scholarly journals Reduction of Arcobacter at Two Conventional Wastewater Treatment Plants in Southern Arizona, USA

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 175 ◽  
Author(s):  
Ghaju Shrestha ◽  
Sherchan ◽  
Kitajima ◽  
Tanaka ◽  
Gerba ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
Pathogenic Bacteria ◽  
Wastewater Treatment Plants ◽  
The United States ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Wwtp Effluent

This study aimed to identify the bacterial community in two wastewater treatment plants (WWTPs) and to determine the occurrence and reduction of Arcobacter, along with virulence genes (ciaB and pldA). A total of 48 samples (24 influent and 24 effluent) were collected at two WWTPs in southern Arizona in the United States, monthly from August 2011 to July 2012. Bacterial DNA extract was utilized for 16S rRNA metagenomic sequencing. Quantification of Arcobacter 16S rRNA gene was conducted using a recently developed SYBR Green-based quantitative PCR assay. Among 847 genera identified, 113 (13%) were identified as potentially pathogenic bacteria. Arcobacter 16S rRNA gene was detected in all influent samples and ten (83%) and nine (75%) effluent samples at each plant, respectively. Log reduction ratios of Arcobacter 16S rRNA gene in Plant A and Plant B were 1.7 ± 0.9 (n = 10) and 2.3 ± 1.5 (n = 9), respectively. The ciaB gene was detected by quantitative PCR in eleven (92%) and twelve (100%) of 12 influent samples from Plant A and Plant B, respectively, while the pldA gene was detected in eight (67%) and six (50%) influent samples from Plant A and Plant B, respectively. The prevalence of potentially pathogenic bacteria in WWTP effluent indicated the need for disinfection before discharge into the environment.

Detection of filamentous genus Gordonia in foam samples using genus-specific primers combined with PCR – denaturing gradient gel electrophoresis analysis

2007 ◽  
Vol 53 (6) ◽  
pp. 768-774 ◽  
Author(s):  
Fo-Ting Shen ◽  
Hsuan-Ru Huang ◽  
A.B. Arun ◽  
Hui-Ling Lu ◽  
Ta-Chen Lin ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Nested Pcr ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wastewater Treatment Plants ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Gradient Gel Electrophoresis

A nested-PCR amplification combined with denaturing gradient gel electrophoresis (PCR–DGGE) approach was used to detect and identify Gordonia populations from wastewater treatment plant foam samples. The PCR-amplified region (position 722–1119) by specifically designed primers G699F and G1096R covered the hypervariable region of the Gordonia 16S rRNA gene sequence. This approach successfully distinguished Gordonia species to the interspecies level. The differential ability of PCR–DGGE analysis was effectively used to separate 12 Gordonia species belonging to different 16S rRNA gene-based phylogenetic lineages into 8 groups. Based on this method, the minimum limit of Gordonia detection was 5 × 104CFU·g–1in the seeded soil samples. The PCR–DGGE bands obtained were excised and identified by sequence analysis. Gordonia polyisoprenivorans , Gordonia amicalis , DGGE type II Gordonia species, and an uncertain Gordonia species dominated the activated sludge foam samples. Results of this study indicate that the detection and analyses of genus Gordonia within a complex microbial community could be accomplished using the PCR–DGGE approach to a larger extent, with certain limitations. Detection of diverse Gordonia populations in foam samples from wastewater treatment plants revealed the significant role of Gordonia in biological foaming during wastewater treatment. The nested-PCR amplification and DGGE can be used as a diagnostic tool for the early detection of foaming incidents in wastewater treatment plants using Gordonia as indicator organism.

16S rRNA gene-based primer pair showed high specificity and quantification accuracy in detecting freshwater Brocadiales anammox bacteria

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Chang Ding ◽  
Lorenz Adrian ◽  
Yongzhen Peng ◽  
Jianzhong He
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wastewater Treatment Plants ◽  
High Specificity ◽  
Amplicon Sequencing ◽  
Anammox Bacteria ◽  
Rrna Gene ◽  
Detection And Quantification

