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At least 19 recordsLinked to original sources
PubMed2024

Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.

UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields. IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.

Saccharum↗
PubMed1976

[Heterogeneity of the population of pseudotuberculosis microbe cultures].

Use of the method of oblique illumination of the colonies permitted to detect four variants of pseudotuberculosis microbe differing by the character of fluorescence, and also by virulence, toxicity and immunogenicity. Strains isolated from sick persons, carriers and rodents were characterized by polychromatic character of fluorescence of the colonies, whereas strains isolated from the external environment were monochromatic. Since colonies with a different fluorescence had different biological properties it can be supposed that the properties of each strain as a whole were determined by its quantitative and qualitative composition as of a heterogeneous population.

Animals↗
PubMed1979

Microbial oxidation of gaseous hydrocarbons: production of methyl ketones from their corresponding secondary alcohols by methane- and methanol-grown microbes.

Cultures of methane- or methanol-utilizing microbes, including obligate (both types I and II) and facultative methylotrophic bacteria, obligate methanol utilizers, and methanol-grown yeasts were isolated from lake water of Warinanco Park, Linden, N.J., and lake and soil samples of Bayway Refinery, Linden, N.J. Resting-cell suspensions of these, and of other known C1-utilizing microbes, oxidized secondary alcohols to their corresponding methyl ketones. The product methyl ketones accumulated extracellularly. Succinate-grown cells of facultative methylotrophs did not oxidize secondary alcohols. Among the secondary alcohols, 2-butanol was oxidized at the highest rate. The optimal conditions for in vivo methyl ketone formation were compared among five different types of C1-utilizing microbes. Some enzymatic degradation of 2-butanone was observed. The product, 2-butanone, did not inhibit the oxidation of 2-butanol. The rate of the 2-butanone production was linear for the first 4 h of incubation for all five cultures tested. A yeast culture had the highest production rate. The optimum temperature for the production of 2-butanone was 35 degrees C for all the bacteria tested. The yeast culture had a higher temperature optimum (40 degrees C), and there was a reasonably high 2-butanone production rate even at 45 degrees C. Metal-chelating agents inhibit the production of 2-butanone, suggesting the involvement of metal(s) in the oxidation of secondary alcohols. Secondary alcohol dehydrogenase activity was found in the cell-free soluble extract of sonically disrupted cells. The cell-free system requires a cofactor, specifically nicotinamide adenine dinucleotide, for its activity. This is the first report of a nicotinamide adenine dinucleotide-dependent, secondary alcohol-specific enzyme.

Butanols↗
PubMed2004

[Rapid pathogens diagnosis of infected keratitis and endophthalmitis using two steps polymerase chain reaction].

OBJECTIVE: To establish a rapid diagnosis technique of the pathogens of infected keratitis and endophthalmitis. METHODS: Fifty-one corneal scraping, tear and 16 vitreous specimens were obtained from 67 cases of infected keratitis and endophthalmitis. Multiplex polymerase chain reaction (MPCR) was performed to differentiate the genes of bacteria, fungi and HSV using their own universal primers. Special-primers PCR were carried out for MPCR positive specimens to detect the genes of common bacteria and fungi respectively. The results were compared with microbe culture and clinical diagnosis. RESULTS: In 67 clinical samples, 52 (77.6%) were positive at least one kind of pathogen by MPCR (two positive pathogens were 8 cases). SPCR revealed that 7 bacteria (25.0%) out of 28 bacteria positive specimens were Staphylococcus aureus, Streptococcus pneumoniae, Pseudomonas aeruginosa. Eight fungi (53.3%)of 15 fungi positive specimens was Candida, Aspergillus, Fusarium. The culture positive rates were 31.3% (21 cases), among them 1 case was found positive for two pathogens. MPCR positive rate was statistically higher than the rate that in culture (chi(2) = 13.50, P < 0.005). The kinds of bacteria and fungi of SPCR positive were as the same as bacteria and fungi of culture positive. Consistency of clinical diagnosis and experimental evidences of infected keratitis was 54.8%. The time for microbe culture needs 72 to 96 hours, but MPCR and SPCR needs 8 hours. CONCLUSION: Two steps PCR is rapid, sensitive method to detect the pathogens of infected keratitis and endophthalmitis.

