Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

Muller, Emilie; Pinel, Nicolás; Gillece, John D.; Schupp, James M.; Price, Lance B.; Engelthaler, David M.; Levantesi, Caterina; Tandoi, Valter; Luong, Khai; Baliga, Nitin S.; Korlach, Jonas; Keim, Paul; Wilmes, Paul

doi:10.1128/jb.01765-12

Cited by 27 publications

(28 citation statements)

References 17 publications

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“…Preliminary details from the annotation of the M. parvicella str. Bio17-1 genome suggest the absence of a nitrite reductase (Muller et al, 2012). However, a BLAST search of this genome with the putative gene from RN1 identified a CDS with 99.9% nucleotide sequence identity.…”

Section: Nitrogen Metabolismmentioning

confidence: 99%

“…Thus, although the discussions focus on the RN1 genome, its features and subsequent proposed metabolic model could be considered relevant generally to M. parvicella. During the review process of this manuscript, a draft genome sequence of the M. parvicella strain Bio17-1 was published (Muller et al, 2012). Genome sequence comparison of the RN1 and Bio17-1 was made using the JSpecies software (Richter and Rosselló-Móra, 2009), giving a calculated average nucleotide identity of 99% over the 89% of the genomes aligned by the programme.…”

Section: Comparison Of Central Pathways In M Parvicellamentioning

confidence: 99%

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Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses

et al. 2013

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'Candidatus Microthrix parvicella' is a lipid-accumulating, filamentous bacterium so far found only in activated sludge wastewater treatment plants, where it is a common causative agent of sludge separation problems. Despite attracting considerable interest, its detailed physiology is still unclear. In this study, the genome of the RN1 strain was sequenced and annotated, which facilitated the construction of a theoretical metabolic model based on available in situ and axenic experimental data. This model proposes that under anaerobic conditions, this organism accumulates preferentially long-chain fatty acids as triacylglycerols. Utilisation of trehalose and/or polyphosphate stores or partial oxidation of long-chain fatty acids may supply the energy required for anaerobic lipid uptake and storage. Comparing the genome sequence of this isolate with metagenomes from two full-scale wastewater treatment plants with enhanced biological phosphorus removal reveals high similarity, with few metabolic differences between the axenic and the dominant community 'Ca. M. parvicella' strains. Hence, the metabolic model presented in this paper could be considered generally applicable to strains in full-scale treatment systems. The genomic information obtained here will provide the basis for future research into in situ gene expression and regulation. Such information will give substantial insight into the ecophysiology of this unusual and biotechnologically important filamentous bacterium.

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Section: Nitrogen Metabolismmentioning

confidence: 99%

Section: Comparison Of Central Pathways In M Parvicellamentioning

confidence: 99%

Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses

et al. 2013

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“…The Long chain fatty acid (LCFA) content in wastewater influents is a significant influencing factor promoting the growth of Candidatus M. parvicella (Dunkel et al, 2015). This organism is responsible for bulking (Martins et al, 2004;Muller et al, 2012) and might be the most frequent in bulking situations (Rossetti et al, 2005;Guo et al, 2013;Santos et al, 2015). Surprisingly, Candidatus M. parvicella was considerably abundant in the non-bulking AS (3.20%), and a previous study showed that >3% Candidatus M. parvicella in AS could cause foaming problems in WWTPs (Kaetzke et al, 2005).…”

Section: Biological and Environmental Factors Causing Sludge Bulkingmentioning

confidence: 99%

Detailed comparison of bacterial communities during seasonal sludge bulking in a municipal wastewater treatment plant

Wang

et al. 2016

Water Research

101

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a b s t r a c tIn this study, pyrosequencing combined with clone library analysis, qPCR, and fluorescent in situ hybridization (FISH) were performed to identify detailed changes of bacterial and filamentous bacterial communities in activated sludge (AS) in 3 types of typical AS samples: sludge bulking (B-AS), excessive bulking (EB-AS), and non-bulking (N-AS). Sludge bulking resulted in a decrease in total bacterial numbers from (6.4 ± 0.18) Â 10 8 gene copies/mL in N-AS to (2.4 ± 0.22) Â 10 8 in EB-AS and a decrease in bacterial diversity from 2757 OTUs in N-AS to 2217 OTUs in EB-AS. With the occurrence of sludge bulking, Actinobacteria and Firmicutes increased sharply, whereas Proteobacteria, which was the predominant phylum in N-AS, decreased markedly. In addition, Nitrospirae, a major lineage of the nitrite-oxidizing bacteria, had quite a low abundance in EB-AS (0.15%), while it was relatively high in N-AS (1.17%). On the other hand, filamentous bacteria accounted for 28.77% and 5.72% of total sequences in EB-AS and N-AS, respectively. More interestingly, 11 types of filamentous bacteria were always present in 3 types of typical AS samples from different stages of sludge bulking, and most of them enriched in EB-AS compared to N-AS. It is noteworthy that, in addition to the frequently reported filamentous bacteria such as Candidatus M. parvicella and Tetrasphaera, novel filamentous species of Trichococcus might exist in this bulking WWTP. Our results reveal that sludge bulking are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the bulking phenomenon in AS.

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“…Therefore, the use of functional genes for multiplex PCR seems to be much easier. Recently, a genome announcement of M. parvicella has been published (Muller et al, 2012). Although the sequence assembly is not complete yet, some functional gene sequence will be soon available and the subsequent development of other quantification tools will be possible.…”

Section: Comparison Between Taqman Sybr Green and Microscopymentioning

confidence: 99%

Development and evaluation of a TaqMan duplex real-time PCR quantification method for reliable enumeration of Candidatus Microthrix

Vanysacker

Denis

Roels

et al. 2014

Journal of Microbiological Methods

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Candidatus Microtrhix parvicella is one of the most common filamentous bacteria reported to be involved in bulking and foaming problems in activated sludge plants worldwide. In order to detect and quantify both M. parvicella and Microthrix calida by quantitative PCR (qPCR), primers targeting 16S rDNA genes were designed. The qPCR reaction was optimized by using the TaqMan technology and an internal positive control was included to ensure the absence of PCR inhibitors. A total of 29 samples originating from different wastewater treatment plants were analyzed and the results were compared by using conventional microscopy, fluorescent in situ hybridization and an existing SYBR Green-based assay. Our assay showed a 100% specificity for both M. parvicella and M. calida, a sensitivity of 2.93 × 10 9 to 29 copy numbers/reaction, an amplification efficiency of 93% and no PCR inhibition. By performing a spiking experiment including different Microthrix concentrations, recovery rates ranging from 65 to 98% were obtained. A positive correlation with the SYBR Green assay (R 2 = 0.85) was found and most of the samples were in accordance with the microscopical observation. In comparison with SYBR Green assay, the probe-based TaqMan assay had a much lower detection limit. Compared with microscopy, some samples had a lower or higher enumeration when using qPCR. In conclusion, a qPCR method is forwarded here that could be useful as an early warning tool for fast and reliable detection of Microthrix in for instance sludge bulking events.

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Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

Cited by 27 publications

References 17 publications

Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses

Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses

Detailed comparison of bacterial communities during seasonal sludge bulking in a municipal wastewater treatment plant

Development and evaluation of a TaqMan duplex real-time PCR quantification method for reliable enumeration of Candidatus Microthrix

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