Despite the recent interest in viruses infecting eucaryotic marine microalgae, only 7 viruses infecting marine phytoplankton have been isolated so far. It is therefore worth reviewing isolation techniques and rationalizing the method for obtaining novel microalgal viruses. I consider 7 steps as critical in the isolation procedure: (1) selection of the target host alga, (2) preparation of target host cultures, (3) collection of sample water for virus isolation, (4) treatment of sample water, (5) screening procedures, (6) cloning and cleaning-up of the isolated viruses and (7) storage and maintenance. In the present review, several observations that may lead to more effective isolation procedures are discussed with regard to (1)~(7).
Sphingomonas sp. S213 is a soil oligotrophic, Gram-negative bacterium capable of degrading lignin-related ferulic acid. In this study, the capacity of strain S213 to degrade ferulic acid was characterized from its growth parameters in batch and continuous cultures and the first steps in the degradation pathway were identified. Batch cultures with different concentrations of ferulate (0-9.8 mM) showed a profile of substrate inhibition of growth; i.e. the growth rate increased with ferulate concentration up to an optimum value (0.15-0.3 mM), after which the inhibitory effect became dominant. In contrast, the ferulate degradation rate decreased progressively with increasing concentration. HPLC analysis and oxygen uptake experiments on resting cell suspensions indicated that the first steps in ferulate degradation involve the conversion to vanillate followed by demethylation to protocatechuate, then ring fission of protocatechuate. In chemostat cultures, the specific rates for converting ferulate to vanillate and for converting vanillate to protocatechuate were a linear function of the growth rate. At growth rates above 0.044 h−1 (medium with 0.02% yeast extract) or 0.054 h−1 (with 0.05% yeast extract), the increase in the rate for converting ferulate to vanillate was not accompanied by a proportional increase in the rate for converting vanillate to protocatechuate. This implied that strain S213 had an overcapacity for the conversion of ferulate to vanillate during ferulate metabolism.
This study relates to the abundance and seasonal distribution of both V. cholerae non-O1 (O2 to 138) and V. mimicus in various aquatic components of the pond ecosystem. Three hundred eighty nine samples comprising aquatic plants (n=52), surface water (n=96), snails (n=90), oysters (n=55) and soil sediment (n=96) were collected from four selected ponds in Matlab at 15-day intervals. The isolation rate of V. cholerae non-O1 and V. mimicus was found to be 16.71% (65/389) and 10.80% (42/389), respectively. The abundance of both V. cholerae non-O1 and V. mimicus was highest with snail (26.6% and 24.4%) and lowest in soil sediment (11.5% and 1.4%, respectively). Seasonal variation in the prevalence of V. cholerae non-O1 and V. mimicus in individual pond ecosystems was also observed. V. cholerae non-O1 was isolated at a higher rate in pond no. 4 (33.3%) followed by pond no. 1 (19.2%). The isolation rate was higher between May and June for most of the ponds except for pond no. 2. The prevalence of V. mimicus was highest in pond no. 3 (16.5%) followed by pond no. 2 (13.3%). The abundance and seasonal distribution pattern of both V. cholerae non-O1 and V. mimicus reveal that Vibrio can survive in association with various aquatic components of the pond ecosystem and may have relevance to the transmission and epidemiology of diarrhoea in Bangladesh.
The potential aminopeptidase activity (APA) in surface sediment (0-1 cm), and important ecological factors of a eutrophicated inlet were monitored for one and a half years on a weekly to biweekly basis to elucidate the fluctuations in extracellular hydrolysis of protein during an annual cycle, and main regulating factors on an annual and/or a seasonal basis. APA was estimated in sediment slurry prepared with unamended bottom water, as the Vmax of the rate of the enzymatic hydrolysis of a coumarine derivative fluorophore at in situ temperatures. APA varied 5-6 fold during the study period with highest values (225-275 nmole AMC h-1 g-1 dry weight) during September-October or early June when the temperature was 22-28°C and dissolved oxygen concentrations (DO) (2-4 mg L-1) in overlying bottom water were high, and much lower values (ca. 50 nmoles AMC h-1 g -1 dry weight) in July-August or December-February. On an annual basis, APA correlated only marginally (p > 0.05; r = 0.25) with the protein content of the surface sediment and not at all with any other variables. However, it showed highly significant correlations (p > 0.001) with temperature (r = 0.81), and protein content (0.65) in mid December-early June, when temperatures were relatively low (ca. 12-22°C) and DO was abundant (ca. 2-6 mg L-1) in overlying bottom water.
Changes in diversity of type I and type II methanotrophs during a biostimulation field experiment were investigated for 73 days after the start of treatment by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rDNA fragments. DGGE profiles of the type I and type II methanotrophs yielded simple banding patterns. The type I methanotrophs' profile showed a single intense band at day 10 of biostimulation, and sequence analysis showed 99% similarity with Methylobacter psychrophilus. The type II methanotrophs' profile showed a single band appeared at day 31, becoming an intense band after day 40. Sequence analysis of this band pattern showed 99% similarity with Methylocystis parvus. These results suggest a possible shift of numerically dominant methanotrophs from type I to type II during the field experiment.
SSU rRNA genes of symbiotic methanogens in the hindgut of four lower Japanese termites and one Australian lower termite Mastotermes darwiniensis as well as a soil sample collected near a nest of Reticulitermes speratus were amplified, cloned and phylogenetically analyzed. Most of the clones found in the lower termites were of the genus Methanobrevibacter. The symbiotic methanogens in the Japanese termites and in the soil sample were related to each other. The clones obtained from M. darwiniensis grouped separately from the clones of Japanese termites. These results suggest that the methanogen community of lower termites reflects host locality rather than phylogeny.
A Pseudomonas strain capable of growing on 4-nitrophenol (4NP) as a sole source of carbon was isolated from a pharmaceutical waste dumpsite after selective enrichment. Experiments revealed that the strain, SF1, utilizes 4-nitrophenol after 6h of adaptation and could degrade up to 2.1 mM of 4NP. Oxygen consumption studies demonstrated that strain SF1 utilized 1,4-benzoquinone and hydroquinone, as well as 4NP. On partial 16S-rDNA sequence analysis, strain SF1 showed highest homology with the Pseudomonas putida strain based on the FASTA program.
The presence of NaCl was essential for cAMP-induced cell aggregation leading to a mat formation in the cyanobacterium Spirulina platensis. The most effective concentration for the mat formation was 0.25 M and higher concentrations were inhibitory. The mat formation occurred under a physiological pH of 7 to 9. Li+ and K+ were less effective than Na+ and divalent cations such as Ca2+ or Mg2+ showed no effect on the mat formation. It was suggested that Na+ enabled the mat formation by supplying energy to cells for aggregation.
The sequences of small subunit ribosomal RNA gene (SSU rDNA) and pigment composition were examined for the five filamentous bacteria isolated from the unialgal cultures of marine microalgae Chattonella marina, Heterosigma akashiwo, or Tetraselmis sp. The SSU rDNA data suggested that the filamentous bacteria were clustered into the same species, which belonged to the Roseobacter group in α-proteobacteria. Sequence similarities of SSU rDNA to each of the other strains were more than 99%. The strains possessed bacteriochlorophyll a, but were different in carotenoid composition: four of the strains contained a carotenoid that was similar to spheroidenone but the other one did not.