Enzymes involved in the anaerobic degradation of phenol by the sulfate-reducing bacterium Desulfatiglans anilini

Biodegradation of phenolic pollutants and bioaugmentation strategies: A review of current knowledge and future perspectives

The widespread use of phenolic compounds renders their occurrence in various environmental matrices, posing ecological risks especially the endocrine disruption effects. Biodegradation-based techniques are efficient and cost-effective in degrading phenolic pollutants with less production of secondary pollution. This review focuses on phenol, 4-nonylphenol, 4-nitrophenol, bisphenol A and tetrabromobisphenol A as the representatives, and summarizes the current knowledge and future perspectives of their biodegradation and the enhancement strategy of bioaugmentation. Biodegradation and isolation of degrading microorganisms were mainly investigated under oxic conditions, where phenolic pollutants are typically hydroxylated to 4-hydroxybenzoate or hydroquinone prior to ring opening. Bioaugmentation efficiencies of phenolic pollutants significantly vary under different application conditions (e.g., increased degradation by 10-95% in soil and sediment). To optimize degradation of phenolic pollutants in different matrices, the factors that influence biodegradation capacity of microorganisms and performance of bioaugmentation are discussed. The use of immobilization strategy, indigenous degrading bacteria, and highly competent exogenous bacteria are proposed to facilitate the bioaugmentation process. Further studies are suggested to illustrate 1) biodegradation of phenolic pollutants under anoxic conditions, 2) application of microbial consortia with synergistic effects for phenolic pollutant degradation, and 3) assessment on the uncertain ecological risks associated with bioaugmentation, resulting from changes in degradation pathway of phenolic pollutants and alterations in structure and function of indigenous microbial community.

Modern Strategies for Carbon Isotope Exchange

In contrast to stable and natural abundant carbon-12, the synthesis of organic molecules with carbon (radio)isotopes must be conceived and optimized in order to navigate through the hurdles of radiochemical requirements, such as high costs of the starting materials, harsh conditions and radioactive waste generation. In addition, it must initiate from the small cohort of available C-labeled building blocks. For long time, multi-step approaches have represented the sole available patterns. On the other side, the development of chemical reactions based on the reversible cleavage of C-C bonds might offer new opportunities and reshape retrosynthetic analysis in radiosynthesis. This review aims to provide a short survey on the recently emerged carbon isotope exchange technologies that provide effective opportunity for late-stage labeling. At present, such strategies have relied on the use of primary and easily accessible radiolabeled C1-building blocks, such as carbon dioxide, carbon monoxide and cyanides, while the activation principles have been based on thermal, photocatalytic, metal-catalyzed and biocatalytic processes.

Recent Advances in Biotechnologies for the Treatment of Environmental Pollutants Based on Reactive Sulfur Species

The definition of reactive sulfur species (RSS) is inspired by the reactivity and variable chemical valence of sulfur. Sulfur is an essential element for life and is a part of global geochemical cycles. Wastewater treatment bioreactors can be divided into two major categories: sulfur reduction and sulfur oxidation. We review the origins of the definition of RSS and related biotechnological processes in environmental management. Sulfate reduction, sulfide oxidation, and sulfur-based redox reactions are key to driving the coupled global carbon, nitrogen, and sulfur co-cycles. This shows the coupling of the sulfur cycle with the carbon and nitrogen cycles and provides insights into the global material-chemical cycle. We also review the biological classification and RSS metabolic mechanisms of functional microorganisms involved in the biological processes, such as sulfate-reducing and sulfur-oxidizing bacteria. Developments in molecular biology and genomic technologies have allowed us to obtain detailed information on these bacteria. The importance of RSS in environmental technologies requires further consideration.

Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico

Mangroves are unique coastal ecosystems, which have many important ecological functions, as they are a reservoir of many marine species well adapted to saline conditions and are fundamental as sites of carbon storage. Although the microbial contribution to nutrient cycling in these ecosystems has been well recognized, there is a lack of information regarding the microbial composition and structure of different ecological types of mangrove forests. In this study, we characterized the microbial community (Bacteria and Archaea) in sediments associated with five ecological types of mangrove forests in a coastal lagoon dominated by Avicennia germinans and Rhizophora mangle, through 16S rRNA-V4 gene sequencing. Overall, Proteobacteria (51%), Chloroflexi (12%), Gemmatimonadetes (5%) and Planctomycetes (6%) were the most abundant bacterial phyla, while Thaumarchaeota (30%), Bathyarchaeota (21%) and Nanoarchaeaeota (18%) were the dominant archaeal phyla. The microbial composition associated with basin mangroves dominated by Avicennia germinans was significantly different from the other ecological types, which becomes relevant for restoration strategies.

