Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole

AbstractBackgroundThiabendazole (TBZ), is a benzimidazole fungicide and anthelminthic whose high persistence and toxicity pose a serious environmental threat. In our quest for environmental mitigation we previously isolated the first TBZ-degrading bacterial consortium and provided preliminary evidence for its composition and the degrading role of a Sphingomonas. Here, we employed a multi-omic approach combined with DNA-stable isotope probing (SIP) to determine the genetic make-up of the key consortium members, to disentangle nutritional and metabolic interdependencies, to identify the transformation pathway of TBZ and to understand the genetic network driving its transformation.ResultsTime-series SIP in combination with amplicon sequencing analysis verified the key role of Sphingomonas in TBZ degradation by assimilating over 80% of the 13C-labelled phenyl moiety of TBZ. Non-target mass spectroscopy (MS) analysis showed the accumulation of thiazole-4-carboxamidine as a single dead-end transformation product and no phenyl-containing derivative, in line with the phenyl moiety assimilation in the SIP analysis. Time series metagenomic analysis of the consortium supplemented with TBZ or succinate led to the assembly of 18 metagenome-assembled genomes (MAGs) with >80% completeness, six (Sphingomonas 3X21F, γ-Proteobacterium 34A, Bradyrhizobiaceae 9B and Hydrogenophaga 19A, 13A, and 23F) being dominant. Meta-transcriptomic and -proteomic analysis suggested that Sphingomonas mobilize a carbazole dioxygenase (car) operon during the initial cleavage of TBZ to thiazole-4-carboxamidine and catechol, the latter is further transformed by enzymes encoded in a catechol ortho-cleavage (cat) operon; both operons being up-regulated during TBZ degradation. Computational docking analysis of the terminal oxygenase component of car, CarAa, showed high affinity to TBZ, comparable to carbazole, reinforcing its high potency for TBZ transformation. These results suggest no interactions between consortium members in TBZ transformation, performed solely by Sphingomonas. In contrast, gene expression network analysis revealed strong interactions between Sphingomonas MAG 3X12F and Hydrogenophaga MAG 23F, with Hydrogenophaga activating its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway along TBZ degradation.ConclusionsOur findings suggest interactions between consortium members which align with the “black queen hypothesis”: Sphingomonas detoxifies TBZ, releasing consortium members by a toxicant; in return for this, Hydrogenophaga 23F provides cobalamin to the auxotrophic Sphingomonas.

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Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes (pdmAB) in a Biobed System

Applied and Environmental Microbiology ◽

10.1128/aem.00474-20 ◽

2020 ◽

Vol 86 (14) ◽

Author(s):

Veronika Storck ◽

Sara Gallego ◽

Sotirios Vasileiadis ◽

Sabir Hussain ◽

Jérémie Béguet ◽

...

Keyword(s):

Bacterial Community ◽

Large Subunit ◽

16S Rrna Gene Sequencing ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Analysis ◽

Gene Encoding ◽

Reverse Transcription Pcr ◽

Dna And Rna

ABSTRACT Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon. IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.

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The role of parental self-regulation and household chaos in parent-toddler interactions: A time-series study.

Journal of Family Psychology ◽

10.1037/fam0000814 ◽

2020 ◽

Author(s):

Sanne B. Geeraerts ◽

Joyce Endendijk ◽

Kirby Deater-Deckard ◽

Jorg Huijding ◽

Marike H. F. Deutz ◽

...

Keyword(s):

Time Series ◽

Self Regulation ◽

Household Chaos ◽

Time Series Study ◽

Series Study

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Exploring the Role of Meteorological Factors in Predicting Incident Pulmonary Tuberculosis: A Time-Series Study in Eastern China

SSRN Electronic Journal ◽

10.2139/ssrn.3667848 ◽

2020 ◽

Author(s):

Zhongqi Li ◽

Hongqiu Pan ◽

Qiao Liu ◽

Jianming Wang

Keyword(s):

Time Series ◽

Pulmonary Tuberculosis ◽

Meteorological Factors ◽

Eastern China ◽

Time Series Study ◽

Series Study

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Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

Scientific Reports ◽

10.1038/s41598-021-91615-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kazutoshi Yoshitake ◽

Gaku Kimura ◽

Tomoko Sakami ◽

Tsuyoshi Watanabe ◽

Yukiko Taniuchi ◽

...

