Complete Genome of Isoprene Degrading Nocardioides sp. WS12

Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene.

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Complete genome sequence and Benzophenone-3 mineralisation potential of Rhodococcus sp. USK10, a bacterium isolated from riverbank sediment.

10.1101/2021.11.04.467327 ◽

2021 ◽

Author(s):

Joseph Donald Martin ◽

Urse Scheel Kruger ◽

Athanasios Zervas ◽

Morten Dencker Schostag ◽

Tue Kjaergaard Nielsen ◽

...

Keyword(s):

Genome Sequence ◽

Dna Sequences ◽

Complete Genome ◽

Aquatic Organisms ◽

Degradation Pathway ◽

Uv Filter ◽

Degrading Bacterium ◽

Wide Range ◽

Mineralisation Potential ◽

Rhodococcus Sp

Benzophenone-3 (BP3) is an organic UV filter whose presence in the aquatic environment has been linked to detrimental developmental impacts in aquatic organisms such as coral and fish. The genus Rhodococcus has been extensively studied and is known for possessing large genomes housing genes for biodegradation of a wide range of compounds, including aromatic carbons. Here, we present the genome sequence of Rhodococcus sp. USK10, which was isolated from Chinese riverbank sediment and is capable of utilising BP3 as the sole carbon source, resulting in full BP3 mineralisation. The genome consisted of 9,870,030 bp in 3 replicons, a G+C content of 67.2%, and 9,722 coding DNA sequences (CDSs). Annotation of the genome revealed that 179 of these CDSs are involved in metabolism of aromatic carbons. The complete genome of Rhodococcus sp. USK10 is the first complete, annotated genome sequence of a Benzophenone-3 degrading bacterium. Through radiolabelling, it is also the first bacterium proven to mineralise Benzophenone-3. Due to the widespread environmental prevalence of Benzophenone-3, coupled to its adverse impact on aquatic organisms, this characterisation provides an integral first step in better understanding the environmentally relevant degradation pathway of the commonly used UV filter. Given USK10's ability to completely mineralise Benzophenone-3, it could prove to be a suitable candidate for bioremediation application.

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Degradation Potential of the Nonylphenol Monooxygenase of Sphingomonas sp. NP5 for Bisphenols and Their Structural Analogs

Microorganisms ◽

10.3390/microorganisms8020284 ◽

2020 ◽

Vol 8 (2) ◽

pp. 284 ◽

Cited By ~ 3

Author(s):

Masahiro Takeo ◽

Junichi Akizuki ◽

Aika Kawasaki ◽

Seiji Negoro

Keyword(s):

Substrate Specificity ◽

Cell Suspension ◽

Structural Similarity ◽

Side Chain ◽

Bisphenol S ◽

Bisphenol F ◽

Degrading Bacterium ◽

Monooxygenase Gene ◽

Wide Range ◽

Endocrine Disrupting

The nonylphenol-degrading bacterium Sphingomonas sp. strain NP5 has a very unique monooxygenase that can attack a wide range of 4-alkylphenols with a branched side chain. Due to the structural similarity, it can also attack bisphenolic compounds, which are very important materials for the synthesis of plastics and resins, but many of them are known to or suspected to have endocrine disrupting effects to fish and animals. In this study, to clarify the substrate specificity of the enzyme (NmoA) for bisphenolic compounds, degradation tests using the cell suspension of Pseudomonas putida harboring the nonylphenol monooxygenase gene (nmoA) were conducted. The cell suspension degraded several bisphenols including bisphenol F, bisphenol S, 4,4′-dihydroxybenzophenone, 4,4′-dihydroxydiphenylether, and 4,4′-thiodiphenol, indicating that this monooxygenase has a broad substrate specificity for compounds with a bisphenolic structure.

