Aromatic Degradation Pathways Research Articles

Deciphering Toxic Pollutants Breakdown Potential in Microbial Community of Chumathang Hot Spring, Ladakh, India via Shotgun Metagenome Sequencing.

Persistent Organic Pollutants (POPs) have been in focus of research due to their massive contamination ofenvironment and bio-accumulation. Bioremediation and high-throughput research have gained momentum to curb the harmful effects of POPs. The present research has explored the microbial diversity of Chumathang Hot Spring, Ladakh, India, through Illumina metagenomic HiSeq 4000 sequencing platform and their potential to degrade persistent pollutants, especially xenobiotics. Taxonomic characterization based on raw metagenomic data illuminated the abundance of members of Pseudomonadota and Actinomyceota. The re-construction of the microbial genomes from assembled contigs and scaffolds using de novo assembler metaSPAdes and their further annotation through contig alignment with available reference genomes elucidated the landscape of the hot spring's microbes. The predominantly occupied key genera reported were Pannonibacter and Novosphingobium. Comparative genomic analysis established evolutionary relationships and functional diversities among hot spring microbial communities. The function annotation through MG-RAST has revealed their metabolic versatility of degrading a wide array of xenobiotic compounds, including caprolactam, dioxin, chlorobenzene, benzoate, and. Further, the hydroxylating dioxygenase (Saro_3901) was identified as a pivotal component in the aromatic degradation pathways, showcasing extensive metabolic interconnectivity. Interestingly, protein interaction network analysis identified hub genes like Saro_1233 (protocatechuate 4,5-dioxygenase alpha subunit), while Saro_3057 (amidase) was noted for its critical role in network communication and control. The resilience of thermal ecosystems, evidenced by robust enzymatic activity and degradation capability among organisms with < 95% genetic similarity, underscores their potential for industrial and bioremediation exploration, emphasizing the importance of preserving and studying biodiverse habitats.

Metabolic engineering of Pseudomonas bharatica CSV86T to degrade Carbaryl (1-naphthyl-N-methylcarbamate) via the salicylate-catechol route.

Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.

The catabolism of lignin-derived p-methoxylated aromatic compounds by Rhodococcus jostii RHA1.

Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C-O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C-C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ΔpobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ΔpcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.IMPORTANCELignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in Rhodococcus, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives.

Erratum for Walton and Buchan, "Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates".

Erratum for Walton and Buchan, "Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates".

Analysis of gut target microbiota and species difference in patients with obstructive sleep apnea based on 16S rRNA sequencing

To explore the difference in gut microbiota composition between patients with obstructive sleep apnea (OSA) and healthy individuals and the role of gut microbiota in the pathogenesis of OSA. Thirty-nine patients with OSA admitted to our hospital between May and December, 2022 and 20 healthy individuals were enrolled in this study. Stool samples were collected from all the participants for analysis of microbiome composition using 16S rRNA high- throughput sequencing analysis. The alpha diversity, beta diversity, and species difference were determined between the two groups and marker species analysis and metabolic pathway function prediction analysis were performed. The species diversity (Shannon and Simpson) indexes, richness (observed species) and evenness (Pielou) of gut microbiota were significantly lower in OSA patients than in the healthy individuals (P < 0.05). The OSA patients had also a significantly lowered community diversity (P < 0.05) with different gut microbial communities from those of the healthy individuals shown by increased relative abundance of potentially pathogenic bacteria such as Pseudomonas and Monocytogenes (P < 0.05). LEfSe analysis showed that the abundance of 23 species of gut microbiota differed significantly between the two groups and the OSA patients had significant increases in the abundance of Pseudomonas, Meganomonas, and Fusobacterium (P < 0.05). The differential marker flora affected host homeostasis. Random Forest and ROC curve analyses confirmed that Pseudomonas could be used as important biomarkers for a differential diagnosis. Metabolic pathway function prediction analysis showed that biosynthesis function had the greatest contribution to maintaining gut microbiota homeostasis, and Pseudomonas affected the occurrence and progression of OSA by participating in aromatic bioamine degradation and ketogluconic acid metabolic pathway. OSA patients have obvious gut microbiota disturbances, and Pseudomonas may affect the development of OSA by participating in substance metabolism to serve as the potential target gut bacteria for OSA treatment.

