Biodegradation of skatole by Burkholderia sp. IDO3 and its successful bioaugmentation in activated sludge systems

Biodegradation of chloroxylenol by an aerobic enrichment consortium and a newly identified Rhodococcus strain

Chloroxylenol is a commonly used antimicrobial agent in antibacterial and disinfection products, which has been detected in various environments, such as wastewater treatment plants, rivers, seawater, and even drinking water, with concentrations ranging from ng/L to mg/L. However, the biodegradation of chloroxylenol received limited attention with only sporadic reports available so far. In this study, an efficient chloroxylenol-degrading consortium, which could degrade 20 mg/L chloroxylenol within two days, was obtained after five months of enrichment. Amplicon sequencing analysis revealed a decrease in the α-diversity (e.g., Shannon index and Inv_Simpson index) of the community during the domestication process. Microbial community dynamics were uncovered, with sequences affiliated to Achromobacter, Pseudomonas, and Rhodococcus identified as the most abundant taxonomic groups. From the consortium, five pure isolates were obtained; however, it was found that only one strain of Rhodococcus could degrade chloroxylenol. Strain Rhodococcus sp. DMU2021 could degrade chloroxylenol efficiently under the conditions of temperature 30-40 °C, and neutral/alkaline conditions. Chloroxylenol was toxic to strain DMU2021 and triggered both enzymatic and non-enzymatic antioxidant systems in response. This study provides novel insights into the biodegradation process of chloroxylenol, as well as valuable bioresources for bioremediation.

Sustainable management and valorization of biomass wastes using synthetic microbial consortia

In response to the persistent expansion of global resource demands, considerable attention has been directed toward the synthetic microbial consortia (SMC) within the domain of microbial engineering, aiming to address the sustainable management and valorization of biomass wastes. This comprehensive review systematically encapsulates the most recent advancements in research and technological applications concerning the utilization of SMC for biomass waste treatment. The construction strategies of SMC are briefly outlined, and the diverse applications of SMC in biomass wastes treatment are explored, with particular emphasis on its potential advantages in waste degradation, hazardous substances control, and high value-added products conversion. Finally, recommendations for the future development of SMC technology are proposed, and prospects for its sustainable application are discussed.

Lactobacillus-driven feed fermentation regulates microbiota metabolism and reduces odor emission from the feces of pigs

IMPORTANCE

Our present study showed that dietary supplementation with feed fermented by Lactobacillus could promote the growth performance of pigs, regulate the microbiota, and inhibit the growth of harmful bacteria. It could prevent the accumulation of toxic substances and reduce odor emission from pig feces, thereby reducing environmental pollution. In addition, one key triumph of the present study was the isolation of Weissella cibaria ZWC030, and the strain could inhibit the production of skatole in vitro in our present results.

Long-term influence of chloroxylenol on anaerobic microbial community: Performance, microbial interaction, and antibiotic resistance gene behaviors

The use of antibacterial and disinfection products is increasing in recent years. Para-chloro-meta-xylenol (PCMX), a widely used antimicrobial agent, has been detected in various environments. Herein, the impacts of PCMX with long-term exposure on anaerobic sequencing batch reactors were investigated. The high concentration (50 mg/L, GH group) PCMX severely inhibited the nutrient removal process, and the low concentration group (0.5 mg/L, GL group) slightly affected the removal efficiency which was recovered after 120 days of adaptation compared to the control group (0 mg/L, GC group). Cell viability tests indicated that PCMX inactivated the microbes. A significant reduction in bacterial α-diversity was observed in the GH but not the GL group. The microbial communities were shifted upon PCMX exposure, among which Olsenella, Novosphingobium, and Saccharibacteria genera incertae Sedis became the predominant genera in the GH groups. Network analyses showed that PCMX significantly reduced the complexity and interactions of the microbial communities, consistent with the negative impacts on bioreactor performance. Real-time PCR analysis indicated that PCMX affected the behavior of antibiotic resistance genes (ARGs), and the relationship between ARGs and bacterial genera gradually became complicated after long-term exposure. Most detected ARGs decreased on Day 60 but increased on Day 120 especially in the GL group, implying the potential risk of environment-relevant concentration of PCMX in the ecosystems. This study provides new insights into the understanding of the impacts and risks of PCMX on wastewater treatment processes.

Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies

3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.