ABSTRACT Anaerobic ammonium oxidizing (anammox) bacteria are widely distributed and contribute significantly to the global nitrogen cycle. Traditionally, identification and quantification based on the 16S rRNA gene were considered not reliable because of low 16S rRNA gene sequence identity within Brocadiales. Here we hypothesize that by using appropriate primers and methodology, 16S-based detection and quantification of anammox bacteria can be accurate. We modified an existing 16S rRNA gene-based primer pair (Amx694F–Amx960R) by changing one nucleotide (Amx694F position 18, G→C) (Amx694PF–Amx960R) so that they match the sequences of most Brocadiales anammox bacteria, and evaluated the modified primer pair with 29 freshwater samples from microcosms, anammox reactors and wastewater treatment plants of various geographical origins. The primer pair showed high specificity in detection and quantification of anammox populations in samples that contained >0.1% anammox bacteria. Quantification of anammox abundance by quantitative real-time PCR and delineation of anammox species by denaturing gradient gel electrophoresis agreed well with amplicon sequencing results. A clear shift of anammox population towards ‘Candidatus Kuenenia’ was observed under laboratory cultivation conditions. With the help of amplicon sequencing, we demonstrated that 16S rRNA gene-based anammox-specific primers are able to achieve qualitative and quantitative monitoring of anammox communities in wastewater treatment plants and natural freshwater environments.2007;73:5261–7.

scholarly journals Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing

2017 ◽  
Vol 6 (3) ◽  
pp. e00443 ◽  
Author(s):  
Tiago Palladino Delforno ◽  
Gileno Vieira Lacerda Júnior ◽  
Melline F. Noronha ◽  
Isabel K. Sakamoto ◽  
Maria Bernadete A. Varesche ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Full Scale ◽  
Uasb Reactor ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing ◽  
Treatment Integration

scholarly journals MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

2021 ◽  
Author(s):  
Morten Simonsen Dueholm ◽  
Marta Nierychlo ◽  
Kasper Skytte Andersen ◽  
Vibeke Rudkjoebing Joergensen ◽  
Simon Knutsson ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Wastewater Treatment Plants ◽  
Species Level ◽  
Full Length ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

Biological wastewater treatment and an increased focus on resource recovery is fundamental for environmental protection, human health, and sustainable development. Microbial communities are responsible for these processes, but our knowledge of their diversity and function is still poor, partly due to the lack of good reference databases and comprehensive global studies. Here, we sequenced more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and used the sequences to construct MiDAS 4, a full-length amplicon sequence variant resolved 16S rRNA gene reference database with a comprehensive taxonomy from the domain to species-level for all references. Using a study-independent amplicon dataset from the Global Water Microbiome Consortium project (269 WWTPs), we showed that the MiDAS 4 database provides much better coverage for bacteria in WWTPs worldwide compared to commonly applied universal references databases, and greatly improved the rate of genus and species-level classification. Hence, MiDAS 4 provides a unifying taxonomy for the majority of prokaryotic diversity in WWTPs globally, which can be used for linking microbial identities with their functions across studies. Taking advantage of MiDAS 4, we carried out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting the V1-V3 and V4 region of the 16S rRNA gene. We found that the V1-V3 primers were generally best suited for this ecosystem, and revealed how environmental conditions and biogeography shape the activated sludge microbiota. We also identified process-critical taxa (core and conditionally rare or abundant taxa), encompassing 966 genera and 1530 species. These represented approximately 80% and 50% of the accumulated read abundance, respectively, and represent targets for further investigations. Finally, we showed that for well-studied functional guilds, such as nitrifiers or polyphosphate accumulating organisms, the same genera were prevalent worldwide, with only a few abundant species in each genus.

scholarly journals Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Francesco Durazzi ◽  
Claudia Sala ◽  
Gastone Castellani ◽  
Gerardo Manfreda ◽  
Daniel Remondini ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Shotgun Sequencing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Experimental Conditions ◽  
Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

scholarly journals The diversity of active microbial groups in an activated sludge process treating painting process wastewater

2020 ◽  
Vol 148 ◽  
pp. 01002
Author(s):  
Herto Dwi Ariesyady ◽  
Mentari Rizki Mayanda ◽  
Tsukasa Ito
Keyword(s):  
Wastewater Treatment ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Biological Treatment ◽  
Rrna Gene ◽  
Activated Sludge Process ◽  
Painting Process ◽  
Process Wastewater