Bacterial catabolism of acetovanillone, a lignin-derived compound

Upgrading lignin, an underutilized component of biomass, is essential for sustainable biorefining. Biocatalysis has considerable potential for upgrading lignin, but our lack of knowledge of relevant enzymes and pathways has limited its application. Herein, we describe a microbial pathway that catabolizes acetovanillone, a major component of several industrial lignin streams. This pathway is unusual in that it involves phosphorylation and carboxylation before conversion to the intermediate, vanillate, which is degraded via the β-ketoadipate pathway. Importantly, the hydroxyphenylethanone catabolic pathway enables bacterial growth on softwood lignin pretreated by oxidative catalytic fractionation. Overall, these insights greatly facilitate the engineering of bacteria to biocatalytically upgrade lignin.

Bacterial catabolic pathways have considerable potential as industrial biocatalysts for the valorization of lignin, a major component of plant-derived biomass. Here, we describe a pathway responsible for the catabolism of acetovanillone, a major component of several industrial lignin streams. Rhodococcus rhodochrous GD02 was previously isolated for growth on acetovanillone. A high-quality genome sequence of GD02 was generated. Transcriptomic analyses revealed a cluster of eight genes up-regulated during growth on acetovanillone and 4-hydroxyacetophenone, as well as a two-gene cluster up-regulated during growth on acetophenone. Bioinformatic analyses predicted that the hydroxyphenylethanone (Hpe) pathway proceeds via phosphorylation and carboxylation, before β-elimination yields vanillate from acetovanillone or 4-hydroxybenzoate from 4-hydroxyacetophenone. Consistent with this prediction, the kinase, HpeHI, phosphorylated acetovanillone and 4-hydroxyacetophenone. Furthermore, HpeCBA, a biotin-dependent enzyme, catalyzed the ATP-dependent carboxylation of 4-phospho-acetovanillone but not acetovanillone. The carboxylase’s specificity for 4-phospho-acetophenone (k_cat/K_M = 34 ± 2 mM⁻¹ s⁻¹) was approximately an order of magnitude higher than for 4-phospho-acetovanillone. HpeD catalyzed the efficient dephosphorylation of the carboxylated products. GD02 grew on a preparation of pine lignin produced by oxidative catalytic fractionation, depleting all of the acetovanillone, vanillin, and vanillate. Genomic and metagenomic searches indicated that the Hpe pathway occurs in a relatively small number of bacteria. This study facilitates the design of bacterial strains for biocatalytic applications by identifying a pathway for the degradation of acetovanillone.

Enhancement effects of decabromodiphenyl ether on microbial sulfate reduction in eutrophic lake sediments: A study on sulfate-reducing bacteria using dsrA and dsrB amplicon sequencing

Although sulfate (SO₄^2-) reduction by sulfate-reducing bacteria (SRB) is an important sulfur cycling processes, little is known about how the persistent organic pollutants affect the SO₄^2- reduction process in the eutrophic lake sediments. Here, we carried out a 120-day microcosm experiment to explore the effects of decabromodiphenyl ether (BDE-209) on SO₄^2- reduction mediated by SRB in sediment collected from Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination significantly enhanced the activity of dissimilatory sulfite reductase (DSR) (r = 0.83), which led to an increased concentration of sulfide produced by SO₄^2- reduction. This stimulatory effect of BDE-209 on DSR activity was closely related to variations in the dsrA- and dsrB-type SRB communities. The abundances and diversities of the dsrA- and dsrB-containing SRB increased and their community composition varied in response to BDE-209 contamination. The gene copies (r = 0.72), Chao 1 (r = 0.50), Shannon (r = 0.55), and Simpson (r = 0.70) indices of dsrB-containing SRB was positively correlated with BDE-209 contamination. Co-occurrence network analysis revealed that network complexity, connectivity, and the interspecific cooperative relationship in SRB were strengthened by BDE-209 contamination. The keystone species identified in the SRB community mainly belonged to the genera Candidatus Sulfopaludibacter for the dsrA-containing SRB and Desulfatiglans for the dsrB-containing SRB, and their relative abundances were positively correlated with DSR activity in the sediment. The relative abundance of the keystone species and SRB diversity were important microbial factors directly contributing to the variations in DSR activity based on structural equation modeling analysis. Notably, the results of abundance, community structure, and interspecific relationships showed that the dsrB-containing SRB may be more sensitive to the BDE-209 contamination than the dsrA-containing SRB. These results will help us understand the effects of BDE-209 on microbial sulfate reduction in eutrophic lakes.

Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea

DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play.

Due to their unique metabolism and important ecological roles, deep-sea hydrothermal archaea have attracted great scientific interest. Among these archaea, DPANN superphylum archaea are widely distributed in hydrothermal vent environments. However, DPANN metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes among 43 reconstructed genomes obtained from deep-sea hydrothermal vent sediments. Phylogenetic analysis suggests 6 phyla, comprised of Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum we have designated Kexuearchaeota. These are included in the 20 DPANN archaeal members, indicating their broad diversity in this special environment. Analyses of their metabolism reveal deficiencies due to their reduced genome size, including gluconeogenesis and de novo nucleotide and amino acid biosynthesis. However, DPANN archaea possess alternate strategies to address these deficiencies. DPANN archaea also have the potential to assimilate nitrogen and sulfur compounds, indicating an important ecological role in the hydrothermal vent system.

IMPORTANCE DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. In this study, we obtained 20 high-quality metagenome-assembled genomes (MAGs) corresponding to 6 phyla of the DPANN group (Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum designated Kexuearchaeota). Further metagenomic analyses provided insights on the metabolism and ecological functions of DPANN archaea to adapt to deep-sea hydrothermal environments. Our study contributes to a deeper understanding of their special lifestyles and should provide clues to cultivate this important archaeal group in the future.

Influence of metallic species for efficient photocatalytic water disinfection: bactericidal mechanism of in vitro results using docking simulation

TiO₂-based heterogeneous photocatalysis systems have been reported with remarkable efficiency to decontaminate and mineralize a range of pollutants present in air and water medium. In the present study, a series of visible light active metal oxide TiO₂ nanoparticle were synthesized and evaluated for their photodegradation efficiency against emerging textile pollutant (Reactive Yellow 145) and antibacterial applications. In the first phase, nanomaterial synthesis was carried out following various synthesis parameters like addition of metallic impurities (different types and concentration) and calcination temperature. In the second phase, synthesized nanomaterials were screened for their performance in terms of photocatalytic degradation of RY145 and the best one (Fe-1-T-3 with 100% RY145 removal within 80 min of irradiation) was further optimized against various reaction parameters. To get knowledge about the insights of nanomaterial performance for degradation of different environmental pollutants, the most important is to understand their physicochemical properties utilizing different characterization techniques. The physical morphology and elemental dispersion of metal-doped TiO₂ nanomaterials were analyzed and results indicated that added metallic impurities were well dispersed onto the substrate surface. The efficient nanomaterials selected from initial screening were further assessed for photocatalytic disinfection efficiency against human pathogenic bacterial strains. Antimicrobial activities of the metal oxide nanomaterial were tested against gram-positive and gram-negative pathogenic bacterial strains. Possible mode of interaction of nanomaterial with bacterial DNA for bacterial cell inactivation was predicted using molecular docking simulation. The research project has the potential to contribute to multiple disciplines like material synthesis, water disinfection, and as green solutions for the textile industry replacing traditional technologies.

