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The high concentrations of commercial sample of Bacillus intermedius 7P ribonuclease (binase) showed a weak mutagenic effect in Ames test and Ara-test. It has been established that binase induces the SOS-functions of microbial cell and prophage induction. The way of exogenic enzyme action through activation of RecA protein is proposed.
The stable isotope ratios of a seized pathogen culture could potentially reveal information about the environment in which the agent was produced. In this paper we describe general relationships between stable isotopes of carbon, nitrogen, and hydrogen in bacteriological culture media and spores of Bacillus subtilis, an endospore-forming soil bacterium. In numerous media that varied both in nutrient composition and water stable isotope ratios, medium to spore enrichment in carbon isotopes was 0.3 +/- 2.0% per thousand (parts per thousand), and in nitrogen, 4.5 +/- 0.7% per thousand. We achieved mass balance for the contribution of hydrogen isotopes from nutrients (70%) and water (30%) to spores in independent experiments by varying the isotope ratios of nutrients or water. A model was derived for predicting the isotope ratio values of spores from those in nutrients and water.
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The evidence for occurring lipopolysaccharide-protein complexes in the outer membrane of gram-negative bacteria has been summarized. The composition and supramolecular structure of these complexes as well as their functions in microbial envelope and substantial role in membrane organization have been discussed. The biological properties of the complexes as endotoxins and O-specific antigens have been considered.
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The importance of comprehensive care treatment planning in dental undergraduate and graduate curricula has long been underestimated. With a decreasing prevalence of dental diseases an increasing interest in the subject has been recognized. Comprehensive care treatment planning requires a strategic approach to resolve a patient's problems in a logical sequence and at a a priori estimation of treatment time and costs. The strategy outlined in this work comprises a phasing of the treatment along urgency criteria. Initially, immediate problems are resolved, followed by microbial problems, functional problems, after which a maintenance plan is established. A treatment planning model is introduced to enable students to hold track of the overall treatment plan and to advice students how to address specific dental problems.
Molecular tools have revealed wide microbial diversity in the human alimentary tract. Most intestinal microorganisms have not been cultured and the in situ functions of distinct groups of the intestinal microbiota are largely unknown but pivotal to understanding the role of these microorganisms in health and disease. Promising strategies to gain more insight into the functionality of the complex microbial communities in the human alimentary tract, including fermentation processes in the colon, are discussed. These research approaches could provide a basis for the definition of a healthy gut based on key properties of microbial functionality. This will also enable the development of direct nutritional strategies for intestinal disease prevention and health promotion.
Modification of the functionality of whey proteins using microbial transglutaminase (TGase) has been the subject of recent studies. However, changes in rheological properties of whey proteins as affected by extensive cross-linking with TGase are not well studied. The factors affecting cross-linking of whey protein isolate (WPI) using both soluble and immobilized TGase were examined, and the rheological properties of the modified proteins were characterized. The enzyme was immobilized on aminopropyl glass beads (CPG-3000) by selective adsorption of the biotinylated enzyme on avidin that had been previously immobilized. WPI (4 and 8% w/w) in deionized water, pH 7.5, containing 10 mM dithiothreitol was cross-linked using enzyme/substrate ratios of 0.12-10 units of activity/g WPI. The reaction was carried out in a jacketed bioreactor for 8 h at 40 degrees C with continuous circulation. The gel point temperature of WPI solutions treated with 0.12 unit of immobilized TGase/g was slightly decreased, but the gel strength was unaffected. However, increasing the enzyme/substrate ratio resulted in extensive cross-linking of WPI that was manifested by increases in apparent viscosity and changes in the gelation properties. For example, using 10 units of soluble TGase/g resulted in extensive cross-linking of alpha-lactalbumin and beta-lactoglobulin in WPI, as evidenced by SDS-PAGE and Western blotting results. Interestingly, the gelling point of WPI solutions increased from 68 to 94 degrees C after a 4-h reaction, and the gel strength was drastically decreased (lower storage modulus, G'). Thus, extensive intra- and interchain cross-linking probably caused formation of polymers that were too large for effective network development. These results suggest that a process could be developed to produce heat-stable whey proteins for various food applications.
