Using high-throughput transcriptome sequencing to investigate the biotransformation mechanism of hexabromocyclododecane with Rhodopseudomonas palustris in water

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.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Mechanisms of BPA Degradation and Toxicity Resistance in Rhodococcus equi

Bisphenol A (BPA) pollution poses an increasingly serious problem. BPA has been detected in a variety of environmental media and human tissues. Microbial degradation is an effective method of environmental BPA remediation. However, BPA is also biotoxic to microorganisms. In this study, Rhodococcus equi DSSKP-R-001 (R-001) was used to degrade BPA, and the effects of BPA on the growth metabolism, gene expression patterns, and toxicity-resistance mechanisms of Rhodococcus equi were analyzed. The results showed that R-001 degraded 51.2% of 5 mg/L BPA and that 40 mg/L BPA was the maximum BPA concentration tolerated by strain R-001. Cytochrome P450 monooxygenase and multicopper oxidases played key roles in BPA degradation. However, BPA was toxic to strain R-001, exhibiting nonlinear inhibitory effects on the growth and metabolism of this bacterium. R-001 bacterial biomass, total protein content, and ATP content exhibited V-shaped trends as BPA concentration increased. The toxic effects of BPA included the downregulation of R-001 genes related to glycolysis/gluconeogenesis, pentose phosphate metabolism, and glyoxylate and dicarboxylate metabolism. Genes involved in aspects of the BPA-resistance response, such as base excision repair, osmoprotectant transport, iron-complex transport, and some energy metabolisms, were upregulated to mitigate the loss of energy associated with BPA exposure. This study helped to clarify the bacterial mechanisms involved in BPA biodegradation and toxicity resistance, and our results provide a theoretical basis for the application of strain R-001 in BPA pollution treatments.

Historical development and prospect of intimately coupling photocatalysis and biological technology for pollutant treatment in sewage: A review

Through the synergistic effect of photocatalysis and biodegradation, intimately coupling photocatalysis and biological (ICPB) technology could improve the removal rate and mineralization rate of refractory pollutants and reduce the toxicity of intermediate products. ICPB system was characterized with the advantages of simple operation, low energy consumption and high treatment efficiency. As a new sewage treatment technology, ICPB system has shown great potential in the treatment of refractory pollutants, and has been widely concerned. In this study, the research progress of photocatalyst, carrier and biofilm in ICPB system were discussed, and the degradation mechanism was introduced. The shortcomings of the current ICPB system were pointed out, and the possible research directions of ICPB in the future were proposed. This review aimed to deepen the understanding of ICPB technology and promoted the further development of ICPB technology in the treatment of refractory pollutants.

Rhodopseudomonas palustris: A biotechnology chassis

Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials

Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene (also known as styrofoam), is among the most commonly produced plastics worldwide and is recalcitrant to microbial degradation. In this study, we assessed changes in the gut microbiome of superworms (Zophobas morio) reared on bran, polystyrene or under starvation conditions over a 3 weeks period. Superworms on all diets were able to complete their life cycle to pupae and imago, although superworms reared on polystyrene had minimal weight gains, resulting in lower pupation rates compared to bran reared worms. The change in microbial gut communities from baseline differed considerably between diet groups, with polystyrene and starvation groups characterized by a loss of microbial diversity and the presence of opportunistic pathogens. Inferred microbial functions enriched in the polystyrene group included transposon movements, membrane restructuring and adaptations to oxidative stress. We detected several encoded enzymes with reported polystyrene and styrene degradation abilities, supporting previous reports of polystyrene-degrading bacteria in the superworm gut. By recovering metagenome-assembled genomes (MAGs) we linked phylogeny and functions and identified genera including Pseudomonas, Rhodococcus and Corynebacterium that possess genes associated with polystyrene degradation. In conclusion, our results provide the first metagenomic insights into the metabolic pathways used by the gut microbiome of superworms to degrade polystyrene. Our results also confirm that superworms can survive on polystyrene feed, but this diet has considerable negative impacts on host gut microbiome diversity and health.

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.

Microbial debromination of hexabromocyclododecanes

Hexabromocyclododecanes (HBCDs), a new sort of brominated flame retardants (BFRs), are globally prevalent and recalcitrant toxic environmental pollutants. HBCDs have been found in many environmental media and even in the human body, leading to serious health concerns. HBCDs are biodegradable in the environment. By now, dozens of bacteria have been discovered with the ability to transform HBCDs. Microbial debromination of HBCDs is via HBr-elimination, HBr-dihaloelimination, and hydrolytic debromination. Biotic transformation of HBCDs yields many hydroxylated and lower brominated compounds which lack assessment of ecological toxicity. Bioremediation of HBCD pollution has only been applied in the laboratory. Here, we review the current knowledge about microbial debromination of HBCDs, aiming to promote the bioremediation applied in HBCD contaminated sites. KEY POINTS: • Microbial debromination of HBCDs is via hydrolytic debromination, HBr-elimination, and HBr-dihaloelimination. • Newly occurred halogenated contaminants such as HBCDs hitch the degradation pathway tamed by previously discharged anthropogenic organohalides. • Strategy that combines bioaugmentation with phytoremediation for bioremediation of HBCD pollution is promising.

