Kristjan Oopkaup

Dynamics of antibiotic resistance genes and their relationships with system treatment efficiency in a horizontal subsurface flow constructed wetland

Municipal wastewater treatment is one of the pathways by which antibiotic resistance genes from anthropogenic sources are introduced into natural ecosystems. This study examined the abundance and proportion dynamics of seven antibiotic resistance genes in the wetland media biofilm and in the influent and effluent of parallel horizontal subsurface flow mesocosm cells of a newly established hybrid constructed wetland treating municipal wastewater. The targeted genes (tetA, tetB, tetM, ermB, sul1, ampC, and qnrS) encode resistance to major antibiotic classes such as tetracyclines, macrolides, sulfonamides, penicillins, and fluoroquinolones, respectively. All targeted antibiotic resistance genes were detectable in the tested mesocosm environments, with the tetA, sul1, and qnrS genes being the most abundant in the mesocosm effluents. After initial fluctuation in the microbial community, target gene abundances and proportions stabilized in the wetland media biofilm. The abundance of 16S rRNA and antibiotic resistance genes, and the proportion of antibiotic resistance genes in the microbial community, were reduced during the wastewater treatment by the constructed wetland. The concentration of antibiotic resistance genes in the system effluent was similar to conventional wastewater treatment facilities; however, the mesocosms reduced sulfonamide resistance encoding sul1 concentrations more effectively than some traditional wastewater treatment options. The concentrations of antibiotic resistance genes in the wetland media biofilm and in effluent were affected by system operation parameters, especially time and temperature. The results also revealed a relationship between antibiotic resistance genes abundance and the removal efficiencies of NO2-N, NH4-N, and organic matter. Correlation analysis between the abundance of individual antibiotic resistance genes in the mesocosms influent, effluent and wetland media biofilm indicated that depending on antibiotic resistance gene type the microbes carrying these genes interact differently with microbial communities already present on the wetland media.

Complementary seminovaginal microbiome in couples

The genital tract microbiome is tightly associated with reproductive health. Although many research studies have been performed on the vaginal microbiome, current knowledge of the male microbiome is scarce, and parallel studies examining couples are extremely rare. In this work, we aimed to compare seminal and vaginal microbiomes in couples and to assess the influence of sexual intercourse on vaginal microbiome. The study included 23 couples. Microbiomes of semen and vaginal fluid (pre- and post-intercourse) were profiled using Illumina HiSeq2000 sequencing of the V6 region of 16S rRNA gene. Seminal communities were significantly more diverse, but with lower total bacterial concentrations than those of the vagina. Gardnerella vaginalis was predominant in half of the women whose partners had significant leukocytospermia, but only in one of 17 women who had a partner without leukocytospermia. There was significant decrease in the relative abundance of Lactobacillus crispatus after intercourse, and high concordance between semen and vaginal samples. Our data support the hypothesis that semen and vaginal microbiomes are in association, inasmuch as the predominance of G. vaginalis in female partners was significantly related to inflammation in male genital tracts.

Highly diverse microbiota in dental root canals in cases of apical periodontitis (data of illumina sequencing).

INTRODUCTION Chronic apical periodontitis (CAP) is a frequent condition that has a considerable effect on a patients quality of life. We aimed to reveal root canal microbial communities in antibiotic-naive patients by applying Illumina sequencing (Illumina Inc, San Diego, CA). METHODS Samples were collected under strict aseptic conditions from 12 teeth (5 with primary CAP, 3 with secondary CAP, and 4 with a periapical abscess [PA]) and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products. RESULTS Root canal specimens displayed highly polymicrobial communities in all 3 patient groups. One sample contained 5-8 (mean = 6.5) phyla of bacteria. The most numerous were Firmicutes and Bacteroidetes, but Actinobacteria, Fusobacteria, Proteobacteria, Spirochaetes, Tenericutes, and Synergistetes were also present in most of the patients. One sample contained 30-70 different operational taxonomic units; the mean (± standard deviation) was lower in the primary CAP group (36 ± 4) than in the PA (45 ± 4) and secondary CAP (43 ± 13) groups (P < .05). The communities were individually different, but anaerobic bacteria predominated as the rule. Enterococcus faecalis was found only in patients with secondary CAP. One PA sample displayed a significantly high proportion (47%) of Proteobacteria, mainly at the expense of Janthinobacterium lividum. CONCLUSIONS This study provided an in-depth characterization of the microbiota of periapical tissues, revealing highly polymicrobial communities and minor differences between the study groups. A full understanding of the etiology of periodontal disease will only be possible through further in-depth systems-level analyses of the host-microbiome interaction.

