scholarly journals Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Baoli Zhu ◽  
Lauren Bradford ◽  
Sichao Huang ◽  
Anna Szalay ◽  
Carmen Leix ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Water Systems ◽  
Rrna Gene ◽  
Molecular Tools ◽  
Content Type ◽  
Microbial Nitrogen ◽  
Wet Weight ◽  
Contaminated Aquifers ◽  
Nitrogen Elimination ◽  
Wastewater Treatment Systems

ABSTRACT It has recently been suggested that oxygenic dismutation of NO into N2 and O2 may occur in the anaerobic methanotrophic “Candidatus Methylomirabilis oxyfera” and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to “Ca. Methylomirabilis oxyfera” and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from “Ca. Methylomirabilis oxyfera” and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 107 to 5.2 × 1010 copies · g−1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. IMPORTANCE NO dismutation into N2 and O2 is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium “Ca. Methylomirabilis oxyfera” and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of nod genes in environmental samples. A surprisingly high diversity and abundance of nod genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future.

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

scholarly journals Bacteria from the Genus Arcobacter Are Abundant in Effluent from Wastewater Treatment Plants

2020 ◽  
Vol 86 (9) ◽  
Author(s):  
Jannie Munk Kristensen ◽  
Marta Nierychlo ◽  
Mads Albertsen ◽  
Per Halkjær Nielsen
Keyword(s):  
Wastewater Treatment ◽  
Pathogenic Bacteria ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Effluent Quality ◽  
Culture Independent ◽  
Influent Wastewater

ABSTRACT Pathogenic bacteria in wastewater are generally considered to be efficiently removed in biological wastewater treatment plants. This understanding is almost solely based on culture-based control measures, and here we show, by applying culture-independent methods, that the removal of species in the genus Arcobacter was less effective than for many other abundant genera in the influent wastewater. Arcobacter was one of the most abundant genera in influent wastewater at 14 municipal wastewater treatment plants and was also abundant in the “clean” effluent from all the plants, reaching up to 30% of all bacteria as analyzed by 16S rRNA gene amplicon sequencing. Metagenomic analyses, culturing, genome sequencing of Arcobacter isolates, and visualization by fluorescent in situ hybridization (FISH) confirmed the presence of the human-pathogenic Arcobacter cryaerophilus and A. butzleri in both influent and effluent. The main reason for the high relative abundance in the effluent was probably that Arcobacter cells, compared to those of other abundant genera in the influent, did not flocculate and attach well to the activated sludge flocs, leaving a relatively large fraction dispersed in the water phase. The study shows there is an urgent need for new standardized culture-independent measurements of pathogens in effluent wastewaters, e.g., amplicon sequencing, and an investigation of the problem on a global scale to quantify the risk for humans and livestock. IMPORTANCE The genus Arcobacter was unexpectedly abundant in the effluent from 14 Danish wastewater treatment plants treating municipal wastewater, and the species included the human-pathogenic A. cryaerophilus and A. butzleri. Recent studies have shown that Arcobacter is common in wastewater worldwide, so the study indicates that discharge of members of the genus Arcobacter may be a global problem, and further studies are needed to quantify the risk and potentially minimize the discharge. The study also shows that culture-based analyses are insufficient for proper effluent quality control, and new standardized culture-independent measurements of effluent quality encompassing most pathogens should be considered.

scholarly journals Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1488-1494 ◽  
Author(s):  
Daichi Fujii ◽  
Fumiko Nagai ◽  
Yohei Watanabe ◽  
Yukio Shirasawa
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two Gram-staining-negative, strictly aerobic, non-endospore-forming, non-motile, rod-shaped bacteria, designated strains YIT 12745T and YIT 12746T, were isolated from sludge from a wastewater treatment plant. 16S rRNA gene sequence analyses indicated that these strains belonged to the genus Flavobacterium . In these analyses, strains YIT 12745T and YIT 12746T were most closely related to the type strains of Flavobacterium caeni and Flavobacterium terrigena , with 16S rRNA gene sequence similarity values of 94.9 % and 96.2 %, respectively. For both novel strains, menaquinone (MK-6) was the only respiratory quinone. The major fatty acids of strain YIT 12745T were iso-C15 : 1 G (14.4 %), iso-C16 : 0 (13.2 %), C15 : 0 (12.9 %), iso-C15 : 0 (12.9 %) and iso-C17 : 0 3-OH (11.5 %). Those of strain YIT 12746T were iso-C15 : 0 (21.5 %), iso-C16 : 0 (13.3 %), C15 : 0 (12.0 %) and iso-C15 : 1 G (11.9 %). The genomic DNA G+C contents of strains YIT 12745T and YIT 12746T were 48.7 and 30.9 mol%, respectively. From their differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus Flavobacterium , for which the names Flavobacterium longum sp. nov. (type strain YIT 12745T = JCM 19141T = DSM 27077T) and Flavobacterium urocaniciphilum sp. nov. (type strain YIT 12746T = JCM 19142T = DSM 27078T) are proposed. Emended descriptions of Flavobacterium caeni and Flavobacterium terrigena are also proposed.

