Sole Carbon Source Utilization Patterns Research Articles

Carbon source utilization patterns in dental plaque and microbial responses to sucrose, lactose, and phenylalanine consumption in severe early childhood caries

ABSTRACT Background Severe early childhood caries (S-ECC) is mainly caused by the interaction of microbiota and environmental factors. However, the metabolic profiles of S-ECC microbial communities and the community-level microbial responses to carbohydrates and amino acids are poorly understood. Methods We collected supragingival plaques from 15 caries-free (CF) and 14 S-ECC children. Cultivation on Biolog AN microplates together with next-generation sequencing was used to analyze sole carbon source utilization patterns and microbial responses to sucrose, lactose and phenylalanine. Results S-ECC plaques had greater overall metabolic activity than those of CF ones. Comparing with CF, S-ECC plaques utilized more sucrose and lactose but less phenylalanine and then had greater response to carbohydrates. A remarkable increase of non-mutans Streptococci was observed in sucrose and lactose consumption. Lactose led to less differently distributed taxa than sucrose in both CF and S-ECC groups. Sucrose made the originally different S-ECC and CF communities eventually became similar to each other, but they remained dissimilar in lactose. Conclusion S-ECC plaques had more active interaction with cariogenic carbohydrates like sucrose and lactose than healthy plaques. We supported lactose has less cariogenicity compared with sucrose from microbial community structural aspect. Phenylalanine may have a potentially inhibitory effect on caries development.

A rhizosphere-associated symbiont, Photobacterium spp. strain MELD1, and its targeted synergistic activity for phytoprotection against mercury.

Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg . kg-1 mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis). While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg . kg-1, 24 h) and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis) and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg) on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA) productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury.

Effects of contamination of single and combined cadmium and mercury on the soil microbial community structural diversity and functional diversity

To assess the effects of single and combined pollution of cadmium (Cd) and mercury (Hg) on soil microbial community structural and functional diversities, an incubation experiment was conducted, by employing two soils, namely, the marine sediment silty loam soil and the yellowish-red soil, in which five levels of Cd, Hg and Cd and Hg in combination were added. After being incubated for 56 days, the phospholipid fatty acids (PLFAs) profile and sole carbon source utilization pattern (BIOLOG) of the samples were tested. The results showed that the composition of the microbial communities changed significantly at different levels of metals application. The principal component analyses (PCA) of PLFAs indicated that the structure of the microbial community was also significantly altered with increasing levels of metals, with increasing PLFAs biomarkers for fungi and actinomycetes, and increasing ratio of Gram-positive to Gram-negative bacteria. Sole carbon source utilization pattern analysis revealed that single and combined application of Cd and Hg inhibited significantly the functional activity of soil microorganisms, the functional diversity indices [Richness (S), Shannon-Wiener indices (H) and Evenness (EH)] were significantly lower in polluted soils than those in non-polluted soils, which also significantly altered with increasing levels of metals. PCA for the sole carbon source utilization pattern also indicated that the metal contamination could result in a variable soil microbial community. The results revealed that the combination of Cd and Hg had higher toxicity to soil microbial community structural and functional diversities than the individual application of Cd or Hg.

Nutritional constraints on displacement of Fusarium pseudograminearum from cereal straw by antagonists