Characterization of the bacterioplankton community and its antibiotic resistance genes in the Baltic Sea.

The residues from human environments often contain antibiotics and antibiotic resistance genes (ARGs) that can contaminate natural environments; the clearest consequence of that is the selection of antibiotic‐resistant bacteria. The Baltic Sea is the second largest isolated brackish water reservoir on Earth, serving as a drainage area for people in 14 countries, which differ from one another in antibiotic use and sewage treatment policies. The aim of this study was to characterize the bacterioplankton structure and quantify ARGs (tetA, tetB, tetM, ermB, sul1, blaSHV, and ampC) within the bacterioplankton community of the Baltic Sea. Quantitative polymerase chain reaction was applied to quantify ARGs from four different sampling sites of the Baltic Sea over 2 years, and the bacterial communities were profiled sequencing the V6 region of the 16S rRNA gene on Illumina HiSeq2000. The results revealed that all the resistance genes targeted in the study were detectable from the Baltic Sea bacterioplankton. The percentage of tetA, tetB, tetM, ermB, and sul1 genes in the sea bacterial community varied between 0.0077% and 0.1089%, 0.0003% and 0.0019%, 0.0001% and 0.0105%, 0% and 0.0136%, and 0.0001% and 0.0438%, respectively. The most numerous ARG detected was the tetA gene and this gene also had the highest proportion in the whole microbial community. A strong association between bacterioplankton ARGs’ abundance data and community phylogenetic composition was found, implying that the abundance of most of the studied ARGs in the Baltic Sea is determined by fluctuations in its bacterial community structure.

Biotransformation of pink water TNT on the surface of a low-cost adsorbent pine bark

This two-week anaerobic batch study evaluated 2,4,6-trinitrotoluene (TNT) removal efficiency from industrial pink water by (1) adsorption on low-cost adsorbent pine bark, and (2) adsorption coupled with TNT biotransformation by specialised microbial communities. Samples of the supernatant and acetonitrile extracts of pine bark were analysed by HPLC, while the composition of the bacterial community of the experimental batches, inocula and pine bark were profiled by high-throughput sequencing the V6 region of the bacterial 16S rRNA gene. Integrated adsorption and biotransformation proved to be the most efficient method for TNT removal from pink water. The type of applied inoculum had a profound effect on TNT removal efficiencies and microbial community structures, which were dominated by phylotypes belonging to the Enterobacteriaceae family. The analysis of acetonitrile extracts of pine bark supported the hypothesis that the microbial community indigenous to pine bark has the ability to degrade TNT.

Seminal microbiome in men with and without prostatitis.

To profile the seminal microbiome applying next generation sequencing.

Effect of pine bark on the biotransformation of trinitrotoluene and on the bacterial community structure in a batch experiment

Pine bark, a low-cost industrial residue, has been suggested as a promising substitute for granular activated carbon in the on-site treatment of water contaminated with 2,4,6-trinitrotoluene (TNT). However, the complex organic structure and indigenous microbial community of pine bark have thus far not been thoroughly described in the context of TNT-contaminated water treatment. This two-week batch study examined the removal efficiency of TNT from water by (1) adsorption on pine bark and (2) simultaneous adsorption on pine bark and biotransformation by specialized TNT-biotransforming microbial inocula. The bacterial community composition of experimental batches, inocula and pine bark, was profiled by Illumina sequencing of the V6 region of the 16S rRNA gene. The results revealed that the inocula and experimental batches were dominated by phylotypes belonging to the Enterobacteriaceae family and that the tested inocula had good potential for TNT biotransformation. The type of applied inocula had the most profound effect on the TNT-transforming bacterial community structure in the experimental batches. The indigenous microbial community of pine bark harboured phylotypes that also have a potential to degrade TNT. Altogether, the combination of a specialized inoculum and pine bark proved to be the most efficient treatment option for TNT-contaminated water.