The microbial community dynamics of a functionally stable, well-mixed, methanogenic reactor fed with glucose were analyzed over a 605-day period. The reactor maintained constant pH and chemical oxygen demand removal during this period. Thirty-six rrn clones from each of seven sampling events were analyzed by amplified ribosomal DNA restriction analysis (ARDRA) for the Bacteria and Archaea domains and by sequence analysis of dominant members of the community. Operational taxonomic units (OTUs), distinguished as unique ARDRA patterns, showed reproducible distribution for three sample replicates. The highest diversity was observed in the Bacteria domain. The 16S ribosomal DNA Bacteria clone library contained 75 OTUs, with the dominant OTU accounting for 13% of the total clones, but just 21 Archaea OTUs were found, and the most prominent OTU represented 50% of the clones from the respective library. Succession in methanogenic populations was observed, and two periods were distinguished: in the first, Methanobacterium formicicum was dominant, and in the second, Methanosarcina mazei and a Methanobacterium bryantii-related organism were dominant. Higher variability in Bacteria populations was detected, and the temporal OTU distribution suggested a chaotic pattern. Although dominant OTUs were constantly replaced from one sampling point to the next, phylogenetic analysis indicated that inferred physiologic changes in the community were not as dramatic as were genetic changes. Seven of eight dominant OTUs during the first period clustered with the spirochete group, although a cyclic pattern of substitution occurred among members within this order. A more flexible community structure characterized the second period, since a sequential replacement of a Eubacterium-related organism by an unrelated deep-branched organism and finally by a Propionibacterium-like species was observed. Metabolic differences among the dominant fermenters detected suggest that changes in carbon and electron flow occurred during the stable performance and indicate that an extremely dynamic community can maintain a stable ecosystem function.
Microbial infection of plants or elicitation of cell cultures initiates substantial metabolic changes directed at the induction of defence reactions. The antimicrobial phytoalexins deserve special attention because they represent one essential component of plant resistance. The great structural diversity of phytoalexins and possible cellular sites for their toxic activity are discussed. Pterocarpan phytoalexin biosynthesis in Cicer arietinum is an example of the induction of extended biosynthetic pathways, their modes of regulation and metabolic links with constitutive secondary product formation. Elicitation of plant tissues represents a technique to induce simultaneously the formation of phytoalexins and increased levels of constitutive or other secondary products that do not normally accumulate. The biological function of phytoalexins and the pathways of their degradation by pathogenic fungi are outlined. Detoxification of phytoalexins by fungi may have important consequences for the practical application of these defence compounds and for the genetic transformation of fungi and plants. Phytoalexins accumulate in plants or cell cultures only transiently, because they are readily degraded or polymerized by extracellular peroxidases.
Snow cover, the extensive terrestrial habitat in Antarctica, sometimes exhibits vivid coloration, yet the structure and function of its microbial communities remain poorly characterized. Using metagenomic sequencing of red snow (RS) and green snow (GS) from the Fildes Peninsula, we found that bacterial, eukaryotic, and archaeal relative abundances were 85.82%, 13.52% and 0.16%, respectively. β-Diversity differed significantly between RS and GS across these three domains (P < 0.05). Dominant bacterial phyla included Bacteroidota (RS: 62.61%; GS: 38.72%) and Pseudomonadota (RS: 32.80%; GS: 54.10%). Among eukaryotes, Chlorophyta (RS: 58.10%; GS: 52.98%) and Basidiomycota (RS: 14.80%; GS: 8.08%) were prevalent. Nanobdellota dominated archaea, with lower abundance in RS than GS. In the algal community, Sanguina, Gonium and Chloromonas were significantly enriched in red snow, while Chlorella and Micractinium were enriched in green snow (P < 0.05). Marker genes associated with carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles were identified in green and red snow. Aerobic respiration and phosphate regulation were significantly enriched in red snow, while CO oxidation, fermentation, and denitrification were significantly enriched in green snow. Key microbial genera associated with these functional pathways also varied. In the denitrification of red snow, Stutzerimonas was the most abundant genus, while Janthinobacterium was abundant in green snow. Nitrification-related genes were detected only in red snow based on the present metagenomic data. The network of the red snow microbial community was potentially more complex and resistant based on topology, which not only benefited its own long-term survival but might also have potentially influenced the positive feedback effect of snowmelt by maintaining a low-albedo snow surface. This provided an ecological implication under climate warming: the expansion of red snow patches showed the potential to the increase nitrate runoff export, which would affect nitrogen nutrient levels in coastal Antarctic waters. Overall, this study used metagenomics to compare the multidomain (bacteria, archaea and eukaryotes) composition and diversity between red snow and green snow, and directly linked key microbial taxa with functional genes of biogeochemical cycles. This study provided new insights into the biological characteristics and functional potential of Antarctic colored snow.
Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime (digital image analysis in microbial ecology), a new computer program integrating 2-D and 3-D image analysis and visualization functionality, which has previously not been available in a single open-source software package. For example, daime automatically finds 2-D and 3-D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with '3D-FISH', which preserves the 3-D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms.
Background/Objectives: Microbial biotransformation of monoterpenoids is a promising approach for obtaining bioactive compounds. Rhodococcus species are attractive biocatalysts due to their metabolic versatility and ability to transform hydrophobic substrates. In this study, we investigated the catalytic potential of Rhodococcus qingshengii IEGM 267 toward carveol isomers and explored genomic features that may underlie this activity. Methods: The strain was cultivated in mineral medium supplemented with (-)-trans-carveol. Biotransformation products were analyzed by TLC and GC-MS. The draft genome was sequenced, assembled, taxonomically assigned, and annotated using standard bioinformatics tools. Results: Rhodococcus qingshengii IEGM 267 efficiently converted (-)-trans-carveol to carvone. Genome analysis confirmed the taxonomic assignment of the strain and revealed a large repertoire of oxidoreductases, including monooxygenases, hydroxylases, and dehydrogenases. Seven genes encoding cytochrome P450-dependent oxygenases were identified as candidate enzymes potentially involved in carveol oxidation. Conclusions: R. qingshengii IEGM 267 is an efficient and stereoselective biocatalyst for (-)-trans-carveol oxidation. The results of bioinformatics analysis suggest an alternative enzymatic basis for this transformation and provide a foundation for future functional characterization.
Six functional replication origins (repGA14, repGA33, repGA70, repSD41, repSD164 and repSD172), obtained from endogenously isolated, broad-host-range (BHR) marine plasmids ranging in size from 5 to 60 kb, were used to determine plasmid occurrence in three coastal marine sediment sites (in California, Georgia and South Carolina, USA). The plasmid-specific replicons were isolated from plasmid-bearing marine sediment bacteria belonging to the alpha and gamma subclasses of the Proteobacteria. The plasmid sources of the endogenous replicons were considered to be cryptic due to a lack of identifiable phenotypic traits. The putative Rep proteins from a number of these replicons showed similarity to replicons of two recognized families: RCR group III (repSD164) and the FIA family of theta group A (repSD41, repSD121, repGA33 and repGA14). Plasmids isolated from marine bacteria belonging to the genera Pseudoalteromonas, Shewanella and Vibrio cultivated from geographically different coastal sites exhibited homology to two of the marine plasmid replicons, repSD41 and repGA70, obtained from a Vibrio sp. The repGA33 plasmid origin, obtained from a Shewanella sp. isolated from coastal Georgia, was detected in 7% of the Georgia marine sediment Shewanella sp. isolates. Microbial community DNA extracted from marine sediments was also screened for the presence of the plasmid replication sequences. Community DNA samples amplified by PCR yielded a positive signal for the repSD172 and repGA14 replication sequences. The replication origin of BHR plasmid RK2 (IncP) was also detected in marine Vibrio sp. and microbial community DNA extracted from the three coastal sites. These findings provide molecular evidence that marine sediment bacteria harbour an untapped population of BHR plasmids.