Displacement of the fungus Fusarium pseudograminearum from stubble by antagonists is a potential means of biocontrol of crown rot in cereals. The role of carbon and nitrogen nutrition in interactions between the pathogen and the antagonists Fusarium equiseti, Fusarium nygamai, Trichoderma harzianum and the non-antagonistic straw fungus Alternaria infectoria was investigated. Sole carbon source utilization patterns on Biolog plates were similar among the three Fusarium species, suggesting a possible role for competition. However, carbon niche overlap was unlikely to be important in antagonism by T. harzianum. Straw medium supplemented with sugars generally reduced the inhibitory effect of antagonists on growth of F. pseudograminearum in dual culture, indicating that availability of simple carbon sources does not limit antagonism. Adding nitrogen as urea, nitrate or ammonium to straw medium had little effect on antagonism by F. equiseti and F. nygamai, but ammonium addition removed the inhibitory effect of T. harzianum on growth of F. pseudograminearum. Displacement of F. pseudograminearum from straw by all fungi in a Petri dish assay was greater when urea or nitrate was used as a nitrogen source than with ammonium. All forms of nitrogen significantly increased displacement of F. pseudograminearum from straw under simulated field conditions when straws were either inoculated with T. harzianum or exposed to resident soil microbes. However, in 2 out of 3 experiments urea and nitrate were more effective than ammonium. The results suggest that availability of nitrogen, but not carbon, is limiting the activities of antagonists of F. pseudograminearum in straw, and the way nitrogen is applied can influence the rate of displacement and mortality of the pathogen in host residues.

Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea.

A novel actinomycete, strain TVU1(T), was isolated from leaves of the indigenous South African plant Tulbaghia violacea. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain TVU1(T) was most closely related to Micromonospora echinospora DSM 43816(T). However, phylogenetic analysis based on gyrB gene sequences showed that strain TVU1(T) was most closely related to the type strains of Micromonospora aurantiaca and Micromonospora chalcea. DNA-DNA relatedness values between strain TVU1(T) and the type strains of M. echinospora, M. aurantiaca and M. chalcea were 7.6+/-4.5, 45.9+/-2.0 and 60.9+/-4.5 %, respectively. Strain TVU1(T) could be distinguished from the type strains of all three of these species by several physiological characteristics, such as colony colour, NaCl tolerance, growth temperature range and sole carbon source utilization pattern. Strain TVU1(T) (=DSM 45142(T)=NRRL B-24576(T)) therefore represents a novel species for which the name Micromonospora tulbaghiae sp. nov. is proposed.

Impact of Elevated O3 on Soil Microbial Community Function Under Wheat Crop

This study was initiated to explore the effects of ozone (O-3) exposure on potted wheat roots and soil microbial community function. Three treatments were performed: (1) Air with daily averaged O-3 concentration of 4-10 ppb (control situation, CK), (2) Air plus 8 h averaged O-3 concentration of 76.1 ppb (O-3-1), and (3) Air plus 8 h averaged O-3 concentration of 118.8 ppb (O-3-2). In treatments with elevated O-3 concentration (O-3-1 and O-3-2), the root and shoot biomass were reduced by 25% and 18%, respectively, compared to the control treatment (CK). On the other hand, root activity was significantly reduced by 58% and 90.8% in the O-3-1 and O-3-2 treatments, respectively, compared to CK. The soil microbial biomass was significantly reduced only in the highest O-3 concentration (O-3-2 treatment) in the rhizosphere soil. Soil microbial community composition was assessed under O-3 stress based on the changes in the sole carbon source utilization profiles of soil microbial communities using the Biolog (TM) system. Principal component analysis showed that there was significant discrimination in the sole-carbon source utilization pattern of soil microbial communities among the O-3 treatments in rhizosphere soil; however, there was none in the bulk soil. In rhizosphere soil, the functional richness of the soil microbial community was reduced by 27% and 38% in O-3-1 and O-3-2 treatments, respectively, compared to CK. O-3-2 treatment remarkably decreased the Shannon diversity index of soil microbial community function in rhizosphere soil, but the O-3-1 treatment did not. In the dominant microorganisms using carbon sources of carbohydrates and amino acids groups were significantly reduced by an elevated O-3 concentration in the rhizosphere soil. Our study shows that the elevated ozone levels may alter microbial community function in rhizosphere soil but not in the bulk soil. Hence, this suggests that O-3 effects on soil microbes are caused by O-3 detriments on the plant, but not by the O-3 direct effects on the soil microbes.