Desulfatiglans anilini Initiates Degradation of Aniline With the Production of Phenylphosphoamidate and 4-Aminobenzoate as Intermediates Through Synthases and Carboxylases From Different Gene Clusters

The anaerobic degradation of aniline was studied in the sulfate-reducing bacterium Desulfatiglans anilini. Our aim was to identify the genes and their proteins that are required for the initial activation of aniline as well as to characterize intermediates of this reaction. Aniline-induced genes were revealed by comparison of the proteomes of D. anilini grown with different substrates (aniline, 4-aminobenzoate, phenol, and benzoate). Most genes encoding proteins that were highly abundant in aniline- or 4-aminobenzoate-grown D. anilini cells but not in phenol- or benzoate-grown cells were located in the putative gene clusters ani (aniline degradation), hcr (4-hydroxybenzoyl-CoA reductase) and phe (phenol degradation). Of these putative gene clusters, only the phe gene cluster has been studied previously. Based on the differential proteome analysis, four candidate genes coding for kinase subunits and carboxylase subunits were suspected to be responsible for the initial conversion of aniline to 4-aminobenzoate. These genes were cloned and overproduced in E. coli. The recombinant proteins were obtained in inclusion bodies but could be refolded successfully. Two subunits of phenylphosphoamidate synthase and two carboxylase subunits converted aniline to 4-aminobenzoate with phenylphosphoamidate as intermediate under consumption of ATP. Only when both carboxylase subunits, one from gene cluster ani and the other from gene cluster phe, were combined, phenylphosphoamidate was converted to 4-aminobenzoate in vitro, with Mn²⁺, K⁺, and FMN as co-factors. Thus, aniline is degraded by the anaerobic bacterium D. anilini only by recruiting genes for the enzymatic machinery from different gene clusters. We conclude, that D. anilini carboxylates aniline to 4-aminobenzoate via phenylphosphoamidate as an energy rich intermediate analogous to the degradation of phenol to 4-hydroxybenzoate via phenylphosphate.

Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations

Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.

Enhanced aniline degradation by Desulfatiglans anilini in a synthetic microbial community with the phototrophic purple sulfur bacterium Thiocapsa roseopersicina

Desulfatiglans anilini is a sulfate-reducing bacterium (SRB) capable of oxidizing aniline, although growth and aniline turnover rates are slow, making it difficult to analyze the metabolism of the strain. Therefore, this study was designed to investigate the effect of sulfide on growth of D. anilini cultures, in order to improve its growth and aniline turnover rates, and study the biochemical mechanisms of sulfide inhibition. Hydrogen sulfide was found to inhibit growth of D. anilini, regardless of whether the strain was grown with aniline or phenol, and complete inhibition was observed at 20mM hydrogen sulfide. For improving the growth of D. anilini with aniline, the sulfide-consuming phototrophic bacterium Thiocapsa roseopersicina was co-cultured in a synthetic microbial community with D. anilini using a co-cultivation device that continuously removed hydrogen sulfide from the culture. The doubling time of D. anilini with aniline was 15 days in the co-cultivation device, compared to 26 days in the absence of a sulfide-oxidizing partner. Moreover, the aniline degradation rate was significantly increased by a factor of 2.66 during co-cultivation of D. anilini with T. roseopersicina. The initial carboxylation reaction during aniline degradation was measured in cell-free extracts of D. anilini with carbon dioxide (CO₂) as a co-substrate in the presence of aniline and ATP. The effects of hydrogen sulfide on this aniline carboxylating system and on phenylphosphate synthase activity for phenol activation were studied, and it was concluded that hydrogen sulfide severely inhibited these enzyme activities.

Carboxylation of Hydroxyaromatic Compounds with HCO3− by Enzyme Catalysis: Recent Advances Open the Perspective for Valorization of Lignin-Derived Aromatics

This review focuses on recent advances in the field of enzymatic carboxylation reactions of hydroxyaromatic compounds using HCO3− (as a CO2 source) to produce hydroxybenzoic and other phenolic acids in mild conditions with high selectivity and moderate to excellent yield. Nature offers an extensive portfolio of enzymes catalysing reversible decarboxylation of hydroxyaromatic acids, whose equilibrium can be pushed towards the side of the carboxylated products. Extensive structural and mutagenesis studies have allowed recent advances in the understanding of the reaction mechanism of decarboxylase enzymes, ultimately enabling an improved yield and expansion of the scope of the reaction. The topic is of particular relevance today as the scope of the carboxylation reactions can be extended to include lignin-related compounds in view of developing lignin biorefinery technology.