Efficient hexabromocyclododecane-biodegrading microorganisms isolated in Taiwan

The potential toxicity of hexabromocyclododecane (HBCD), its persistence in the environment, and its high bioaccumulation characteristics pose a need to remediate HBCD in the environment. Bacillus cereus and B. subtilis species complexes we isolated from Taiwan soil are capable of degrading HBCD. B. cereus can degrade HBCD with a half-life only 0.911 days. The highest efficiency of HBCD degradation by B. cereus was achieved at pH 7.0, 35 °C, and 0.10 ppm HBCD. The removal mechanism of HBCD by B. cereus is debromination and its pathway was proposed. The addition of surfactant Tween 60 improved HBCD removal but the addition of CaO₂, slow-releasing oxygen, did not. These findings can facilitate the bioremediation of HBCD in the environment.

Aerobic degradation and the effect of hexabromocyclododecane by soil microbial communities in Taiwan

Hexabromocyclododecane (HBCD) is one of the most frequently used brominated flame retardants (BFRs) in the industries nowadays. Despite being listed as persistent organic pollutant (POP), it is still in use until 2025. Because of its bio-accumulative and toxic characteristics, the applicable remediation approach is required. The aim of this study is to identify the microbial community from soil with HBCD degradation ability. The soil suspension and soil samples from Chiang Chun Soil and River Bank Soil showed to degrade HBCD by 60% 4 days after treatment, the debromination ratio was around 60%, and the total HBCD removal ratio reached 70% and 77.9%, respectively. The HBCD debromination metabolites, and oxidation metabolites were identified by GC-MS. The microbial taxonomic diversity was observed with DGGE approach to evaluate the effect of HBCD of microbial community. Bacillus spp. and Clostridium spp. were identified as the dominant microbes in the Chiang Chun Soil, but the amount of Bacillus spp. were showed to be affected by HBCD. In conclusion, HBCD could be removed by the microbial consortium in soil under aerobic culturing condition by various metabolic pathways.

Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens

The cecal microbiota plays a critical role in energy harvest and nutrient digestion, influencing intestinal health and the performance of chickens. Feed efficiency (FE) is essential for improving economic efficiency and saving social resources in chicken production and may be affected by the cecal microbiota. Therefore, to investigate the composition and functional capacity of cecum microbes related to FE in Xiayan chicken, an indigenous breed in Guangxi province, metagenome sequencing was performed on chicken cecal contents. 173 male and 167 female chickens were divided into high and low FE groups according to the residual feed intake. The cecal microbial genome was extracted and sequenced. The results showed that the genera Bacteroides, Prevotella, and Alistipes were the 3 most abundant in each cecal microbiome. The linear discriminant analysis effect size revealed 6 potential biomarkers in male and 14 in female chickens. Notably, the relative abundance of Lactobacillus in the high FE group was higher than that of the low FE group both in the male and female chickens, and the species Limosilactobacillus oris has a higher score in the high FE group of male chickens. In contrast, some potentially pathogenic microorganisms such as Campylobacter avium in females and Helicobacter pullorum in males were enriched in the low FE group. Predictive functional analysis showed that the high FE group in male chickens had a greater ability of xenobiotics biodegradation and metabolism and signaling molecules and interaction. In addition, the host sex was found to exert effects on the cecal microbial composition and function associated with FE. These results increased our understanding of the cecal microbial composition and identified many potential biomarkers related to FE, which may be used to improve the FE of the chickens.

Molecular response mechanism in Escherichia coli under hexabromocyclododecane stress

The effects of hexabromocyclododecane (HBCD) on the relationship between physiological responses and metabolic networks remains unclear. To this end, cellular growth, apoptosis, reactive oxygen species, exometabolites and the proteome of Escherichia coli were investigated following exposure to 0.1 and 1 μM HBCD. The results showed that although there were no significant changes in the pH value, apoptosis and reactive oxygen species under HBCD stress, cell growth was inhibited. The metabolic network formed by glycolysis, oxidative phosphorylation, amino acids biosynthesis, membrane proteins biosynthesis, ABC transporters, glycogen storage, cell recognition, compound transport and nucleotide excision repair was disrupted. Cell chemotaxis and DNA damage repair were the effective approaches to alleviate HBCD stress. This work improves our understanding of HBCD toxicity and provides insight into the toxicological mechanism of HBCD at the molecular and network levels.