Activated sludge process is one of the wastewater treatment method that is applied for many wastewater types including painting process wastewater of automotive industry. This wastewater is well-known to have high heavy metals concentration which could deteriorate water environment if appropriate performance of the wastewater treatment could not be achieved. In this study, we monitored microbial community diversity in a Painting Biological Treatment (PBT) system. We applied a combination of cultivation and genotypic biological methods based on 16S rRNA gene sequence analysis to identify the diversity of active microbial community. The results showed that active microbes that could grow in this activated sludge system were dominated by Gram-negative bacteria. Based on 16S rRNA gene sequencing analysis, it was revealed that their microbial diversity has close association with Bacterium strain E286, Isosphaera pallida, Lycinibacillus fusiformis, Microbacterium sp., Orchobactrum sp., Pseudomonas guariconensis, Pseudomonas sp. strain MR84, Pseudomonas sp. MC 54, Serpens sp., Stenotrophomonas acidaminiphila, and Xylella fastidiosa with similarity of 86 – 99%. This findings reflects that microbial community in a Painting Biological Treatment (PBT) system using activated sludge process could adapt with xenobiotics in the wastewater and has a wide range of diversity indicating a complex metabolism mechanism in the treatment process.

scholarly journals Metagenome-validated Parallel Amplicon Sequencing and Text Mining-based Annotations for Simultaneous Profiling of Bacteria and Fungi: Vaginal Microbiome and Mycobiota in Healthy Women

2021 ◽  
Author(s):  
Seppo Virtanen ◽  
Schahzad Saqib ◽  
Tinja Kanerva ◽  
Pekka Nieminen ◽  
Ilkka Kalliala ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Extensive Literature ◽  
Metagenomic Sequencing ◽  
Text Extraction ◽  
Healthy Women ◽  
Bacteria And Fungi

Abstract Background: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial populations. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS-1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing. Results: Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment guided tool provided ecosystem specific annotations that were confirmed by Metagenomic Phylogenetic Analysis (MetaPhlAn). The metagenome analysis revealed distinct functional differences between the bacterial community types while fungi were undetected, despite being identified in all samples based on ITS amplicons. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.Conclusion: Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Text extraction-based annotation tool facilitates the characterization and interpretation of defined microbial communities from rapidly accumulating sequencing and metadata readily available through public databases.

scholarly journals Alone Yet Not Alone: Frankia Lives Under the Same Roof With Other Bacteria in Actinorhizal Nodules

2021 ◽  
Vol 12 ◽  
Author(s):  
Faten Ghodhbane-Gtari ◽  
Timothy D’Angelo ◽  
Abdellatif Gueddou ◽  
Sabrine Ghazouani ◽  
Maher Gtari ◽  
...  
Keyword(s):  
16S Rrna ◽  
Plant Growth ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Actinorhizal Plants ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Metagenomic Sequencing ◽  
Plant Growth Promoting ◽  
Growth Promoting

Actinorhizal plants host mutualistic symbionts of the nitrogen-fixing actinobacterial genus Frankia within nodule structures formed on their roots. Several plant-growth-promoting bacteria have also been isolated from actinorhizal root nodules, but little is known about them. We were interested investigating the in planta microbial community composition of actinorhizal root nodules using culture-independent techniques. To address this knowledge gap, 16S rRNA gene amplicon and shotgun metagenomic sequencing was performed on DNA from the nodules of Casuarina glauca. DNA was extracted from C. glauca nodules collected in three different sampling sites in Tunisia, along a gradient of aridity ranging from humid to arid. Sequencing libraries were prepared using Illumina NextEra technology and the Illumina HiSeq 2500 platform. Genome bins extracted from the metagenome were taxonomically and functionally profiled. Community structure based off preliminary 16S rRNA gene amplicon data was analyzed via the QIIME pipeline. Reconstructed genomes were comprised of members of Frankia, Micromonospora, Bacillus, Paenibacillus, Phyllobacterium, and Afipia. Frankia dominated the nodule community at the humid sampling site, while the absolute and relative prevalence of Frankia decreased at the semi-arid and arid sampling locations. Actinorhizal plants harbor similar non-Frankia plant-growth-promoting-bacteria as legumes and other plants. The data suggests that the prevalence of Frankia in the nodule community is influenced by environmental factors, with being less abundant under more arid environments.

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