Influence of Tea Cultivation on Soil Microbial Biomass and Substrate Utilization Pattern

The study was conducted to evaluate the effect of tea cultivation on soil microbial biomass and community structure. Soil pH, extractable aluminum (Al), organic carbon (Corg) and total nitrogen were considerably modified by tea cultivation. Long‐term tea cultivation resulted in the increase of microbial biomass C (Cmic), microbial biomass N (Nmic), and basal respiration. The metabolic quotient declined as the tea cultivation age increased. The adjacent citrus orchard soil showed a higher Cmic/Corg ratio than the tea orchard soils. Microtitration plates with 21 carbon sources and two different pH levels (4.7 and 7.0) were used to determine the substrate utilization pattern of these soils. The average well color development (AWCD) of the carbon sources in the plates did not vary in a consistent manner with the microbial biomass. Multivariate analysis of sole carbon source utilization pattern demonstrated that land‐use history had a significant effect on substrate utilization pattern. The pH 4.7 characterization medium can increase the discrimination of this technique and is more adequate than the conventional neutral medium for the tea orchard soils.

Effect of heavy metals on substrate utilization pattern, biomass, and activity of microbial communities in a reclaimed mining wasteland of red soil area

The microbial biomass, basal respiration, and substrate utilization pattern in a copper mining wasteland of red soil area, southern China, were investigated, and indicated that soil microflora were obviously affected by heavy metals. Microbial biomass and basal respiration were negatively affected by comparatively high heavy metal levels. Two important microbial ecophysiological parameters, namely, the microbial biomass C ( C mic)/microbial biomass N ( N mic) ratio and the metabolic quotient ( qCO 2) were significantly correlated to heavy metal stress. There was a significant decrease in the C mic/ N mic ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of Biolog data for sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and functional diversity. All the results showed that soil microbiological parameters could have great potential as sensitive, effective, and liable indicators of the stresses or perturbations in soils of mining ecosystems.

Rhizobacterial community-level, sole carbon source utilization pattern affects the delay in the bacterial wilt of tomato grown in rhizobacterial community model system

Characterizing rhizomicrobial community structure is important to our understanding of the mechanisms of suppressive soils towards soilborne plant diseases. We investigated whether the bacterial community structure, i.e., the number of the constituent bacterial strains and the community-level, sole carbon source utilization pattern of rhizobacteria estimated by BIOLOG EcoPlates, affects bacterial wilt of tomato. To assess their impact on the bacterial wilt, we used 15 artificial soil systems into which 5–20 rhizobacterial isolates from a disease-suppressive soil were inoculated. Although most of the tomato plants wilted by 16 days after pathogen inoculation, significant negative relationships were observed between the number of wilted plants, the number of the bacterial strains and the number of carbon sources that the rhizobacterial community was able to utilize. BIOLOGs showed that several carbon sources were utilized by the pathogen but not by the rhizobacterial community from the fastest-wilting treatments, suggesting that competition between the pathogen and the other rhizobacteria for carbon sources played an important role in suppressing the growth of the pathogen.

Effects of lead and cadmium nitrate on biomass and substrate utilization pattern of soil microbial communities

A study was conducted to evaluate the effects of different concentrations of lead (Pb) and cadmium (Cd) applied as their nitrates on soil microbial biomass carbon (C mic) and nitrogen (N mic), and substrate utilization pattern of soil microbial communities. The C mic and N mic contents were determined at 0, 14, 28, 42 and 56 days after heavy metal application (DAA). The results showed a significant decline in the C mic for all Pb and Cd amended soils from the start to 28 DAA. From 28 to 56 DAA, C mic contents changed non-significantly for all other treatments except for 600 mg kg −1 Pb and 100 mg kg −1 Cd in which it declined significantly from 42 to 56 DAA. The N mic contents also decreased significantly from start to 28 DAA for all other Pb and Cd treatments except for 200 mg kg −1 Pb which did not show significant difference from the control. Control and 200 mg kg −1 Pb had significantly lower soil microbial biomass C:N ratio as compared with other Pb treatments from 14 to 42 DAA, however at 56 DAA, only 1000 mg kg −1 Pb showed significantly higher C:N ratio compared with other treatments. No significant difference in C:N ratio for all Cd treated soils was seen from start to 28 DAA, however from 42 to 56 DAA, 100 mg kg −1 Pb showed significantly higher C:N ratio compared with other treatments. On 56 DAA, substrate utilization pattern of soil microbial communities was determined by inoculating Biolog ECO plates. The results indicated that Pb and Cd addition inhibited the functional activity of soil microbial communities as indicated by the intensity of average well color development (AWCD) during 168 h of incubation. Multivariate analysis of sole carbon source utilization pattern demonstrated that higher levels of heavy metal application had significantly affected soil microbial community structure.

