Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal

Matsuura, Norihisa; Masakke, Yalkhin; Karthikeyan, Smruthi; Kanazawa, Sui; Honda, Ryo; Yamamoto-Ikemoto, Ryoko; Konstantinidis, Konstantinos T.

doi:10.1007/s00253-021-11113-4

Cited by 28 publications

(5 citation statements)

References 61 publications

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“…The HotStarTaq plus DNA polymerase kit (Qiagen, Hilden, Germany) was used for amplification of 25 μL of the final reaction volume in duplicate. The PCR conditions were as described elsewhere . Then, gel electrophoresis was performed using 1% agarose gel to confirm the length of the PCR products.…”

Section: Materials and Methodsmentioning

confidence: 99%

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Quantitative 16S rRNA Gene Amplicon Sequencing for Comprehensive Pathogenic Bacterial Tracking in a Municipal Wastewater Treatment Plant

et al. 2023

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Quantification of bacterial pathogens in the environment is crucial for determining their potential risk of pathogenicity and infection. Here, we applied quantitative sequencing (qSeq) based on the 16S rRNA gene with spike-in internal standards for comprehensive pathogen quantification in a municipal wastewater treatment plant (WWTP). A novel bacterial pathogen database based on biosafety levels (BSLs) was constructed for rapid pathogen identification. Pathogen taxonomies were obtained from the constructed database using a basic local alignment search tool, and amounts of pathogens were quantified by regression analysis of spike-in internal standards. The total pathogen concentrations were gradually decreased from 6.8 ± 4.9 × 107 copies/mL in the influent to 1.6 ± 1.4 × 105 copies/mL in the effluent. BSL2 pathogens (e.g., Aeromonas spp., Mycobacterium spp., Klebsiella spp., and pathogenic Escherichia spp.) were detected more than 4.0 × 103 copies/mL at the effluent. The genus Arcobacter (BSL1) showed the highest abundance throughout the WWTP (8.8 ± 8.1 × 104 to 2.5 ± 3.5 × 107 copies/mL). BSL2 Mycobacterium spp. noticeably increased at the anaerobic treatment (2.3 × 106 copies/mL) and showed least removal at the effluent. The qSeq analysis with the pathogen database provided a holistic view of the microbial pathogen dynamics and ecology in the WWTP.

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Section: Materials and Methodsmentioning

confidence: 99%

“…The PCR conditions were as described elsewhere. 30 Then, gel electrophoresis was performed using 1% agarose gel to confirm the length of the PCR products. The PCR products were purified using an Agencourt AMPure XP Beads kit (Beckman Coulter, Pasadena, CA).…”

Section: Mixed Sample Preparation For Amplification and Illumina Miseqmentioning

confidence: 99%

Quantitative 16S rRNA Gene Amplicon Sequencing for Comprehensive Pathogenic Bacterial Tracking in a Municipal Wastewater Treatment Plant

et al. 2023

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“…After homogenizing each sample by using a Vortex-Genie 2 (Scientific Industries, USA), total DNA was extracted using the DNeasy PowerSoil Pro kit and automatic DNA extractor QIAcube Connect (Qiagen, Germany), following the manufacturer’s protocol. Amplicon libraries were prepared using a two-step tailed PCR method ( 6 ) with 515F and 806R primers targeting the V4 region of the prokaryotic 16S rRNA gene ( 7 ). Illumina adapter sequences were attached to the 5′ end of the forward and reverse sequencing primers.…”

Section: Announcementmentioning

confidence: 99%

Microbial diversity in shallow-sea sediment from Tsukumo Bay, Japan, determined by 16S rRNA gene amplicon sequencing

Kato,

Sugitani,

Niiyama

et al. 2024

Microbiol Resour Announc

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“…Li et al (2022) showed that sulphur reduction genes are mainly dominated by the cys genes, and also showed the core linking of the network co-occurrence of the C-N-S genes in coal seams. Besides, sulphates and other substances participate in reactions that convert organic substances into acetate (Matsuura et al, 2021). The existence of these desulphurising Methanoculleus sp.…”

Section: Main Metabolic Pathwaymentioning

confidence: 99%

Insights into the ecological roles of assembling genomes for stimulated methanogenic archaea Methanoculleus in coal seams

Liu

2023

J. Natn. Sci. Foundation Sri Lanka

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Biogenic coalbed methane is produced by biological processes mediated by the synergistic interaction of microbial complexes in coal seams. However, the comprehensive ecological role of methanogenic archaea in biogenic coalbed methane production remains poorly understood. Here, we study the metagenome assembled genomes (MAGs) of Methanoculleus from coal seams, which were stimulated by minimal salts plus yeast media in anaerobic conditions. The Methanoculleus genus accounted for the highest proportion of archaea (80.4 ± 2.8%) once the CH4 concentration in the headspace increased to 15.0 ± 2.6% on the 50th day. The Methanoculleus MAGs were closely related to M. thermophiles; even so, 30 genes were detected in MAGs which were lacking in the genomes of M. thermophiles ATCC 33837. A deeper look at the metabolic pathway showed several metabolic pathways, including methanogenesis, glycolysis, urea cycle, TCA cycle and sulphur reduction. The CO2 and acetate were the primary carbon sources of these cells for the methanogenesis pathway. Glycolysis and sulphate reduction processes were the main processes for providing acetate. In addition, the cells had a variety of other functions, including nitrogen fixation and hydrogen production. Overall, this study enabled a better understanding of the ecological roles of Methanoculleus for biogenic methane in coal seams by combining bioinformatic techniques.

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Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal

Cited by 28 publications

References 61 publications

Quantitative 16S rRNA Gene Amplicon Sequencing for Comprehensive Pathogenic Bacterial Tracking in a Municipal Wastewater Treatment Plant

Quantitative 16S rRNA Gene Amplicon Sequencing for Comprehensive Pathogenic Bacterial Tracking in a Municipal Wastewater Treatment Plant

Microbial diversity in shallow-sea sediment from Tsukumo Bay, Japan, determined by 16S rRNA gene amplicon sequencing

Insights into the ecological roles of assembling genomes for stimulated methanogenic archaea Methanoculleus in coal seams

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