The aim of this study was to evaluate the suitability of several mathematical functions for describing microbial growth curves. The nonlinear functions used were: three-phase linear, logistic, Gompertz, Von Bertalanffy, Richards, Morgan, Weibull, France and Baranyi. Two data sets were used, one comprising 21 growth curves of different bacterial and fungal species in which growth was expressed as optical density units, and one comprising 34 curves of colony forming units counted on plates of Yersinia enterocolitica grown under different conditions of pH, temperature and CO(2) (time-constant conditions for each culture). For both sets, curves were selected to provide a wide variety of shapes with different growth rates and lag times. Statistical criteria used to evaluate model performance were analysis of residuals (residual distribution, bias factor and serial correlation) and goodness-of-fit (residual mean square, accuracy factor, extra residual variance F-test, and Akaike's information criterion). The models showing the best overall performance were the Baranyi, three-phase linear, Richards and Weibull models. The goodness-of-fit attained with other models can be considered acceptable, but not as good as that reached with the best four models. Overall, the Baranyi model showed the best behaviour for the growth curves studied according to a variety of criteria. The Richards model was the best-fitting optical density data, whereas the three-phase linear showed some limitations when fitting these curves, despite its consistent performance when fitting plate counts. Our results indicate that the common use of the Gompertz model to describe microbial growth should be reconsidered critically, as the Baranyi, three-phase linear, Richards and Weibull models showed a significantly superior ability to fit experimental data than the extensively used Gompertz.
Bioaugmentation of bioreactors focuses on the removal of xenobiotics, with little attention typically paid to the recovery of disrupted reactor functions such as ammonium-nitrogen removal. Chloroanilines are widely used in industry as a precursor to a variety of products and are occasionally released into wastewater streams. This work evaluated the effects on activated-sludge reactor functions of a 3-chloroaniline (3-CA) pulse and bioaugmentation by inoculation with the 3-CA-degrading strain Comamonas testosteroni I2 gfp. Changes in functions such as nitrification, carbon removal, and sludge compaction were studied in relation to the sludge community structure, in particular the nitrifying populations. Denaturing gradient gel electrophoresis (DGGE), real-time PCR, and fluorescent in situ hybridization (FISH) were used to characterize and enumerate the ammonia-oxidizing microbial community immediately after a 3-CA shock load. Two days after the 3-CA shock, ammonium accumulated, and the nitrification activity did not recover over a 12-day period in the nonbioaugmented reactors. In contrast, nitrification in the bioaugmented reactor started to recover on day 4. The DGGE patterns and the FISH and real-time PCR data showed that the ammonia-oxidizing microbial community of the bioaugmented reactor recovered in structure, activity, and abundance, while the number of ribosomes of the ammonia oxidizers in the nonbioaugmented reactor decreased drastically and the community composition changed and did not recover. The settleability of the activated sludge was negatively influenced by the 3-CA addition, with the sludge volume index increasing by a factor of 2.3. Two days after the 3-CA shock in the nonbioaugmented reactor, chemical oxygen demand (COD) removal efficiency decreased by 36% but recovered fully by day 4. In contrast, in the bioaugmented reactor, no decrease of the COD removal efficiency was observed. This study demonstrates that bioaugmentation of wastewater reactors to accelerate the degradation of toxic chlorinated organics such as 3-CA protected the nitrifying bacterial community, thereby allowing faster recovery from toxic shocks.
A photosynthetic microbial mat was investigated in a large pond of a Mediterranean saltern (Salins-de-Giraud, Camargue, France) having water salinity from 70 per thousand to 150 per thousand (w/v). Analysis of characteristic biomarkers (e.g., major microbial fatty acids, hydrocarbons, alcohols and alkenones) revealed that cyanobacteria were the major component of the pond, in addition to diatoms and other algae. Functional bacterial groups involved in the sulfur cycle could be correlated to these biomarkers, i.e. sulfate-reducing, sulfur-oxidizing and anoxygenic phototrophic bacteria. In the first 0.5 mm of the mat, a high rate of photosynthesis showed the activity of oxygenic phototrophs in the surface layer. Ten different cyanobacterial populations were detected with confocal laser scanning microscopy: six filamentous species, with Microcoleus chthonoplastes and Halomicronema excentricum as dominant (73% of total counts); and four unicellular types affiliated to Microcystis, Chroococcus, Gloeocapsa, and Synechocystis (27% of total counts). Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments confirmed the presence of Microcoleus, Oscillatoria, and Leptolyngbya strains (Halomicronema was not detected here) and revealed additional presence of Phormidium, Pleurocapsa and Calotrix types. Spectral scalar irradiance measurements did not reveal a particular zonation of cyanobacteria, purple or green bacteria in the first millimeter of the mat. Terminal-restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA gene fragments of bacteria depicted the community composition and a fine-scale depth-distribution of at least five different populations of anoxygenic phototrophs and at least three types of sulfate-reducing bacteria along the microgradients of oxygen and light inside the microbial mat.