmids of molecular weights 77 X 10(6) to 182 X 10(6) as determined by electron microscopy. One strain contained only a smaller plasmid (50 X 10(6) daltons). Several strains had both large and small (ca. 11 X 10(6) daltons) plasmids; one strain contained two large plasmids (112 X 10(6) and 136 X 10(6) daltons). Hybridization reactions of virulence plasmids from Agrobacterium tumefaciens strains C58 and A6 with plasmids from each of the A. radiobacter strains revealed that some A. radiobacter plasmids had less than 10% homology to either the C58 or A6 plasmids. Plasmids from some strains had approximately 50% homology with the C58 plasmid, but only one A. radiobacter plasmid contained more than 10% homology to the A6 plasmid. The presence of large plasmids in A. radiobacter strains did not correlate with sensitivity to agrocin 84; however, the utilization of the amino acid derivatives octopine and nopaline was generally correlated to partial base sequence homology to the C58 plasmid. We conclude that all large plasmids found in Agrobacterium strains are not virulence associated, although they may share base sequence homology with a virulence-associated plasmid. Further, plasmids from tumorigenic strains may be more closely related by base sequence homology to plasmids from nonpathogenic strains than to plasmids from other pathogenic strains.     

Lyrella cassiteridum, a new species of marine epipelic diatom

Lyrella cassiteridum sp. nov. is described from the Isles of Scilly, SW Britain. It is an epipelic species and was found in samples taken from marine sandflats in the intertidal and uppermost subtidal zones. In LM, L. cassiteridum is most similar to L. abrupta , from which it can be distinguished by its larger size and coarser structure. The ultrastructure of the frustule is documented and discussed with respect to that of other Lyrella species and the related genus Petroneis. A brief review of the nomenclatural history of Lyrella is given.     

High number of diatom species in first-year ice from the Chukchi Sea

Our study describes the species composition of microalgae, primarily diatoms, in two ice cores collected from the Chukchi Sea in early June 1998. At least 251 species were present in 2 cores collected 10 m apart in first-year ice. This is a greater number of algal species in ice from one locality than has been recorded from any other area of the Arctic. Microalgae were distributed throughout the 173-cm-long core, but abundance and species composition varied among different sections of the core, with maximum species richness (108 and 103 species in the 94- to 103- and 103- to 113-cm sections, respectively) occurring in the middle sections. More than 237 species were recorded from this core. Only the bottom 20 cm of the shorter (110 cm) core was analysed and it contained 135 algal species, still an extraordinarily high number of species. Marine species dominated both cores, but typical brackish and freshwater species were also present. None of these species, however, had more than 1% relative abundance. It should be noted, though, that there were several distinct, but unidentified, species of unknown origin. Characteristic ice algal species (e.g. Nitzschia frigida, Navicula pelagica, solitary Navicula spp., in addition to Cylindrotheca closterium) were the numerical dominants in most sections of the long core, but phytoplankton and benthic species were quite abundant in some sections. One section was dominated by a blue-green bacterium, presumably of the genus Anabaena. The species composition is consistent with several different mechanisms for algal incorporation into ice (i.e. seawater filtration ice, seeding from the sea floor, freshwater input). Over time, ice dynamics and sources of ice in the Chukchi Sea appear to result in high numbers of algal species in the ice. It is also likely that season of collection contributed to the high number of species observed. Determining the geographical area of origin for the different species is however difficult, due to the large-scale pattern of ice circulation.     

Coexistence of two Cyclotella diatom species in the plankton of Lake Baikal

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