Heterotrophic Community‐Level Physiological Profiles of Domestic Wastewater Following Treatment by Small Constructed Subsurface Flow Wetlands

Seasonal treatment performance of small-surface flow wetlands was evaluated during their second operational year and compared with community-level physiological profiles (CLPP) of the heterotrophic bacterial community obtained from sole-carbon source utilization patterns in BIOLOG GN (Haywood, California) microplates. The CLPP patterns varied significantly by season, indicating reduced functional diversity in the heterotrophic community during warmer months of active plant growth (April through October). Principal component analysis (PCA) suggested that the functional community differed in planted versus unplanted wetlands during the growing season. Wetlands generally improved wastewater quality; however, treatment performance was reduced in the second year. Despite differences in the heterotrophic community suggested by CLPP, treatment efficiency with respect to removal of five-day biochemical oxygen demand or reduction in fecal indicator organisms generally was not significantly changed as a function of growing season or plant treatment.

Substrate utilization pattern, biomass and activity of microbial communities in a sequence of heavy metal-polluted paddy soils

The microbial biomass, activity and substrate utilization pattern of seven Chinese paddy soils with different heavy metal concentrations in the vicinity of a Cu–Zn smelter was investigated. Microbial biomass and basal respiration were negatively affected by the elevated metal levels. Two important biological parameters, namely, the microbial biomass-C (C mic)/organic C (C org) ratio and metabolic quotient were closely correlated to heavy metal stress. There was a significant decrease in the C mic/C org ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and there was a threshold metal concentration for substrate utilization pattern. However, the average well colour development (AWCD) of the carbon sources in Biolog plates did not vary in a consistent manner with the microbial biomass or heavy metal concentration.

Attached and unattached microbial communities in a simulated basalt aquifer under fracture- and porous-flow conditions.

Bench scale column studies were used to examine the partitioning of microorganisms between groundwater and a geologic medium and to examine the effect of hydrogeology (i.e., porous- versus fracture-flow) on organism partitioning. Replicated columns were constructed with intact basalt core segments that contained natural fractures and with the same basalt crushed into particles. The columns were perfused with groundwater, and upon reaching a steady state, the columns were sacrificed and the attached and unattached communities were analyzed by multiple approaches. The analyses included the total number of cells, the phylogenetic affiliation of the cells (i.e., the alpha, beta, and gamma subclasses of the class Proteobacteria and gram positives with high G+C DNA content) by fluorescent in situ hybridization (FISH), number and taxonomic affiliation by fatty acid methyl ester profiles of culturable heterotrophs, most-probable-number estimates of methanotrophs and phenol oxidizers, and whole-community sole carbon source utilization patterns from Biolog GN microplates. In the packed columns, about 99% of the total biomass (per cubic centimeter of porous medium) was attached to the geologic medium. Lack of equitable units precluded a comparison of attached and unattached biomasses in the fractured columns where the attached biomass was expressed per unit of surface area. Compositional differences in the attached and unattached communities were evidenced by (i) the recovery of Pseudomonas stutzeri, an Enterococcus sp., and Bacillus psychrophilus from the groundwater and not from the basalt, (ii) differences between community carbon source utilization patterns, and (iii) the relative abundances of different phylogenetic groups estimated by FISH in both column types. In the packed columns, attached communities were depleted of members of the alpha- and beta-Proteobacteria subclasses in comparison to those in the corresponding groundwater. In the fractured columns, attached communities were enriched in gram-positive Bacteria and gamma-Proteobacteria and depleted of beta-Proteobacteria, in comparison to those in the corresponding groundwater. Segregation of populations and their activities, possibly modified by attachment to geologic media, may influence contaminant fate and transport in the subsurface and impact other in situ applications.