scholarly journals Burkholderia zhejiangensis sp. nov., a methyl-parathion-degrading bacterium isolated from a wastewater-treatment system

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1337-1341 ◽  
Author(s):  
Peng Lu ◽  
Liu-Qiang Zheng ◽  
Jin-Jin Sun ◽  
Hong-Ming Liu ◽  
Shun-Peng Li ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Type Species ◽  
Methyl Parathion ◽  
Treatment System ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Wastewater Treatment System ◽  
Link Type ◽  
Degrading Bacterium

The taxonomic status of a methyl-parathion-degrading strain, OP-1T, isolated from a wastewater-treatment system in China, was determined using a polyphasic approach. The rod-shaped cells were Gram-staining-negative, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain belonged to the genus Burkholderia , as it appeared closely related to Burkholderia glathei ATCC 29195T (97.4 % sequence similarity), Burkholderia sordidicola KCTC 12081T (96.5 %) and Burkholderia bryophila LMG 23644T (96.3 %). The major cellular fatty acids, C16 : 0, C17 : 0 cyclo and C18 : 1ω7c, were also similar to those found in established members of the genus Burkholderia . The genomic DNA G+C content of strain OP-1T was 59.4 mol%. The level of DNA–DNA relatedness between the novel strain and the closest recognized species, Burkholderia glathei ATCC 29195T, was only 30 %. Based on the phenotypic, genotypic and phylogenetic evidence, strain OP-1T represents a novel species of the genus Burkholderia , for which the name Burkholderia zhejiangensis sp. nov. is proposed. The type strain is OP-1T ( = CCTCC AB 2010354T = KCTC 23300T).

scholarly journals Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant

2020 ◽  
Vol 70 (6) ◽  
pp. 3718-3723 ◽  
Author(s):  
Tomohiko Tamura ◽  
Satomi Saito ◽  
Moriyuki Hamada ◽  
Yingqian Kang ◽  
Yasutaka Hoshino ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two novel actinobacteria, designated NBRC 107696T and NBRC 107697T, were isolated from sludge samples from a wastewater treatment plant and their taxonomic positions were investigated by a polyphasic approach. The cells of the strains were aerobic, rod-shaped, non-motile and non-endospore-forming. The strains contained glutamic acid, alanine and meso-diaminopimelic acid in the peptidoglycan. Galactose and arabinose were detected as cell-wall sugars. The predominant menaquinone was identified as MK-9(H2) and the major fatty acids were C16  :  0, C18 : 1ω9c and C16 : 1ω7c. The DNA G+C contents of NBRC 107696T and NBRC 107697T were 68.07 and 68.99 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that NBRC 107696T and NBRC 107697T were a clade with members of the genus Gordonia . The highest 16S rRNA gene sequence similarity values were obtained with Gordonia araii IFM 10211T (98.9 %) for NBRC 107697T, and Gordonia malaquae IMMIB WWCC-22T, Gordonia neofelifaecis AD-6T and Gordonia humi CC-12301T (98.1 %) for NBRC 107696T, respectively. The digital DNA–DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel separate species. The names proposed to accommodate these two strains are Gordonia spumicola sp. nov. and Gordonia crocea sp. nov., and the type strains are NBRC 107696T (=IFM 10067T=TBRC 11239T) and NBRC 107697T (=IFM 10881T=TBRC 11240T), respectively.

Sphingobium jiangsuense sp. nov., a 3-phenoxybenzoic acid-degrading bacterium isolated from a wastewater treatment system

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 800-805 ◽  
Author(s):  
Jun Zhang ◽  
Zhi-Fei Lang ◽  
Jin-Wei Zheng ◽  
Bao-Jian Hang ◽  
Xiao-Qin Duan ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A non-sporulating, non-motile, catalase- and oxidase-positive, Gram-negative, rod-shaped bacterial strain, designated BA-3T, was isolated from activated sludge of a wastewater treatment facility. The strain was able to degrade about 95 % of 100 mg 3-phenoxybenzoic acid l−1 within 2 days of incubation. Growth occurred in the presence of 0–2 % (w/v) NaCl [optimum, 0.5 % (w/v) NaCl], at pH 5.5–9.0 (optimum, pH 7.0) and at 10–37 °C (optimum, 28 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BA-3T was a member of the genus Sphingobium ; it showed highest gene sequence similarity to Sphingobium qiguonii X23T (98.2 %), and similarities of <97.0 % with strains of other Sphingobium species. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium . Strain BA-3T showed low DNA–DNA relatedness values (21.3±0.8 %) with Sphingobium qiguonii X23T. Based on phenotypic, genotypic and phylogenetic data, strain BA-3T represents a novel species of the genus Sphingobium , for which the name Sphingobium jiangsuense sp. nov. is proposed; the type strain is BA-3T ( = CCTCC AB 2010217T = KCTC 23196T = KACC 16433T).

