Dataset Information

Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals.

ABSTRACT:

Background

In our previous study, Citrobacter sp. XT1-2-2 was isolated from high cadmium-contaminated soils, and demonstrated an excellent ability to decrease the bioavailability of cadmium in the soil and inhibit cadmium uptake in rice. In addition, the strain XT1-2-2 could significantly promote rice growth and increase rice biomass. Therefore, the strain XT1-2-2 shows great potential for remediation of cadmium -contaminated soils. However, the genome sequence of this organism has not been reported so far. RESULTS: Here the basic characteristics and genetic diversity of the strain XT1-2-2 were described, together with the draft genome and comparative genomic results. The strain XT1-2-2 is 5040459 bp long with an average G + C content of 52.09%, and contains a total of 4801 genes. Putative genomic islands were predicted in the genome of Citrobacter sp. XT1-2-2. All genes of a complete set of sulfate reduction pathway and various putative heavy metal resistance genes in the genome were identified and analyzed.

Conclusions

These analytical results provide insights into the genomic basis of microbial immobilization of heavy metals.

SUBMITTER: Shan S

PROVIDER: S-EPMC9764585 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Publications

Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals.

Shan Shiping S Cheng Wei W Li Yilu Y Zhang Min M Liu Zhudong Z Wang Yushuang Y Wei Xiaowu X Fu Zujiao Z Wu Shandong S Du Dongxia D Guo Zhaohui Z

BMC genomics 20221219 1

<h4>Background</h4>In our previous study, Citrobacter sp. XT1-2-2 was isolated from high cadmium-contaminated soils, and demonstrated an excellent ability to decrease the bioavailability of cadmium in the soil and inhibit cadmium uptake in rice. In addition, the strain XT1-2-2 could significantly promote rice growth and increase rice biomass. Therefore, the strain XT1-2-2 shows great potential for remediation of cadmium -contaminated soils. However, the genome sequence of this organism has not b ...[more]

PMID: 36536293

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Project description:To enhance the adsorption capacity of biochar (BC), herein a novel multifunction modified biochar (SDMBC) was prepared by directly crosslinking of the nanomicelle of sodium dodecyl sulfate/sapindus-saponin (SDS/SAP) composite system onto the BC through a simple, environmental friendly approach. Result showed that the adsorption performance of SDMBC has been greatly improved, compared with BC or using alone SDS and SAP, adsorption ability increased by 48.83%, 29.50%, 36.44%, respectively, the best modified effect was appeared when the concentration of SAP to SDS was 0.8 and 0.8 CMC. SDMBC exhibited high adsorption abilities of 130.23, 108.43, 277.09 125.27, 112.78 mg/g for heavy metal ions lead Pb(II), Cadmium Cd(II) and organic pollutants with different chemical properties bisphenol A(BPA), Methylene blue (MB), P-nitrophenol (PNP), respectively, higher than most previously reported adsorbents, importantly, SDMBC can still efficient removal capabilities even in the binary competition. Subsequently, the SDMBC and BC was characterized by Fourier Transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), Zeta potential (Zeta), it found SDMBC has a more layered structure, richer functional groups and more amorphous structure compared with BC, which are closely related with improving its adsorption capacity. The adsorption behavior of SDMBC for MB show that process was found to be spontaneous, propitious, endothermic, the adsorption isotherms fitted Freundlich models well, pseudo-second-order best describes kinetics adsorption, suggesting that the process is multi-layer chemical adsorption. The little affected by ionic strength and coexisting substances, could remained removal rate over a wide pH range, SDMBC still keep high removal rates even after 5 reuses. Based on FT-IR analysis, plausible adsorption mechanism proposed, including hydrogen bond, electrostatic attraction and π-π bonding. Cost analysis manifests that the SDMBC are high efficiency and cheap eco-adsorbents compared with commercial activated carbon, and the SDMBC dosage required for the removal of 99% of a fixed amount of MB in different volumes of effluent was predicted. Seven machine learning (ML) models were used to predict the MB (60 mg/L) adsorption of the SDMBC, using Shapley Additive Explanations (SHAP) for model interpretation. Finding Extreme Gradient Boosting (XGBoost) exhibited best performance, the order of feature importance as time> Ratio> pH> concentration> temperature. Thus, SDMBC as a new cheap and eco-adsorbents, can be used to effectively remove various types of pollutants, has a great application potential in sewage treatment, while the accurate ML prediction model presented a valuable advice for designing efficient adsorbents and optimization operating conditions in the future.

Dataset Information

Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals.

Background

Conclusions

Publications

Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals.

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