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Complete genome sequence of Alcanivorax xenomutans P40, an alkane-degrading bacterium isolated from deep seawater

Marine Genomics ◽

10.1016/j.margen.2017.05.010 ◽

2018 ◽

Vol 38 ◽

pp. 1-4 ◽

Cited By ~ 8

Author(s):

Xiaoteng Fu ◽

Qiliang Lai ◽

Chunming Dong ◽

Wanpeng Wang ◽

Zongze Shao

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Deep Seawater ◽

Degrading Bacterium

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Effects of sulfate concentration and sludge retention time on the interaction between methane production and sulfate reduction for butyrate

Water Science & Technology ◽

10.2166/wst.1994.0378 ◽

1994 ◽

Vol 30 (8) ◽

pp. 45-54 ◽

Cited By ~ 56

Author(s):

O. Mizuno ◽

Y. Y. Li ◽

T. Noike

Keyword(s):

Sulfate Reduction ◽

Retention Time ◽

Methane Production ◽

Electron Flow ◽

Degradation Pathway ◽

Sulfate Concentration ◽

High Concentration ◽

Total Electron ◽

Sludge Retention Time ◽

Wide Range

The effects of sulfate concentration and COD/S ratio on the anaerobic degradation of butyrate were investigated by using 2.0 L anaerobic chemostat-type reactor at 35°C. The study was conducted over a wide range of the COD/S ratio (1.5 to 148) by varying COD concentrations (2500–10000 mg/L) and sulfate concentrations (68–1667 mg-S/L) in the substrate. The sludge retention time at each COD/S ratio was changed from 5 to 20 days. The interaction between methane producing bacteria (MPB) and sulfate-reducing bacteria (SRB) was evidently influenced by COD/S ratio in the substrate. When COD/S ratio was 6.0 or more, methane production was the predominate reaction and over 80% of the total electron flow was used by MPB. At the COD/S ratio of 1.5, SRB utilzed over 50% of the total electron flow. A large amount of sulfate reduction resulted in not only the decrease of methane production, but also the rapid increase of the bacterial growth. The degradation pathway of butyrate and the composition of bacterial populations in the reactor were also dominated by COD/S ratio. In sulfate depleted condition, butyrate was degraded to methane via acetate and hydrogen by MPB. On the other hand, butyrate was firstly degraded into sulfide and acetate in sulfate rich conditions by SRB, and the produced acetate was then degraded by acetate consuming MPB and SRB. The methanogenesis from acetate was inhibited by the high concentration of sulfide.

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The Complete Genome Sequence of the Nicotine-Degrading Bacterium Shinella sp. HZN7

Frontiers in Microbiology ◽

10.3389/fmicb.2016.01348 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 10

Author(s):

Jiguo Qiu ◽

Youjian Yang ◽

Junjie Zhang ◽

Haixia Wang ◽

Yun Ma ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Degrading Bacterium

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Complete Genome Sequence of the Polychlorinated Biphenyl Degrader Rhodococcus sp. WB1

Genome Announcements ◽

10.1128/genomea.00996-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 4

Author(s):

Yuxin Xu ◽

Man Yu ◽

Alin Shen

Keyword(s):

Gene Cluster ◽

Genome Sequence ◽

Contaminated Soil ◽

Complete Genome Sequence ◽

Complete Genome ◽

Polychlorinated Biphenyl ◽

Xenobiotic Metabolism ◽

Rhodococcus Sp

Rhodococcus sp. WB1 is a polychlorinated biphenyl degrader which was isolated from contaminated soil in Zhejiang, China. Here, we present the complete genome sequence. The analysis of this genome indicated that a biphenyl-degrading gene cluster and several xenobiotic metabolism pathways are harbored.

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Complete genome sequence of the cyprodinil-degrading bacterium Acinetobacter johnsonii LXL_C1

Microbial Pathogenesis ◽

10.1016/j.micpath.2018.11.016 ◽

2019 ◽

Vol 127 ◽

pp. 246-249 ◽

Cited By ~ 2

Author(s):

Weijun Wang ◽

Xiaoxin Chen ◽

Hai Yan ◽

Jiye Hu ◽

Xiaolu Liu

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Acinetobacter Johnsonii ◽

Degrading Bacterium

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Identification and Characterization of Cotinine Hydroxylase CotA that Initiates biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195

Applied and Environmental Microbiology ◽

10.1128/aem.00923-21 ◽

2021 ◽

Author(s):

Lingling Zhao ◽

Zhenyang Zhao ◽

Kaiyun Zhang ◽

Xuan Zhang ◽

Siqiong Xu ◽

...