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates.

Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.

Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats.

Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.

Fecal microbiota transplantation improves hepatic fibro-inflammation via regulating oxidative stress in experimental NASH

Nonalcoholic steatohepatitis (NASH) is associated with imbalance of gut microbiome, indicating participation of gut environment in hepatic health status. Therefore, modulating gut environment via fecal microbiota transplantation (FMT) is a promising therapeutic procedure for NASH patients. However, the effect and mechanism of the FMT remains largely unknown. Here, we investigated the gut-liver axis to understand the FMT-mediated hepatic improvement in NASH. Feces from specific pathogen free mice were infused allogeneically into gastrointestinal tract of mice fed with high fat, high cholesterol and fructose (HFHCF), resulting in suppressing hepatic pathogenic events, featured by decreasing inflammatory and fibrotic mediators. The FMT elevated NF-E2-related factor 2 (NRF2), a key transcription factor that regulates antioxidant enzymes, in livers. The HFHCF-induced NASH increased intestinal permeability with abundant Facklamia and Aerococcus, an imbalanced gut environment that was significantly improved by the FMT, characterized with restoration of intestinal barrier function and an enrichment of Clostridium. Notably, the gut environment created by FMT was inferred to produce metabolites from the aromatic biogenic amine degradation pathway, specifically 4-hydroxyphenylacetic acid (4-HPA), which is known to ameliorate liver injury. We suggest that gut-derived molecules, related to hepatic improvement such as 4-HPA are the potential therapeutic agents for preventing and treating NASH.

Microbial responses to increased salinity in oiled upper tidal shorelines

The microbial degradation of crude oil stranded on seashores is usually much slower than that of dispersed oil at sea. This is usually attributed to nutrient limitation and higher oil concentrations on beaches than in dispersed plumes, in addition to the low moisture content and transient hypersaline conditions of the upper intertidal and supratidal zones. Here, we investigated the effect of hypersaline conditions, oil concentration, and nutrient limitation on the hydrocarbonoclastic activity. Beach sand, with oil concentrations of 1 and 10 mL/kg, was infiltrated with seawater at salinities of 30, 90, and 160 g/L to 20% saturation, with and without the addition of nutrients. Oil chemistry, 16 S rRNA gene amplicon, and metagenomic sequencing analyses were conducted every 30 days for 180 days. The biodegradation of aromatic hydrocarbons was much slower at higher salinities, while that of alkanes was not noticeably affected, and the addition of nutrients only marginally enhanced the biodegradation of hydrocarbons. The relative abundance and diversity of genera varied substantially with the increase in pore water salinity, whereby halophilic hydrocarbon-degrading microorganisms, particularly in the Marinobacter genus, were significantly abundant only under hypersaline conditions. The enzymes were considerably less abundant at high salinities, mainly for those associated to aromatic hydrocarbon degradation pathways. Consequently, occasional inundation of the upper parts of oiled sandy beaches with seawater to decrease the pore water salinity and reseed the contaminated region with indigenous hydrocarbon degraders, along with the concomitant addition of fertilizers, could be a suitable, non-destructive, and inexpensive response tool for enhancing the biodegradation of beached crude oil, particularly that of the aromatic fraction.

Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation.

Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.

Parkinson's Disease and the Gut Microbiome in Rural California.

Increasing evidence connects the gut microbiome to Parkinson's disease (PD) etiology, but little is known about microbial contributions to PD progression and its clinical features. We aim to explore the association between the gut microbiome with PD, and the microbial association with PD-specific clinical features. In a community-based case-control study of 96 PD patients and 74 controls, microbiome data were obtained from 16S rRNA gene sequencing of fecal samples, and analyzed for microbial diversity, taxa abundance, and predicted functional pathways that differed in PD patients and controls, and their association with PD-specific features (disease duration, motor subtypes, L-DOPA daily dose, and motor function). PD patients' gut microbiome showed lower species diversity (p = 0.04) and were compositionally different (p = 0.002) compared to controls but had a higher abundance of three phyla (Proteobacteria, Verrucomicrobiota, Actinobacteria) and five genera (Akkermansia, Enterococcus, Hungatella, and two Ruminococcaceae) controlling for sex, race, age, and sequencing platform. Also, 35 Metacyc pathways were predicted to be differentially expressed in PD patients including biosynthesis, compound degradation/utilization/assimilation, generation of metabolites and energy, and glycan pathways. Additionally, the postural instability gait dysfunction subtype was associated with three phyla and the NAD biosynthesis pathway. PD duration was associated with the Synergistota phylum, six genera, and the aromatic compound degradation pathways. Two genera were associated with motor function. PD patients differed from controls in gut microbiome composition and its predicted metagenome. Clinical features were also associated with bacterial taxa and altered metabolic pathways of interest for PD progression.