A comparison of sole carbon source utilization patterns and phospholipid fatty acid profiles to detect changes in the root microflora of hydroponically grown crops

A comparison of sole carbon source utilization patterns and phospholipid fatty acid profiles to detect changes in the root microflora of hydroponically grown crops

Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use.

The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone.

Functional diversity and community structure of microorganisms in uncontaminated and creosote-contaminated soils as determined by sole-carbon-source-utilization

Functional diversities of microorganisms from uncontaminated and creosote-contaminated soils were assessed using sole-carbon source-utilization patterns. The microorganisms were extracted from soil samples and inoculated into Gram-negative Biolog plates incubated at 23°C. Measurement of Shannon diversity, richness, and evenness indices, principal component analysis (PCA), and colour development rank (CDR) plots were based upon substrate utilization. Calculations incorporated data from both the 95 regular Gram-negative Biolog microplate wells and a selection of 23 carbon substrates that are included on Biolog Ecoplates. There did not appear to be significant differences in Shannon diversity and richness indices, PCA, or CDR plots between aminated and creosote-contaminated soils. Significant differences in Shannon diversity and evenness indices that were apparent with the use of the 23 ecologically relevant microplate wells were mostly absent based on calculations that incorporated the regular 95 Gram-negative Biolog microplate wells. Resolution of microbial communities by PCA, however, appeared to be reduced by the use of the 23 Biolog microplate wells compared to the regular 95 carbon sources.

Trichloroethylene (TCE) and toluene effects on the structure and function of the soil community

The effects of trichloroethylene (TCE) and toluene on indigenous soil communities were examined in soil microcosms, with special emphasis on community structure and function. Soil communities were exposed to TCE (1, 30 and 60 μg ml −1) plus toluene (20 μg ml −1), TCE only (1, 30 and 60 μg ml −1), and toluene only (20, 60, 100 and 200 μg ml −1) (all concentrations given as μg ml −1 soil solution after taking into account sorption and volatilization). Soil microbial populations exposed to 30 or 60 μg TCE ml −1 plus 20 μg toluene ml −1, or to toluene concentrations greater than 60 μg toluene ml −1, exhibited different sole carbon source utilization patterns than control soils, as revealed by Biolog Gram negative (GN) plates. These differences remained even 30 days after all the TCE and toluene had been removed from the system. Exposure to TCE alone did not alter Biolog patterns to the same degree as TCE combined with toluene. Thirty and 60 μg TCE ml −1, either in the presence or absence of 20 μg toluene ml −1, slightly reduced basal respiration after 28 days of incubation, whereas substrate induced respiration was not affected. Total culturable heterotrophs were not sensitive to TCE and toluene, and were only slightly reduced after exposure to 200 μg ml −1 toluene for 45 days. Most protozoa were insensitive to TCE and toluene, but TCE was toxic to flagellates. Significant decreases in numbers of nematode types occurred after exposure to 30 or 60 μg TCE ml −1. The nematode maturity index (MI), an index of diversity based on trophic groupings, was not sensitive to TCE or to TCE combined with toluene in an agricultural soil, whereas the MI in a riparian soil was reduced by concentrations of 30 μg TCE ml −1. These results indicate that TCE and toluene adversely affect the biota of the soil ecosystem, sometimes for prolonged periods.