Mitigating the inhibition of antibacterial agent chloroxylenol on nitrification system-The role of Rhodococcus ruber in a bioaugmentation system

The chloroxylenol (PCMX) degrading strain was successfully isolated from sludge and identified as Rhodococcus ruber (R. ruber). Afterwards, a bioaugmentation system was constructed by seeding R. ruber into nitrifying sludge to fasten degradation efficiency of highly toxic PCMX from wastewater. Results showed that R. ruber presented high PCMX-degrading performance under aerobic conditions, 25 °C, pH 7.0 and inoculum sizes of 4% (v/v). These optimized conditions were used in subsequent bioaugmentation experiment. In bioaugmentation system, R. ruber could detoxify nitrifiers by degrading PCMX, and the content of polysaccharide in extracellular polymeric substances increased. The quantitative polymerase chain reaction results exhibited that the absolute abundance of 16S rRNA gene and ammonia oxidizing bacteria (AOB) slightly elevated in bioaugmentation system. After analyzing the results of high-throughput sequencing, it was found that the loaded R. ruber can colonize successfully and turn into dominant strains in sludge system. Molecular docking simulation showed that PCMX had a weaker suppressed effect on AOB than nitrite oxidizing bacteria, and R. ruber can alleviate the adverse effect. This study could provide a novel strategy for potential application in reinforcement of PCMX removal in wastewater treatment.

Transcriptomic profiling reveals the molecular responses of Rhodococcus aetherivorans DMU1 to skatole stress

Skatole is a typical malodor compound in animal wastes. Several skatole-degrading bacterial strains have been obtained, whereas the molecular response of strains to skatole stress has not been well elucidated. Herein, the skatole degradation by a Gram-positive strain Rhodococcus aetherivorans DMU1 was investigated. Strain DMU1 showed high efficiency in skatole degradation under the conditions of 25-40 °C and pH 7.0-10.0. It could utilize various aromatics, including cresols, phenol, and methylindoles, as the sole carbon source for growth, implying its potential in the bioremediation application of animal wastes. Transcriptomic sequencing revealed that 328 genes were up-regulated and 640 genes were down-regulated in strain DMU1 when grown in the skatole-containing medium. Skatole increased the gene expression levels of antioxidant defense systems and heat shock proteins. The expression of ribosome-related genes was significantly inhibited which implied the growth inhibition of skatole. A rich set of oxidoreductases were changed, and a novel gene cluster containing the flavoprotein monooxygenase and ring-hydroxylating oxygenase genes was highly up-regulated, which was probably involved in skatole upstream degradation. The upregulation pattern of this gene cluster was further verified by qRT-PCR assay. Furthermore, skatole should be mainly degraded via the catechol ortho-cleavage pathway with cat25170 as the functional gene. The gene cat25170 was cloned and expressed in E. coli BL21(DE3). Pure enzyme assays showed that Cat25170 could catalyze catechol with Km 9.96 μmol/L and kcat 12.36 s-1.

Skatole: A thin red line between its benefits and toxicity

Skatole (3-methylindole) is a heterocyclic compound naturally found in the feces of vertebrates and is produced by certain flowers. Skatole has been used in specific products of the perfume industry or as a flavor additive in ice cream. Additionally, skatole is formed by tryptophan pyrolysis of tobacco and has been demonstrated to be a mutagen. Skatole-induced pulmonotoxicity was reliably described in ruminants and rodents, but no studies have been conducted in humans. Initially, we provide basic knowledge and a historical overview of skatole. Then, skatole bacterial formation in the intestine is described, and the importance of the microbiome during this process is evaluated. Increased skatole concentrations could serve as a marker for intestinal disease development. Therefore, the human molecular targets of skatole that may have significant effects on various processes in the human body are described. Ultimately, we suggest a link between skatole intestinal formation in humans and skatole-induced pulmonotoxicity, which should be explored further in the future.

The application of bioremediation in wastewater treatment plants for microplastics removal: a practical perspective