Mucilaginibacter defluvii sp. nov., isolated from a dye wastewater treatment facility

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 565-571 ◽  
Author(s):  
Yeoung Min Hwang ◽  
Keun Sik Baik ◽  
Chi Nam Seong
Keyword(s):  
Wastewater Treatment ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Dye Wastewater ◽  
Treatment Facility ◽  
Content Type ◽  
Link Type ◽  
Wastewater Treatment Facility ◽  
The Republic

A non-motile, rod-shaped bacterium, designated strain A5T, was isolated from a dye wastewater treatment facility in the Republic of Korea. Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 0, C18 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and the major polar lipid was phosphatidylethanolamine. The strain contained MK-7 as the only isoprenoid quinone and the DNA G+C content was 41.2 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain A5T forms an evolutionary lineage within the radiation encompassing the members of genus Mucilaginibacter , with Mucilaginibacter lutimaris BR-3T as its nearest neighbour (96.6 % sequence similarity). A number of phenotypic characteristics distinguished strain A5T from the members of the genus Mucilaginibacter . On the basis of the evidence presented in this study, strain A5T represents a novel species, for which the name Mucilaginibacter defluvii sp. nov. is proposed. The type strain is A5T ( = KCTC 23922T = JCM 18283T).

scholarly journals Microbial Community Composition and Dynamics of Moving Bed Biofilm Reactor Systems Treating Municipal Sewage

2011 ◽  
Vol 78 (3) ◽  
pp. 855-864 ◽  
Author(s):  
Kristi Biswas ◽  
Susan J. Turner
Keyword(s):  
Wastewater Treatment ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Biofilm Reactor ◽  
Rrna Gene ◽  
Moving Bed Biofilm Reactor ◽  
Moving Bed ◽  
Content Type ◽  
Suspended Biomass

ABSTRACTMoving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescencein situhybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated byClostridiaand sulfate-reducing members of theDeltaproteobacteria(SRBs). FISH analyses indicated morphological differences in theDeltaproteobacteriadetected at the two plants and also revealed distinctive clustering between SRBs and members of theMethanosarcinales, which were the onlyArchaeadetected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of theGammaproteobacteriaandBetaproteobacteria.This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.

scholarly journals Anaerobic Methyltert-Butyl Ether-Degrading Microorganisms Identified in Wastewater Treatment Plant Samples by Stable Isotope Probing

2012 ◽  
Vol 78 (8) ◽  
pp. 2973-2980 ◽  
Author(s):  
Weimin Sun ◽  
Xiaoxu Sun ◽  
Alison M. Cupples
Keyword(s):  
Wastewater Treatment ◽  
Stable Isotope ◽  
Wastewater Treatment Plant ◽  
Treatment Plant ◽  
Stable Isotope Probing ◽  
Rrna Gene ◽  
Butyl Ether ◽  
Content Type ◽  
Plant Samples ◽  
Mtbe Degradation

ABSTRACTAnaerobic methyltert-butyl ether (MTBE) degradation potential was investigated in samples from a range of sources. From these 22 experimental variations, only one source (from wastewater treatment plant samples) exhibited MTBE degradation. These microcosms were methanogenic and were subjected to DNA-based stable isotope probing (SIP) targeted to both bacteria and archaea to identify the putative MTBE degraders. For this purpose, DNA was extracted at two time points, subjected to ultracentrifugation, fractioning, and terminal restriction fragment length polymorphism (TRFLP). In addition, bacterial and archaeal 16S rRNA gene clone libraries were constructed. The SIP experiments indicated bacteria in the phylaFirmicutes(familyRuminococcaceae) andAlphaproteobacteria(genusSphingopyxis) were the dominant MTBE degraders. Previous studies have suggested a role forFirmicutesin anaerobic MTBE degradation; however, the putative MTBE-degrading microorganism in the current study is a novel MTBE-degrading phylotype within this phylum. Two archaeal phylotypes (generaMethanosarcinaandMethanocorpusculum) were also enriched in the heavy fractions, and these organisms may be responsible for minor amounts of MTBE degradation or for the uptake of metabolites released from the primary MTBE degraders. Currently, limited information exists on the microorganisms able to degrade MTBE under anaerobic conditions. This work represents the first application of DNA-based SIP to identify anaerobic MTBE-degrading microorganisms in laboratory microcosms and therefore provides a valuable set of data to definitively link identity with anaerobic MTBE degradation.

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