Efficient hexabromocyclododecane-biodegrading microorganisms isolated in Taiwan

Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation

Hexabromocyclododecane (HBCD) poses significant environmental risks, and identifying HBCD-degrading microbes and their enzymatic mechanisms is challenging due to the complexity of microbial interactions and metabolic pathways. This study aimed to identify critical genes involved in HBCD biodegradation through two approaches: functional annotation of metagenomes and the interpretation of machine learning-based prediction models. Our functional analysis revealed a rich metabolic potential in Chiang Chun soil (CCS) metagenomes, particularly in carbohydrate metabolism. Among the machine learning algorithms tested, random forest models outperformed others, especially when trained on datasets reflecting the degradation patterns of species like Dehalococcoides mccartyi and Pseudomonas aeruginosa. These models highlighted enzymes such as EC 1.8.3.2 (thiol oxidase) and EC 4.1.1.43 (phenylpyruvate decarboxylase) as inhibitors of degradation, while EC 2.7.1.83 (pseudouridine kinase) was linked to enhanced degradation. This dual-methodology approach not only deepens our understanding of microbial functions in HBCD degradation but also provides an unbiased view of the microbial and enzymatic interactions involved, offering a more targeted and effective bioremediation strategy.

Biotransformation of HBCDs by the microbial communities enriched from mangrove sediments

1,2,5,6,9,10-Hexabromocyclododecanes (HBCDs) are a sort of persistent organic pollutants (POPs). This research investigated 12 microbial communities enriched from sediments of four mangroves in China to transform HBCDs. Six microbial communities gained high transformation rates (27.5-97.7%) after 12 generations of serial transfer. Bacteria were the main contributors to transform HBCDs rather than fungi. Analyses on the bacterial compositions and binning genomes showed that Alcanivorax (55.246-84.942%) harboring haloalkane dehalogenase genes dadAH and dadBH dominated the microbial communities with high transformation rates. Moreover, expressions of dadAH and dadBH in the microbial communities and Alcanivorax isolate could be induced by HBCDs. Further, it was found that purified proteins DadAH and DadBH showed high conversion rates on HBCDs in 36 h (91.9 ± 7.4 and 101.0 ± 1.8%, respectively). The engineered Escherichia coli BL21 strains harbored two genes could convert 5.7 ± 0.4 and 35.1 ± 0.1% HBCDs, respectively, lower than their cell-free crude extracts (61.2 ± 5.2 and 56.5 ± 8.7%, respectively). The diastereoisomer-specific transforming trend by both microbial communities and enzymes were γ- > α- > β-HBCD, differed from α- > β- > γ-HBCD by the Alcanivorax isolate. The identified transformation products indicated that HBCDs were dehalogenated via HBr elimination (dehydrobromination), hydrolytic and reductive debromination pathways in the enriched cultures. Two enzymes converted HBCDs via hydrolytic debromination. The present research provided theoretical bases for the biotransformation of HBCDs by microbial community and the bioremediation of HBCDs contamination in the environment.

Transformation of HBCDs by Rhodococcus sp. stu-38

1,2,5,6,9,10-Hexabromocyclododecanes (HBCDs) are brominated flame retardants causing serious environmental pollution. HBCDs in the environment could be transformed to various products. Identification of transformation products has been performed using various mass-spectrometric techniques. However, bacterial transformation of HBCDs yielding low-level products was not well studied. In this paper, a Rhodococcus strain stu-38 which could stereoselectively transform HBCDs in mineral salt medium, seawater, and growth medium was isolated. Seven potential biotransformation products of HBCDs were identified by using GC-MS. These products, including brominated alkenes, dibromocyclododecadiene and bromocyclododecatriene; brominated alkenols, bromocyclododecadienol and bromocyclododecatrienol; fully debrominated compounds, cyclododecadiendiol, 1,2-epoxy-5,9-cyclododecadiene, and cyclododecadienol, were presented in rather low level which could lead to false negative results. The low-level transformation products should not be ignored because their toxicity was less assessment. This research highlighted identification of the low-level transformation products to reveal the complicated stereoselective biotransformation of HBCDs.

A metagenomics study of hexabromocyclododecane degradation with a soil microbial community

Hexabromocyclododecanes (HBCDs) are globally prevalent and persistent organic pollutants (POPs) listed by the Stockholm Convention in 2013. They have been detected in many environmental media from waterbodies to Plantae and even in the human body. Due to their highly bioaccumulative characterization, they pose an urgent public health issue. Here, we demonstrate that the indigenous microbial community in the agricultural soil in Taiwan could decompose HBCDs with no additional carbon source incentive. The degradation kinetics reached 0.173 day^-1 after the first treatment and 0.104 day^-1 after second exposure. With additional C-sources, the rate constants decreased to 0.054-0.097 day^-1. The hydroxylic debromination metabolites and ring cleavage long-chain alkane metabolites were identified to support the potential metabolic pathways utilized by the soil microbial communities. The metagenome established by Nanopore sequencing showed significant compositional alteration in the soil microbial community after the HBCD treatment. After ranking, comparing relative abundances, and performing network analyses, several novel bacterial taxa were identified to contribute to HBCD biotransformation, including Herbaspirillum, Sphingomonas, Brevundimonas, Azospirillum, Caulobacter, and Microvirga, through halogenated / aromatic compound degradation, glutathione-S-transferase, and hydrolase activity. We present a compelling and applicable approach combining metagenomics research, degradation kinetics, and metabolomics strategies, which allowed us to decipher the natural attenuation and remediation mechanisms of HBCDs.