Enhanced brewery wastewater purification and microalgal production through algal-bacterial synergy

Previous studies on microalgae-based brewery wastewater treatment paid insufficient attention to the relative contributions of microalgae and bacteria on nutrient removal, bacterial community structure and metabolic function, and also the microalgae-bacteria interaction, hindering the large-scale application. This study demonstrated that the bacteria in brewery wastewater promoted the growth of Chlorella sorokiniana to 1.41 g L−1. Collaboration between bacteria and microalgae enhanced the ammonia nitrogen removal up to 96.0% (mainly driven by microalgae) and accelerated dissolved organic carbon degradation (mainly driven by bacteria). Increased humic acid-like substances and reduced soluble microbial by-product-like substances were observed. Functional annotation of prokaryotic taxa (FAPROTAX) analysis demonstrated that bacteria in the brewery wastewater with addition of microalgae (ABS) possessed less abundance of aromatic compound degradation pathway than the treatment without microalgae. Co-occurrence network analysis showed that microalgae induced the dominance of bacteria from module III and exacerbated intraspecies competition within the microbial community in ABS for nutrients. The microalgal biomass in ABS contained high lipid content of 34.9% with good properties for the biodiesel production. Similar results were obtained in 14 L panel photobioreactor with unsterilized brewery wastewater. These results revealed that bacteria and microalgae exerted synergistic effects on the enhanced microalgal growth and brewery wastewater treatment, serving to the promotion of microalgae-based brewery wastewater treatment in a large scale.

Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation.

The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.

Collaborative removal of NOx and toluene in flue gas driven by aerobic denitrifying biotrickling filter

Nitrogen oxides (NOx) and volatile organic compounds (VOCs) may cause ozone formation and photochemical smog pollution, which may damage to human health and ecological environment seriously. An aerobic Denitrifying BioTrickling Filter (DBTF) for collaborative removal of nitrogen oxides (NOx) and toluene in flue gas was investigated. NOx and toluene removal efficiency were up to 90% and 95%, respectively. Mycobacterium, Comamonas and Pseudomonas were predominant bacteria; Mycobacterium, Pseudomonas, Comamonas, Microbacterium, Reyranella, Stenotrophomonas and Alicycliphilus were the core toluene oxidizing-denitrifying genera, denitrification genes (narGHI, nirK, nasB, napAB, nosZ and norC) and toluene oxidation genes (tom, E1.14.13.7, xyl, cat, todE, tes, mhp, pch, pob, pca, lig, gal) responsible for bacterial oxidation of toluene and NOx reduction, as shown by16S rDNA and metagenomic sequencing. Bacterial oxidation of toluene was coupled to NOx reduction in which toluene served as the electron donor while NOx served as the electron acceptor and thereby redox between toluene and NOx was formed, toluene was degraded through the classical aerobic aromatic compound degradation pathway. DBTF was capable of both toluene oxidation and NOx reduction by denitrification. These results show that the DBTF is achievable and open new possibilities for applying the DBTF to simultaneous removal of NOx and VOCs.

Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing

Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. We integrated stable isotope probing (SIP), genome-resolved metagenomics, and enzyme characterization to investigate the degradation of high-molecular weight, 13C-ring-labeled synthetic lignin by microbial communities from moderately thermophilic hot spring sediment (52 °C) and a woody “hog fuel” pile (53 and 62 °C zones). 13C-Lignin degradation was monitored using IR-GCMS of 13CO2, and isotopic enrichment of DNA was measured with UHLPC-MS/MS. Assembly of 42 metagenomic libraries (72 Gb) yielded 344 contig bins, from which 125 draft genomes were produced. Fourteen genomes were significantly enriched with 13C from lignin, including genomes of Actinomycetes (Thermoleophilaceae, Solirubrobacteraceae, Rubrobacter sp.), Firmicutes (Kyrpidia sp., Alicyclobacillus sp.) and Gammaproteobacteria (Steroidobacteraceae). We employed multiple approaches to screen genomes for genes encoding putative ligninases and pathways for aromatic compound degradation. Our analysis identified several novel laccase-like multi-copper oxidase (LMCO) genes in 13C-enriched genomes. One of these LMCOs was heterologously expressed and shown to oxidize lignin model compounds and minimally transformed lignin. This study elucidated bacterial lignin depolymerization and mineralization in thermal ecosystems, establishing new possibilities for the efficient valorization of lignin at elevated temperature.

Metagenomic Insight of a Full Scale Eco-Friendly Treatment System of Textile Dye Wastewater Using Bioaugmentation of the Composite Culture CES-1.

Effects of bioaugmentation of the composite microbial culture CES-1 on a full scale textile dye wastewater treatment process were investigated in terms of water quality, sludge reduction, dynamics of microbial community structures and their functional genes responsible for degradation of azo dye, and other chemicals. The removal efficiencies for Chemical Oxygen Demand (COD), Total Nitrogen (T-N), Total Phosphorus (T-P), Suspended Solids (SS), and color intensity (96.4%, 78.4, 83.1, 84.4, and 92.0, respectively) 300–531 days after the augmentation were generally improved after bioaugmentation. The denitrification linked to T-N removal appeared to contribute to the concomitant COD removal that triggered a reduction of sludge (up to 22%) in the same period of augmentation. Azo dye and aromatic compound degradation and other downstream pathways were highly metabolically interrelated. Augmentation of CES-1 increased microbial diversity in the later stages of augmentation when a strong microbial community selection of Acinetobacter parvus, Acinetobacter johnsonii, Marinobacter manganoxydans, Verminephrobacter sp., and Arcobacter sp. occurred. Herein, there might be a possibility that the CES-1 augmentation could facilitate the indigenous microbial community successions so that the selected communities made the augmentation successful. The metagenomic analysis turned out to be a reasonable and powerful tool to provide with new insights and useful biomarkers for the complex environmental conditions, such as the full scale dye wastewater treatment system undergoing bioaugmentation.

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.

We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderia aspalathi, Paraburkholderia madseniana, Paraburkholderia sediminicola, Paraburkholderia caffeinilytica, Paraburkholderia solitsugae and Paraburkholderia elongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA–DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.

Articles of Significant Interest in This Issue

Solvent-tolerant bacteria constitute promising platforms for biobased production of aromatic compounds and biopolymer building blocks. In Pseudomonas putida, solvent tolerance is associated with megaplasmids carrying solvent pumps and aromatic degradation pathways. Kusumawardhani et al. (e00041-21) succeeded in restoring solvent tolerance in P. putida S12 lacking its megaplasmid, by using adaptive laboratory evolution (ALE). Availability of a promiscuous resistance-nodulation-division (RND) extrusion pump, combined with metabolic flexibility, proved essential. This work underscores the importance of ALE as a tool to identify targets for strain optimization in general and to enhance solvent tolerance in P. putida and in other non-solvent-tolerant bacteria.

Anaerobic reactor applied to laundry wastewater treatment: Unveiling the microbial community by gene and genome-centric approaches

