Comparative analysis of DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) on unraveling dimethoate degraders

doi:10.1007/s11783-024-1765-x

Front. Environ. Sci. Eng.

2024, Vol. 18

Issue (1) : 5 https://doi.org/10.1007/s11783-024-1765-x

RESEARCH ARTICLE

Comparative analysis of DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) on unraveling dimethoate degraders

Luning Lian^1,^2,³, Yi Xing^1,^2,³(

), Dayi Zhang⁴, Longfei Jiang⁵, Mengke Song⁶, Bo Jiang^1,^2,^3,⁷(

)

¹. School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, China
². Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing 100083, China
³. National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing 100083, China
⁴. College of New Energy and Environment, Jilin University, Changchun 130021, China
⁵. Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
⁶. College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
⁷. National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China

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Abstract

● Dimethoate degraders were identified via MMI and DNA-SIP.

● MMI identified Pseudomonas, Bacillus, Ramlibacter, Arthrobacter , and Rhodococcus.

● DNA-SIP identified Ramlibacter , Rhodococcus and Arthrobacter.

● Both oph B and oph C2 were involved in dimethoate metabolism.

● MMI shows higher resolution than DNA-SIP in identifying functional microbes.

Microorganisms are crucial in the bioremediation of organophosphorus pesticides. However, most functional microorganisms (> 99%) are yet to be cultivated. This study applied two cultivation-independent approaches, DNA-SIP and magnetic-nanoparticle mediated isolation (MMI), to identify the functional microorganisms in degrading dimethoate in agricultural soils. MMI identified five dimethoate degraders: Pseudomonas, Bacillus, Ramlibacter, Arthrobacter, and Rhodococcus, whereas DNA-SIP identified three dimethoate degraders: Ramlibacter, Arthrobacter, and Rhodococcus. Also, MMI showed higher resolution than DNA-SIP in identifying functional microorganisms. Two organic phosphohydrolase (OPH) genes: ophC2 and ophB, were involved in dimethoate metabolism, as revealed by DNA-SIP and MMI. The degradation products of dimethoate include omethoate, O,O,S-trimethyl thiophosphorothioate, N-methyl-2-sulfanylacetamide, O,O-diethyl S-hydrogen phosphorodithioate, O,O,O-trimethyl thiophosphate, O,O,S-trimethyl thiophosphorodithioate, and O,O,O-trimethyl phosphoric. This study emphasizes the feasibility of using SIP and MMI to explore the functional dimethoate degraders, expanding our knowledge of microbial resources with cultivation-independent approaches.

Keywords Stable isotope probing (SIP) Magnetic-nanoparticle mediated isolation (MMI) Dimethoate Biodegradation Cultivation-independent approach

Corresponding Author(s): Yi Xing,Bo Jiang

Issue Date: 09 August 2023

Cite this article:

Luning Lian,Yi Xing,Dayi Zhang, et al. Comparative analysis of DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) on unraveling dimethoate degraders[J]. Front. Environ. Sci. Eng., 2024, 18(1): 5.

URL:

https://academic.hep.com.cn/fese/EN/10.1007/s11783-024-1765-x
https://academic.hep.com.cn/fese/EN/Y2024/V18/I1/5

Fig.1 (A) Relative abundance of soil microbial community on phylum level in 12C-R-SIP, 13C-R-SIP, and MMI-R treatments. The selected taxa have a minimal relative abundance greater than 5%. (OS-0d represents the original microbial community in soil. MMI-R-7, 21, 35 represents MMI-R on different days; 12C-R-SIP-7, 21, 35 represents 12C-R-SIP on different days; 13C-R-SIP-7, 21, 35 represents 13C-R-SIP on different days; MFC-R-7, 21, 35 represents MFC-R on different days). (B) Relative abundance of soil microbial community on genus level in 12C-R-SIP, 13C-R-SIP, and MMI-R treatments. The selected taxa have a minimal relative abundance greater than 5%. (C) PCoA score plots illustrating the distance between microbial communities of the 12C-R-SIP, 13C-R-SIP, and MMI-R treatments. Principal coordinate 1 (PCoA1) and 2 (PCoA2) explain 31.0% and 27.0% of the total variance in microbial community structure. 13C-7, 21, 35 represents 13C-R-SIP on different days; 12C-7, 21, 35 represents 12C-R-SIP on different days.SIP on different days.

Fig.2 Shift tendency of OTU-11, OTU-62, and OTU-84 fragments. The relative abundance of the OTU-11, OTU-62, and OTU-84 fragments is in the fractions of different buoyant density (BD) of DNA extracted from the wastewater amended with either ¹²C- or ¹³C-labeled dimethoate.

Fig.3 Phylogenetic tree of DNA-SIP identified OTUs responsible for dimethoate degradation. Neighbor-joining tree based on 16S rRNA gene sequences showing the phylogenetic position of the bacteria corresponding to OTU-11, OTU-62, OTU-84, and their representatives of some other related taxa.

Fig.4 (A) Phylogenetic analysis of amplified oph gene based on the amino acid sequences from 12C-R-SIP, 13C-R-SIP, and MMI-R treatments. (B) Copy numbers of oph gene collected from the CsCl₂ gradient fractions from the SIP with 12C-dimethoate or 13C-dimethoate, respectively. Bacterial template distribution within each density gradient fraction was quantified with qPCR. (C) Copy numbers of oph gene in the MMI and the heavy DNA fractions of the 13C-SIP treatments.

Fig.5 The dimethoate degradation metabolites and pathways by all treatments (MMI, DNA-SIP, and cultivable degraders by Rhodococcus sp. L-1).

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