Adolescent↗
PubMed1978

[Effectiveness of the tularemia-antibody erythrocyte diagnostic agent for the detection of specific antigen and antibodies to it].

The authors demonstrated the efficacy of utilization of tularemia antibody erythrocytic diagnostic agent. Data are presented indicating a strict specificity and a high sensitivity of this diagnostic agent for detection of the Vi-antigen both in the tularemia microbe cultures and in the suspensions of the organs of rodents which perished of tularemia, irrespective of the state of cadaver. There was revealed relationship between the sensitivity of the diagnostic agent and the virulence of the tularemia microbe cultures. A possibility of using the diagnostic agent in the antigen neutralization test for detection of specific antibodies in the sera of patients, who sustained the disease, and of the vaccinated humans and animals was revealed.

Animals↗
PubMed1991

[Virological and bacteriological study of materno-fetal infections in Brazzaville].

Serological study of serum samples taken from pregnant women and umbilical cord and bacteriological study of vaginal secretions samples and cerebrospinal fluid (CSF) showed in mothers: T. pallidum antibody (Tp ab) 9%, Rubella virus antibody (Ru ab) 85%; HBs Ag 16%, HIV antibody (HIV ab) 4%. Microbe culture showed: S. aureus 18%, Streptococcus sp. 9%, E. coli 4.9%, Klebsiella 3.6%, Citrobacter 3.6%, Candida albicans 15%; direct immunofluorescence: Chlamydia 26%. In infants: IgG umbilical cord: Tp ab 4.8%, Rub ab: 80.6%, HIV ab 4/4, Hbs Ag 11.3% Microbe culture in CSF: global frequency: 5.1%; Streptococcus sp. 31.8%, Staphylococcus 20.5%, enterobacteriaceae 27.2%, other Gram negative bacilli 20.5%.

Adolescent↗
PubMed2002

Tolerance to biodegraded crude oil in marine invertebrate embryos and larvae is associated with expression of a multixenobiotic resistance transporter.

The toxicity of water-soluble fractions of biodegraded crude oil (BWSF) to embryos and larvae of two marine invertebrates, the white sea urchin (Lytechinus anamesus) and the fat innkeeper (Urechis caupo), was studied. Santa Barbara Channel crude oil was artificially weathered and subjected to biodegradation using a mixed microbe culture obtained from natural oil seep sites. The degradation culture inoculated with seep sediment microbes accumulated 43.7 microg/l water-soluble hydrocarbons. In contrast water-soluble fractions from the non-degraded cultures (NWSF) only accumulated 3.05 microg/l. BWSF proved deleterious to Lytechinus embryo development at low concentrations (EC50 = 0.33 mg/l) but was essentially non-toxic to Urechis embryos/larvae up to 3.0 mg/l. An established mechanism for handling of a wide array of xenobiotics in Urechis embryos is the multixenobiotoic resistance transporter multixenobiotic response (MXR, also known as multidrug resistance, MDR). This mechanism is primarily mediated by ATP-dependent, efflux pumps that extrude a wide array of xenobiotic compounds. In this study, we show that Lytechinus larvae do not appear to express MXR efflux protein nor MXR mediated dye efflux capacity. In contrast, BWSF acts as a competitive inhibitor of MXR transport-mediated dye efflux in Urechis larvae. These results suggest that MXR may be an important mechanism for extrusion of the by-products of crude oil degradation by microbes, and that the level of its expression may determine the susceptibility of organisms to degraded oil hydrocarbons.

Adaptation, Physiological↗
PubMed1982

[Production of pesticins on synthetic nutrient media].

It was found that 96.2 per cent of the plague microbe cultures studied had a capacity to produce pesticin I on solid and liquid minimum synthetic nutrient media providing growth of the cultures. No pesticin III was detected in the spheroplasts of plague microbes, when they were grown on the synthetic nutrient medium, while on the complete nutrient medium the inhibition zones were observed which was indicative of pesticin III synthesis. The average value characterizing the titer of pesticin I produced by the rod-shaped forms of the plague microbe on the complete and synthetic nutrient media was 320. An increase in the titer of the spheroplast pesticin was shown, while the pesticin titer of the rod-shaped forms was low (1 : 20--1 : 320). As a result the average titer of the spheroplast pesticin was higher than that of pesticin of the rod-like forms. On the complete nutrient medium it was 1280 and on the synthetic medium it was 640.