Gene and genome-centric approaches were applied to investigate the microbial taxonomic and metabolic diversity profiles from a lab-scale anaerobic reactor applied to laundry wastewater treatment with increasing concentrations of linear alkylbenzene sulfonate (LAS). Therefore, metagenomic analysis was carried out with reactor samples collected under three conditions, (i) Stage I, the reactor was fed with synthetic medium, (ii) Stage II, synthetic medium was replaced by diluted laundry wastewater with specific LAS loading rates (SLLRs) of 1.0 ± 0.3 mgLASgTVS−1d−1 and (iii) Stage III, SLLRs increased to 2.7 ± 0.7 mgLASgTVS−1d−1. Shotgun metagenomic sequencing was performed on an Illumina HiSeq 2 × 150 bp platform. Gene-centric analysis of each step of the metabolic pathway (fumarate addition, β-oxidation, ring cleavage and desulfonation) for anaerobic aromatic degradation showed eight over-representative genera (Achromobacter, Pelodictyon, Pseudomonas, Psychrobacter, Rhodococcus, Stenotrophomonas, Sulfurovum and Syntrophobacter), suggesting a microbial core with an important role in LAS biodegradation. Some of these genera were also recovered through a differential binning method, representing fifteen bacterial and one archaeal metagenome-assembled genomes (MAGs). Biodegradation pathway reconstruction of LAS using six MAGs unveiled the syntrophism for complete degradation of the LAS molecule. Only the MAGs with taxonomic annotation for Syntrophobacter showed genetic potential for fumarate addition, whereas in the ring cleavage, there was a predominance of genes in MAGs with taxonomic annotation for Pseudomonas fragi and Rhodococcus. This work represents the first report of genome-centric approach to study biological reactors applied in anionic surfactant degradation, contributing with detailed metabolic information of the key microbial actors in LAS degradation and opening perspectives for future biotechnological strategies aiming at bioaugmentation and/or biostimulation of indigenous microbial populations.

Genomic analysis of Burkholderia sp. ISTR5 for biofunneling of lignin-derived compounds

BackgroundLignin is the second most abundant natural polymer on earth. Industries using lignocellulosic biomass as feedstock generate a considerable amount of lignin as a byproduct with minimal usage. For a sustainable biorefinery, the lignin must be utilized in improved ways. Lignin is recalcitrant to degradation due to the complex and heterogeneous structure. The depolymerization of lignin and its conversion into specific product stream are the major challenges associated with lignin valorization. The blend of oligomeric, dimeric and monomeric lignin-derived compounds (LDCs) generated during depolymerization can be utilized by microbes for production of bioproducts.ResultsIn the present study, a novel bacterium Burkholderia sp. strain ISTR5 (R5), a proteobacteria belonging to class betaproteobacteria, order Burkholderiales and family Burkholderiaceae, was isolated and characterized for the degradation of LDCs. R5 strain was cultured on 12 LDCs in mineral salt medium (MSM) supplemented with individual compounds such as syringic acid, p-coumaric acid, ferulic acid, vanillin, vanillic acid, guaiacol, 4-hydroxybenzoic acid, gallic acid, benzoic acid, syringaldehyde, veratryl alcohol and catechol. R5 was able to grow and utilize all the selected LDCs. The degradation of selected LDCs was monitored by bacterial growth, total organic carbon (TOC) removal and UV–Vis absorption spectra in scan mode. TOC reduction shown in the sample contains syringic acid 80.7%, ferulic acid 84.1%, p-coumaric acid 85.9% and benzoic acid 83.2%. In UV–Vis absorption spectral scan, most of the lignin-associated peaks were found at or near 280 nm wavelength in the obtained absorption spectra. Enzyme assay for the ligninolytic enzymes was also performed, and it was observed that lignin peroxidase and laccase were predominantly expressed. Furthermore, the GC–MS analysis of LDCs was performed to identify the degradation intermediates from these compounds. The genomic analysis showed the robustness of this strain and identified various candidate genes responsible for the degradation of aromatic or lignin derivatives, detoxification mechanism, oxidative stress response and fatty acid synthesis. The presence of peroxidases (13%), laccases (4%), monooxygenases (23%), dioxygenase (44%), NADPH: quinone oxidoreductases (16%) and many other related enzymes supported the degradation of LDCs.ConclusionNumerous pathway intermediates were observed during experiment. Vanillin was found during growth on syringic acid, ferulic acid and p-coumaric acid. Some other intermediates like catechol, acetovanillone, syringaldehyde and 3,4-dihydroxybenzaldehyde from the recognized bacterial metabolic pathways existed during growth on the LDCs. The ortho- and meta cleavage pathway enzymes, such as the catechol-1,2-dioxygenase, protocatechuate 3,4-dioxygenase, catechol-2,3-dioxygenase and toluene-2,3-dioxygenase, were observed in the genome. In addition to the common aromatic degradation pathways, presence of the epoxyqueuosine reductase, 1,2-epoxyphenylacetyl-CoA isomerase in the genome advocates that this strain may follow the epoxy Coenzyme A thioester pathway for degradation.