Detection of the unknown components of the oral microflora of teeth with periapical radiolucencies in a Turkish population using next-generation sequencing techniques.

AIM: To detect the unknown components of the oral microbiome and the effects of root canal treatment in a Turkish population and to evaluate the changes in microbial diversity in the root canals before and after treatment. METHODOLOGY: Single-rooted central and lateral maxillary incisors with one canal were chosen from 20 patients. Baseline samples of intact intracanal microbiota were collected from 20 root canals of permanent teeth with necrotic pulps using sterile paper points. After root canal preparation, the root canals were filled with a calcium hydroxide paste for 7 days. Calcium hydroxide was removed from root canal with 2.5% sodium hypochlorite and 17% EDTA using passive ultrasonic irrigation (PUI). A second bacteriologic samples were taken with sterile paper points prior to root filling. The samples were processes with DNase-I treatment using next-generation sequencing (NGS). Reduction in bacterial numbers during root canal treatment was evaluated using real-time quantitative PCR (qPCR). All statistical analyses were conducted using the MINITAB 17 software (Minitab Ltd. Co., Coventry, UK). A one-sample t-test was used to analyse the data. Statistical significance was accepted at P < 0.05. RESULTS: Relative abundances of Mycoplasma sp., Paludibacter sp., Tannerella sp., Prevotella spp. and an uncultured species from the order Bacteroidales decreased with root canal preparation and medication (98.7%, 99.8%, 98.8%, 97.7% and 99.3%, respectively), whilst the relative abundances of Methylobacterium sp., Corynebacterium sp. and Streptococcus infantis increased (93.1%, 94.8% and 99.4%, respectively). Considerable numbers of Streptophyta species were detected before and after treatment. The ratio of Agrobacterium sp. in the treated teeth community and the ratio of order Streptophyta in the infected canals had negative correlations with the success of bacterial elimination. CONCLUSIONS: The combination of NGS and qPCR techniques resulted in detection of previously unknown components of the oral microbiome and the effects of root canal treatment on their relative abundance in a Turkish population.

Effects of temperature - heavy metal interactions, antioxidant enzyme activity and gene expression in wheat (Triticum aestivum L.) seedlings.

In this study, the effect of heat and chromium (Cr) heavy metal interactions on wheat seedlings (Triticum aestivum L. cv. Ç-1252 and Gun91) was investigated by measuring total chlorophyll and carotenoid levels, catalase (CAT) and ascorbate peroxidase (APX) antioxidant enzyme activities, and MYB73, ERF1 and TaSRG gene expression. Examination of pigment levels demonstrated a decrease in total chlorophyll in both species of wheat under combined heat and heavy metal stress, while the carotenoid levels showed a slight increase. APX activity increased in both species in response to heavy metal stress, but the increase in APX activity in the Gun91 seedlings was higher than that in the Ç-1252 seedlings. CAT activity increased in Gun91 seedlings but decreased in Ç-1252 seedlings. These results showed that Gun91 seedling had higher resistance to Cr and Cr + heat stresses than the Ç-1252 seedling. The quantitative molecular analyses implied that the higher resistance was related to the overexpression of TaMYB73, TaERF1 and TaSRG transcription factors. The increase in the expression levels of these transcription factors was profound under combined Cr and heat stress. This study suggests that TaMYB73, TaERF1 and TaSRG transcription factors regulate Cr and heat stress responsive genes in wheat.

Spatial and temporal changes in microbial diversity of the Marmara Sea sediments.

Spatial (10 different locations) and temporal (2 years) changes in characteristics of the Marmara Sea Sediments were monitored to determine interactions between the chemical and microbial diversity. The sediments were rich in terms of hydrocarbon, nitrate, Ni and microbial cell content. Denitrifying, sulfate reducing, fermentative and methanogenic organisms were co-abundant in 15 cm below the sea floor. The local variations in the sediments' characteristics were more distinctive than the temporal ones. The sulfate and nitrate contents were the main drivers of the changes in the microbial community compositions. N and P were limited for microbial growth in the sediments, and their levels determined the total cell abundance and activity. Seasonal shifts in temperatures of the shallow sediments were also reflected in the active cell abundances. It was concluded that the Marmara Sea is a promising ecosystem for the further investigation of the ecologically important microbial processes.

Methanogenic and sulphate reducing bacterial population levels in a full-scale anaerobic reactor treating pulp and paper industry wastewater using fluorescence in situ hybridisation.

In this study, specific methanogenic activity (SMA) test and fluorescence in situ hybridisation (FISH) were respectively used to determine acetoclastic methanogenic capacity, and composition and number of methanogenic and sulphate reducing bacterial (SRB) populations within a full scale anaerobic contact reactor treating a pulp and paper industry effluent. The sludge samples were collected from three different heights along the anaerobic reactor having a difficulty of completely stirring. Performance of the anaerobic reactor in terms of COD removal efficiency varied between 47 and 55% at organic loading rates in a range of 1.6-1.8 kg COD m(-3) d(-1) and methane yield varied between 0.18 and 0.20 m3CH4kg CODrem(-1). The anaerobic reactor was not operated for 2 weeks during the monitoring period. According to SMA test results, potential methane production rate was 276 mLCH4 gVSS(-1) d(-1) before the off period of the reactor, however it decreased to 159 mL CH4 gVSS(-1) d(-1) after this period. SMA test and FISH results along the reactor height showed that the acetoclastic methanogenic activity of the sludge samples, the relative abundance of acetoclastic methanogens, hydrogenotrophic methanogens and acetate oxidising SRB decreased as the reactor height increased, however the relative abundance of non-acetate oxidising SRB increased.

Methanogenic community change in a full-scale UASB reactor operated at a low F/M ratio.

A full-scale upflow anaerobic sludge blanket (UASB) reactor was investigated in terms of archaeal composition, acetoclastic methanogenic capacity and performance over a 2-year period. Performance of the reactor in terms of COD removal efficiency varied between 60% and 80% at organic loading rates (OLRs) in the range of 2.5-12 kg COD m-3 d-1. The reactor had been operated under a F/M (food to microorganisms) ratio of 0.02-0.03 gCOD gTVS-1 d-1, which is much lower than the typical values reported for similar reactors. According to specific methanogenic activity (SMA) tests the anaerobic sludge was operating at only 12-34% of its potential acetoclastic methanogenic capacity. These results demonstrated that the UASB reactor was under loaded compared to its maximum loading capacity. All other operational parameters had been maintained within their desired ranges. The SMA test and Fluorescence in situ hybridization (FISH) results revealed that a decrease in the acetoclastic methanogenic activity of the UASB sludge from 344 mL CH4 gTVS-1 d-1 to 109 mL CH4 gTVS-1 d-1 coincided with a decrease in the relative abundance of acetoclastic Methanosaeta from 90%+/-1.2 to 79%+/-1.4 of the archaeal population, and an increase in the relative abundance of hydrogenotrophic Methanobacteriales from non-detectable levels to 24%+/-0.7% of the archaeal population during the 2-year operation of the reactor. The relative abundance of archaeal cells within the UASB sludge was in the range of 15-17%.