Keyword(s):

Gene Cluster ◽

Tobacco Consumption ◽

Hydroxyl Group ◽

Carbon And Nitrogen ◽

Enzymatic Transformation ◽

Degrading Bacterium ◽

Hydroxylase Gene ◽

Urine Cotinine ◽

Genetic Mechanisms

Cotinine is a stable toxic contaminant, produced as a byproduct of smoking. It is of emerging concern due to its global distribution in aquatic environments. Microorganisms have the potential to degrade cotinine, however, the genetic mechanisms of this process are unknown. Nocardioides sp. strain JQ2195 is a pure culture strain that has been reported to degrade cotinine at micropollutant concentrations. This strain utilizes cotinine as its sole carbon and nitrogen source. In this study, a 50 kb gene cluster (designated as cot ) involved in cotinine degradation, was predicted based on genomic and transcriptomic analyses. A novel three-component cotinine hydroxylase gene (designated as cotA1A2A3 ), which initiated cotinine catabolism was identified and characterized. CotA from Shinella sp. HZN7 was heterologously expressed and purified, and shown to convert cotinine into 6-hydroxycotinine. H 2 18 O-labelling and ESI-MS analysis confirmed that the hydroxyl group incorporated into 6-hydroxycotinine was derived from water. This study provides new molecular insights into the microbial metabolism of heterocyclic chemical pollutants. IMPORTANCE In the human body, cotinine is the major metabolite of nicotine, and 10–15% of generated cotinine is excreted in urine. Cotinine is a structural analogue of nicotine and is much more stable than nicotine. Increased tobacco consumption has led to high environmental concentrations of cotinine, which may have detrimental effects on aquatic ecosystems and human health. Nocardioides sp. strain JQ2195 is a unique cotinine-degrading bacterium. However, the underlying genetic and biochemical foundations of cotinine degradation are still unknown. In this study, a 50 kb gene cluster (designated cot ) was identified by genomic and transcriptomic analyses as being involved in the degradation of cotinine. A novel three-component cotinine hydroxylase gene (designated cotA1A2A3 ) catalyzed cotinine to 6-hydroxy-cotinine. This study provides new molecular insights into the microbial degradation and enzymatic transformation of cotinine.

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micrIO: An Open-Source Autosampler and Fraction Collector for Automated Microfluidic Input-Output

10.1101/655324 ◽

2019 ◽

Author(s):

Scott A. Longwell ◽

Polly M. Fordyce

Keyword(s):

Open Source ◽

Positive Pressure ◽

Cross Contamination ◽

Wide Spread ◽

Fraction Collector ◽

Input And Output ◽

Wide Range ◽

Molecular Separations ◽

Multiwell Plates

Microfluidic devices are an empowering technology for many labs, enabling a wide range of applications spanning high-throughput encapsulation, molecular separations, and long-term cell culture. In many cases, however, their utility is limited by a ‘world-to-chip’ barrier that makes it difficult to serially interface samples with these devices. As a result, many researchers are forced to rely on low-throughput, manual approaches for managing device input and output (IO) of samples, reagents, and effluent. Here, we present a hardware-software platform for automated microfluidic IO (micrIO). The platform, which is uniquely compatible with positive-pressure microfluidics, comprises an ‘AutoSipper’ for input and a Fraction Collector for output. To facilitate wide-spread adoption, both are open-source builds constructed from components that are readily purchased online or fabricated from included design files. The software control library, written in Python, allows the platform to be integrated with existing experimental setups and to coordinate IO with other functions such as valve actuation and assay imaging. We demonstrate these capabilities by coupling both the AutoSipper and Fraction Collector to a microfluidic device that produces beads with distinct spectral codes, and an analysis of the collected bead fractions establishes the ability of the platform to draw from and output to specific wells of multiwell plates with no detectable cross-contamination between samples.

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Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

Microbiology Resource Announcements ◽

10.1128/mra.00013-21 ◽

2021 ◽

Vol 10 (7) ◽

Author(s):

Kentaro Miyazaki ◽

Hikaru Suenaga ◽

Mamoru Oshiki ◽

Shuichi Kawano ◽

Toshikazu Fukushima

Keyword(s):

Activated Sludge ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Coke Oven ◽

Rrna Genes ◽

Trna Genes ◽

Circular Chromosome ◽

Protein Coding ◽

Degrading Bacterium

ABSTRACT A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

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