Wastewater treatment plants (WWTPs) play the role of intercepting microplastics in the environment and provide a platform for bioremediation to remove microplastics. Despite, this opportunity has not been adequately studied. This paper shows the potential ways microplastics-targeted bioremediation could be incorporated into wastewater treatment through the review of relevant literature on bioaugmentation of water treatment processes for pollutants removal. Having reviewed more than 90 papers in this area, it highlights that bioremediation in WWTPs can be employed through bioaugmentation of secondary biological treatment systems, particularly the aerobic conventional activated sludge, sequencing batch reactor, membrane bioreactor and rotating biological contactor. The efficiency of microplastics removal, however, is influenced by the types and forms of microorganisms used, the polymer types and the incubation time (100% for polycaprolactone with Streptomyces thermoviolaceus and 0.76% for low-density polyethylene with Acinetobacter iwoffii). Bioaugmentation of anaerobic system, though possible, is constrained by comparatively less anaerobic microplastics-degrading microorganisms identified. In tertiary system, bioremediation through biological activated carbon and biological aerated filter can be accomplished and enzymatic membrane reactor can be added to the system for deployment of biocatalysts. During sludge treatment, bioaugmentation and addition of enzymes to composting and anaerobic digestion are potential ways to enhance microplastics breakdown. Limitations of bioremediation in wastewater treatment include longer degradation time of microplastics, incomplete biodegradation, variable efficiency, specific microbial activities and uncertainty in colonization. This paper provides important insight into the practical applications of bioremediation in wastewater treatment for microplastics removal.

Simultaneous removal of aromatic pollutants and nitrate at high concentrations by hypersaline denitrification:Long-term continuous experiments investigation

If we can use toxic aromatic compounds as supplementary carbon source, the simultaneous removal of nitrate (NO₃^-) and aromatic compounds may be achieved at much lower chemical costs. This study uses the expanded granular sludge bed (EGSB) reactors to investigate the hypersaline (> 3%) denitrification performance, the removal of aromatic compounds, i.e., aniline, phenol, and their mixture, and the mechanisms involved in. The four reactors exhibit high removal efficiency of NO₃^- (> 92.8%) and aromatic compounds (> 73.9%) at 0-1200 mg/L of aromatic compounds. The formation of toxic intermediates such as catechol and azo dyes is revealed by gas chromatography mass spectrometry (GC-MS) with and without N,O-Bis(trimethylsilyl) trifluoroacetamide (BSTFA) derivation, and their toxic effects lead to the lower cell survival ratios after exposing to phenol (64.2% ∼ 68.9%) than to aniline and mixture (72.7% ∼ 78.0%). The stable performance is associated with the more secretion of extracellular polymeric substances (EPS) and the adsorption of pollutants on EPS, and this was indicated from the higher fluorescence intensity in three-dimensional excitation-emission matrix (3D-EEM). Moreover, the Halomonas and Azoarcus show high abundance and play important roles in the removal of both NO₃^- and aromatic compounds. Besides, quantitative real time PCR (RT-qPCR) results demonstrate the key role of highly abundant nosZ and nirS genes in denitrification. The toxic organics in industrial wastewaters are potentially feasible carbon sources for denitrification even under high-salinity stress.

Indole metabolism by phenol-stimulated activated sludges: Performance, microbial communities and network analysis

Indole and phenol often coexist in the coking wastewater, while the effects of phenol on microbial communities of indole metabolism were less explored. In this study, the microbial interactions within activated sludge microbial communities stimulated by indole (group A) or by indole and phenol (group B) were systematically investigated in sequencing batch reactors (SBRs). The results showed that the removal of indole was increased by adding phenol. By using high-throughput sequencing technology, it was found that α-diversity was reduced in both groups. According to the relative abundance analysis, the indole-degrading genus Comamonas was the core genus in both groups (33.94% and 61.40%). But another indole-degrading genus Pseudomonas was only enriched in group A with 12.22% relative abundance. Meanwhile, common aromatic degrading genus Dyella and Thermomonas were enriched only in group B. It was found that the relative abundance of cytochrome P450 and styrene degradation enzymes were increased in group B by PICRUSt analysis. Based on the phylogenetic molecular ecological networks (pMENs), module hub OTU_1149 (Burkholderia) was only detected in group B, and the positive interactions between the key functional genus Burkholderia and other bacteria were increased. This study provides new insights into our understanding of indole metabolism communities stimulated by phenol, which would provide useful information for practical coking wastewater treatment.

Effects of biodegradable film mulching on bacterial diversity in soils

The spread of biodegradable plastic films (BDFs) not only increases grain yield but also reduces environmental pollution from plastic film to a large extent. Soil microbes are considered to be involved in biodegradation processes. However, the study of microbe diversity in soil mulched with biodegradable plastic film remains limited. Here, we compared the diversity of microbes between soils with biodegradable film and nonbiodegradable film (NBDF) mulch. The results showed that BDFs affected total C, P and NH₄⁺-N, especially organism C content, as well as microbe species richness (ACE; Chao1) and diversity (Simpson index; Shannon index). In terms of dominant phyla and genera, BDFs and NBDF can influence the abundance of disparate species. Furthermore, BDFs could also contribute to improving the richness of the important functional bacterial groups in soil, e.g., Pedomicrobium and Comamonas, both of which are involved in the degradation of plastic residues in soil. Finally, we found that BDFs improved the transformation of nitrogen by significantly increasing the abundances of Nitrobacter and Nitrospira. Our results highlight the impact of BDF mulch on the abundance of functional bacteria in the soil.