Bacteriocins↗
PubMed2006

Novel quantitative biosystem for modeling physiological fluid shear stress on cells.

The response of microbes to changes in the mechanical force of fluid shear has important implications for pathogens, which experience wide fluctuations in fluid shear in vivo during infection. However, the majority of studies have not cultured microbes under physiological fluid shear conditions within a range commonly encountered by microbes during host-pathogen interactions. Here we describe a convenient batch culture biosystem in which (i) the levels of fluid shear force can be varied within physiologically relevant ranges and quantified via mathematical models and (ii) large numbers of cells can be planktonically grown and harvested to examine the effect of fluid shear levels on microbial genomic and phenotypic responses. A quantitative model based on numerical simulations and in situ imaging analysis was developed to calculate the fluid shear imparted by spherical beads of different sizes on bacterial cell cultures grown in a rotating wall vessel (RWV) bioreactor. To demonstrate the application of this model, we subjected cultures of the bacterial pathogen Salmonella enterica serovar Typhimurium to three physiologically-relevant fluid shear ranges during growth in the RVW and demonstrated a progressive relationship between the applied fluid shear and the bacterial genetic and phenotypic responses. By applying this model to different cell types, including other bacterial pathogens, entire classes of genes and proteins involved in cellular interactions may be discovered that have not previously been identified during growth under conventional culture conditions, leading to new targets for vaccine and therapeutic development.

Bacterial Proteins↗
PubMed1977

Airborne micro-organisms and prevalence of byssinotic symptoms in cotton mills.

The concentration of airborne microbes, their endotoxins and the prevalence of byssinotic symptoms among workers were measured in the cardrooms of seven cotton spinning, a wool spinning and two cotton waste mills and in a dusty workroom of a group of five willowing mills, a tea-packing plant and a pipe tobacco factory. The concentration of microbes cultured on endoagar plates were found to correlate with byssinosis prevalence (r greater than 0.95, P less than 0.001). The concentration of nutrient agar microbes correlated with prevalence less well (r greater than 0.77, P less than 0.01) and that of fungi and endotoxins not at all.

Air Microbiology↗
PubMed2001

In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I.

We previously showed that very thin filamentous bacteria affiliated with the division green non-sulfur bacteria were abundant in the outermost layer of thermophilic methanogenic sludge granules fed with sucrose and several low-molecular-weight fatty acids (Y. Sekiguchi, Y. Kamagata, K. Nakamura, A. Ohashi, H. Harada, Appl. Environ. Microbiol. 65:1280-1288, 1999). Further 16S ribosomal DNA (rDNA) cloning-based analysis revealed that the microbes were classified within a unique clade, green non-sulfur bacteria (GNSB) subdivision I, which contains a number of 16S rDNA clone sequences from various environmental samples but no cultured representatives. To investigate their function in the community and physiological traits, we attempted to isolate the yet-to-be-cultured microbes from the original granular sludge. The first attempt at isolation from the granules was, however, not successful. In the other thermophilic reactor that had been treating fried soybean curd-manufacturing wastewater, we found filamentous microorganisms to outgrow, resulting in the formation of projection-like structures on the surface of granules, making the granules look like sea urchins. 16S rDNA-cloning analysis combined with fluorescent in situ hybridization revealed that the projections were comprised of the uncultured filamentous cells affiliated with the GNSB subdivision I and Methanothermobacter-like cells and the very ends of the projections were comprised solely of the filamentous cells. By using the tip of the projection as the inoculum for primary enrichment, a thermophilic, strictly anaerobic, filamentous bacterium, designated strain UNI-1, was successfully isolated with a medium supplemented with sucrose and yeast extract. The strain was a very slow growing bacterium which is capable of utilizing only a limited range of carbohydrates in the presence of yeast extract and produced hydrogen from these substrates. The growth was found to be significantly stimulated when the strain was cocultured with a hydrogen-utilizing methanogen, Methanothermobacter thermautotrophicus, suggesting that the strain is a sugar-fermenting bacterium, the growth of which is dependent on hydrogen consumers in the granules.

Animals↗