Keyword(s):

Time Series ◽

Microbial Communities ◽

Pacific Coast ◽

Three Dimensional ◽

Amplicon Sequencing ◽

Metagenomic Data ◽

Shotgun Metagenomics ◽

Functional Features ◽

Pacific Coast Of Japan ◽

Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

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The Role of Assumptions in Ohlson Model Performance: Lessons for Improving Equity-Value Modeling

Mathematics ◽

10.3390/math9050513 ◽

2021 ◽

Vol 9 (5) ◽

pp. 513

Author(s):

Olga Fullana ◽

Mariano González ◽

David Toscano

Keyword(s):

Time Series ◽

Model Performance ◽

Listed Firms ◽

Valuation Model ◽

Residual Income Valuation ◽

Equity Value ◽

Short Run ◽

Time Series Approach ◽

Linear Information

In this paper, we test whether the short-run econometric conditions for the basic assumptions of the Ohlson valuation model hold, and then we relate these results with the fulfillment of the short-run econometric conditions for this model to be effective. Better future modeling motivated us to analyze to what extent the assumptions involved in this seminal model are not good enough approximations to solve the firm valuation problem, causing poor model performance. The model is based on the well-known dividend discount model and the residual income valuation model, and it adds a linear information model, which is a time series model by nature. Therefore, we adopt the time series approach. In the presence of non-stationary variables, we focus our research on US-listed firms for which more than forty years of data with the required cointegration properties to use error correction models are available. The results show that the clean surplus relation assumption has no impact on model performance, while the unbiased accounting property assumption has an important effect on it. The results also emphasize the uselessness of forcing valuation models to match the value displacement property of dividends.

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Calibrating the CreditRisk+ Model at Different Time Scales and in Presence of Temporal Autocorrelation †

Mathematics ◽

10.3390/math9141679 ◽

2021 ◽

Vol 9 (14) ◽

pp. 1679

Author(s):

Jacopo Giacomelli ◽

Luca Passalacqua

Keyword(s):

Time Series ◽

Default Risk ◽

Real Life ◽

Statistical Error ◽

Real Data ◽

Sampling Period ◽

Calibration Procedure ◽

Industry Standards ◽

Default Rate

The CreditRisk+ model is one of the industry standards for the valuation of default risk in credit loans portfolios. The calibration of CreditRisk+ requires, inter alia, the specification of the parameters describing the structure of dependence among default events. This work addresses the calibration of these parameters. In particular, we study the dependence of the calibration procedure on the sampling period of the default rate time series, that might be different from the time horizon onto which the model is used for forecasting, as it is often the case in real life applications. The case of autocorrelated time series and the role of the statistical error as a function of the time series period are also discussed. The findings of the proposed calibration technique are illustrated with the support of an application to real data.

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Seasonality in extra-pulmonary tuberculosis notifications in Germany 2004-2014- a time series analysis

BMC Public Health ◽

10.1186/s12889-021-10655-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Tanja Charles ◽

Matthias Eckardt ◽

Basel Karo ◽

Walter Haas ◽

Stefan Kröger

Keyword(s):

Time Series ◽

Time Series Analysis ◽

Disease Onset ◽

Age Groups ◽

Age Group ◽

Pulmonary Tb ◽

Series Analysis ◽

Disease Site ◽

Extra Pulmonary

Abstract Background Seasonality in tuberculosis (TB) has been found in different parts of the world, showing a peak in spring/summer and a trough in autumn/winter. The evidence is less clear which factors drive seasonality. It was our aim to identify and evaluate seasonality in the notifications of TB in Germany, additionally investigating the possible variance of seasonality by disease site, sex and age group. Methods We conducted an integer-valued time series analysis using national surveillance data. We analysed the reported monthly numbers of started treatments between 2004 and 2014 for all notified TB cases and stratified by disease site, sex and age group. Results We detected seasonality in the extra-pulmonary TB cases (N = 11,219), with peaks in late spring/summer and troughs in fall/winter. For all TB notifications together (N = 51,090) and for pulmonary TB only (N = 39,714) we did not find a distinct seasonality. Additional stratified analyses did not reveal any clear differences between age groups, the sexes, or between active and passive case finding. Conclusion We found seasonality in extra-pulmonary TB only, indicating that seasonality of disease onset might be specific to the disease site. This could point towards differences in disease progression between the different clinical disease manifestations. Sex appears not to be an important driver of seasonality, whereas the role of age remains unclear as this could not be sufficiently investigated.

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