Lipid degrading microbe consortium driving micro-ecological evolvement of activated sludge for cooking wastewater treatment

In this study, a lipid degrading microbe consortium (LDMC) was assembled to improve the performance of activated sludge (AS) on cooking wastewater purification. LDMC can rapidly degrade high-level oil (efficiency beyond 93.0% at 5.0 g/L) as sole carbon source under various environmental conditions (10.0-45.0 °C, pH 2.0-12.0). With LDMC inoculation, AS' water treatment performance was significantly enhanced, which removed 36.10 and 48.93% more chemical oxygen demand (COD) and ammonia nitrogen from wastewater than control. A better settling property and smaller bulking risk were found with LDMC inoculation, indicated by a lower SV₃₀ and SVI index but a higher MLSS. By GC/MS analysis, a gradual degradation on the end of the fatty acid chain was suggested. LDMC inoculation significantly changed AS's microbial community structure, improved its stability, decreased the microbial community diversity, facilitated the enrichment of lipid degraders and functional genes related to lipid bio-degradation. Lipid degraders including Nakamurella sp. and Stenotrophomona sp., etc. played a crucial role during oil degradation. Sludge structure maintainers such as Kineosphaera sp. contributed largely to the stability of AS under exogenous stress. This study provided an efficient approach for cooking wastewater treatment along with the underlying mechanism exploration, which should give insights into oil-containing environmental remediation.

Performance and microbial community analysis of bioaugmented activated sludge for nitrogen-containing organic pollutants removal

Nitrogen-containing organic pollutants (quinoline, pyridine and indole) are widely distributed in coking wastewater, and bioaugmentation with specific microorganisms may enhance the removal of these recalcitrant pollutants. The bioaugmented system (group B) was constructed through inoculation of two aromatics-degrading bacteria, Comamonas sp. Z1 (quinoline degrader) and Acinetobacter sp. JW (indole degrader), into the activated sludge for treatment of quinoline, indole and pyridine, and the non-bioaugmented activated sludge was used as the control (group C). Both groups maintained high efficiencies (> 94%) for removal of nitrogen-containing organic pollutants and chemical oxygen demand (COD) during the long-term operation, and group B was highly effective at the starting period and the operation stage fed with raw wastewater. High-throughput sequencing analysis indicated that nitrogen-containing organic pollutants could shape the microbial community structure, and communities of bioaugmented group B were clearly separated from those of non-bioaugmented group C as observed in non-metric multidimensional scaling (NMDS) plot. Although the inoculants did not remain their dominance in group B, bioaugmentation could induce the formation of effective microbial community, and the indigenous microbes might play the key role in removal of nitrogen-containing organic pollutants, including Dokdonella, Comamonas and Pseudoxanthomonas. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis suggested that bioaugmentation could facilitate the enrichment of functional genes related to xenobiotics biodegradation and metabolism, probably leading to the improved performance in group B. This study indicated that bioaugmentation could promote the removal of nitrogen-containing organic pollutants, which should be an effective strategy for wastewater treatment.

Bacterial and fungal community compositions and structures of a skatole-degrading culture enriched from pig slurry

In this study, the aerobic activated sludge for skatole removal was enriched from pig slurry in three parallel sequencing batch reactors. The sludge system exhibited a satisfactory performance for skatole removal during the 40 days operation. High-throughput sequencing results showed that the α-diversity remained unchanged before and after the operation process. However, the structures of bacterial and fungal communities notably shifted. Particularly, Arthrobacter increased to be the major bacterial genus from 2.15 ± 0.76% (day 0) to 23.80 ± 24.36% (day 40), and Fusicolla became the major fungal genus from 1.20 ± 0.48% (day 0) to 37.17 ± 7.47% (day 40). These results indicated that Arthrobacter and Fusicolla might participate in skatole removal in sludge systems, though both genera were not reported to be able to degrade skatole. This is the first study describing skatole-degrading bacterial and fungal communities in the enrichment from pig slurry to the best of our knowledge, providing important guidance for skatole control and bioremediation.