Biochar enhances plant growth and nutrient removal in horizontal subsurface flow constructed wetlands

Biochar has shown great potential as an amendment to improve soil quality and promote plant growth, as well as to adsorb pollutants from water. However, information about the effect of biochar on the wastewater treatment efficiency in horizontal subsurface flow (HSSF) constructed wetlands (CWs) is still scarce. In this study, we assessed the effect of biochar amendment on the purification efficiency of pretreated municipal wastewater in planted (Typha latifolia) experimental horizontal subsurface flow filters filled with lightweight expanded clay aggregates (LECA). The addition of wood-derived biochar (10% v/v) to LECA significantly increased plant biomass production and enhanced the wastewater treatment efficiency of the planted filters. Both the aboveground plant biomass and belowground plant biomass were higher (1.9- and 1.5-fold, respectively) in the filters of the LBP (LECA + biochar + plants) treatments compared to the LP (LECA + plants) filters. The water pH was significantly lower in the planted filters (LBP < LP < LB-LECA + biochar). The efficiencies of TN and TP removal from wastewater were highest in the LBP filters (20.0% and 22.5%, respectively), followed by the LP (13.7% and 16.2%, respectively) and LB (9.5% and 15.6%, respectively) filters. More N and P were incorporated into the plant biomass from wastewater in the presence of biochar in the filter medium. The study results confirm that biochar can be an advantageous supplement for planted HSSF CWs to enhance the treatment efficiency of these systems.

Reduction of antibiotic resistome and integron-integrase genes in laboratory-scale photobioreactors treating municipal wastewater

Wastewater treatment systems receiving municipal wastewater are major dissemination nodes of antibiotic resistance genes (ARGs) between anthropogenic and natural environments. This study examined the fate of antibiotic resistome and class 1-3 integron-integrase genes in photobioreactors that were treating municipal wastewater diluted (70/30) with lake or tap water for the algal biomass production. A combined approach of metagenomic and quantitative (qPCR) analysis was undertaken. Municipal wastewater treatment in the photobioreactors led to reduced antibiotic resistome proportion, number of ARG subtypes, and abundances of individual ARGs in the bacterial community. The ARGs and intI1 gene abundances and relative abundances in the discharges of the photobioreactors were either comparable or lower than the respective values in the effluents of conventional wastewater treatment plants. The reduction of the resistome proved to be strongly related to the changes in the bacterial community composition during the wastewater treatment process as it was responding to rising pH levels caused by intense algal growth. Several bacterial genera (e.g., Azoarcus, Dechloromonas, and Sulfuritalea) were recognized as potential hosts of multiple antibiotic resistance types. Although the lake water contributed a diverse and abundant resistome and intI genes profile to the treatment system, it proved to be considerably more beneficial for wastewater dilution than the tap water. The diversity (number of detected resistance types and subtypes) and proportion of the antibiotic resistome, the amount of plasmid borne integron-integrase gene reads, and the abundances and relative abundances of the majority of quantified ARGs (aadA, sul1, tetQ, tetW, qnrS, ermB, blaOXA2-type) and intI1 gene as well as the amount of multi-resistance determinants were significantly lower in the discharges of photobioreactors where lake water was used to dilute wastewater.

Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils

Tropical peatlands, which play a crucial role in the maintenance of different ecosystem services, are increasingly drained for agriculture, forestry, peat extraction and human settlement purposes. The present study investigated the differences between natural and drained sites of a tropical peatland in the community structure of soil bacteria and archaea and their potential to perform nitrogen transformation processes. The results indicate significant dissimilarities in the structure of soil bacterial and archaeal communities as well as nirK, nirS, nosZ, nifH and archaeal amoA gene-possessing microbial communities. The reduced denitrification and N2-fixing potential was detected in the drained tropical peatland soil. In undisturbed peatland soil, the N2O emission was primarily related to nirS-type denitrifiers and dissimilatory nitrate reduction to ammonium, while the conversion of N2O to N2 was controlled by microbes possessing nosZ clade I genes. The denitrifying microbial community of the drained site differed significantly from the natural site community. The main reducers of N2O were microbes harbouring nosZ clade II genes in the drained site. Additionally, the importance of DNRA process as one of the controlling mechanisms of N2O fluxes in the natural peatlands of the tropics revealed from the results of the study.