Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases

The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.

Meta-omics assisted microbial gene and strain resources mining in contaminant environment

Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.

Changes in Lolium perenne L. rhizosphere microbiome during phytoremediation of Cd- and Hg-contaminated soils

The contamination of soil and water by metals such as mercury (Hg) and cadmium (Cd) has been increasing in recent years, because of anthropogenic activities such as mining and agriculture, respectively. In this work, the changes in the rhizosphere microbiome of Lolium perenne L. during the phytoremediation of soils contaminated with Hg and Cd were evaluated. For this, two soil types were sampled, one inoculated with mycorrhizae and one without. The soils were contaminated with Hg and Cd, and L. perenne seeds were sown and harvested after 30 days. To assess changes in the microbiome, DNA isolation tests were performed, for which samples were subjected to two-step PCR amplification with specific 16S rDNA V3-V4 primers (337F and 805R). With mycorrhizae, changes had been found in the absorption processes of metals and a new distribution. While with respect to microorganisms, families such as the Enterobacteriaceae have been shown to have biosorption and efflux effects on metals such as Hg and Cd. Mycorrhizae then improve the efficiency of removal and allow the plant to better distribute the absorbed concentrations. Overall, L. perenne is a species with a high potential for phytoremediation of Cd- and Hg-contaminated soils in the tropics. Inoculation with mycorrhizae modifies the phytoremediation mechanisms of the plant and the composition of microorganisms in the rhizosphere. Mycorrhizal inoculation and changes in the microbiome were associated with increased plant tolerance to Cd and Hg. Microorganism-assisted phytoremediation is an appropriate alternative for L. perenne.

Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics

The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.

Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation

Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) by gene-targeted metagenomic and qPCR analysis. Overall, PAHs species significantly affected the composition and abundance of pahE gene within the PAHs-degrading bacteria in each treatment and different pahE of PAHs-degrading bacteria involved in the different stages of PAHs degradation. Noted that new pahE genotypes were also discovered in all PAHs treatment groups, indicating that some potential new PAHs-degrading bacterial genera were also involved in PAHs degradation. Besides, all three PAH removal rates were significantly positively related with pahE gene abundances (R² = 0.908 ~ 0.922, p < 0.01), demonstrating that pahE could be a good indicator of PAHs degradation activity or potential. This is the first study focusing on the dynamic changes of the pahE gene within PAHs-degrading bacterial community during the degradation of PAHs in mangrove sediment, providing novel insights into the use of pahE gene as the functional marker to indicate PAH degradation.

DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation

Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.

Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2-17

A new bacterium, Rhodococcus sp. S2-17, which could completely degrade an emerging organic pollutant, benzophenone-3 (BP-3), was isolated from contaminated sediment through an enrichment procedure, and its BP-3 catabolic pathway and genes were identified through metabolic intermediate and transcriptomic analyses and biochemical and genetic studies. Metabolic intermediate analysis suggested that strain S2-17 may degrade BP-3 using a catabolic pathway progressing via the intermediates BP-1, 2,4,5-trihydroxy-benzophenone, 3-hydroxy-4-benzoyl-2,4-hexadienedioic acid, 4-benzoyl-3-oxoadipic acid, 3-oxoadipic acid, and benzoic acid. A putative BP-3 catabolic gene cluster including cytochrome P450, flavin-dependent oxidoreductase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, and α/β hydrolase genes was identified through genomic and transcriptomic analyses. Genes encoding the cytochrome P450 complex that demethylates BP-3 to BP-1 were functionally verified through protein expression, and the functions of the other genes were also verified through knockout mutant construction and intermediate analysis. This study suggested that strain S2-17 might have acquired the ability to catabolize BP-3 by recruiting the cytochrome P450 complex and α/β hydrolase, which hydrolyzes 4-benzoyl-3-oxoadipic acid to benzoic acid and 3-oxoadipic acid, genes, providing insights into the recruitment of genes of for the catabolism of emerging organic pollutants.

Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone

In this study, the diversity of bphA genes was assessed in a ¹³C-enriched metagenome upon stable isotope probing (SIP) of microbial populations in legacy PCB-contaminated soil with ¹³C-biphenyl (BP). In total, 13 bphA sequence variants (SVs) were identified in the final amplicon dataset. Of these, one SV comprised 59% of all sequences, and when it was translated into a protein sequence, it exhibited 87, 77.4, and 76.7% identity to its homologs from Pseudomonas furukawaii KF707, Cupriavidus sp. WS, and Pseudomonas alcaliphila B-367, respectively. This same BphA sequence also contained unusual amino acid residues, Alanine, Valine, and Serine in region III, which had been reported to be crucial for the substrate specificity of the corresponding biphenyl dioxygenase (BPDO), and was accordingly designated BphA_AVS. The DNA locus of 18 kbp containing the BphA_AVS-coding sequence retrieved from the metagenome was comprised of 16 ORFs and was most likely borne by Paraburkholderia sp. The BPDO corresponding to bphAE_AVS was cloned and heterologously expressed in E. coli, and its substrate specificity toward PCBs and a spectrum of flavonoids was assessed. Although depleting a rather narrow spectrum of PCB congeners, the efficient transformation of flavone and flavanone was demonstrated through dihydroxylation of the B-ring of the molecules. The homology-based functional assignment of the putative proteins encoded by the rest of ORFs in the AVS region suggests their potential involvement in the transformation of aromatic compounds, such as flavonoids. In conclusion, this study contributes to the body of information on the involvement of soil-borne BPDOs in the metabolism of flavonoid compounds, and our paper provides a more advanced context for understanding the interactions between plants, microbes and anthropogenic compounds in the soil.

A large-scale metagenomic study for enzyme profiles using the focused identification of the NGS-based definitive enzyme research (FINDER) strategy

Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of 'focused identification of next-generation sequencing-based definitive enzyme research' enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples.

'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions

An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.

Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria

An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.

A brief guide for the measurement and interpretation of microbial functional diversity

The importance of functional diversity for the functioning and behaviour of microbial communities is clear, yet the widespread incorporation of functional diversity measurements into environmental microbiology study designs remains surprisingly limited. This may, at least to some extent, be a consequence of the unique conceptual and methodological challenges to measuring functional diversity in microbial communities. To facilitate the increased incorporation of functional diversity measurements into environmental microbiology study designs, we review here the process and some key caveats for measuring functional diversity and provide specific examples. We highlight three main decision points and provide guidance to making these decisions based on the underlying mechanisms for how functional diversity relates to an ecosystem process or property of interest. We discuss the selection of an appropriate type of functional trait, selection of the specificity at which functional diversity will be measured, and selection of an appropriate metric for estimating functional diversity from quantitative measures of those traits. We further discuss decisions regarding the use of one- or multi-dimensional measures of functional diversity and how advances in the field of trait-based community ecology could be applied or adapted to address questions in environmental microbiology.

Comparative Genomics of the Rhodococcus Genus Shows Wide Distribution of Biodegradation Traits

The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.

Rhizoremediation of weathered PCBs in a heavily contaminated agricultural soil: Results of a biostimulation trial in semi field conditions

This paper describes the results of a rhizoremediation greenhouse experiment planned to select the best plant species and soil management for the bioremediation of weathered polychlorinated biphenyls (PCBs). We evaluated the ability of different plant species to stimulate activity and diversity of the soil microbial community leading to the reduction of PCB concentrations in a heavily contaminated soil (at mg kg-1 dw level), of the national priority site for remediation (SIN) "Brescia-Caffaro" in Italy. Biostimulation was determined in large size (6kg) pots, to reflect semi-field conditions with a soil/root volume ratio larger than in most rhizoremediation experiments present in the literature. In total, 10 treatments were tested in triplicates comparing 7 plant species (grass and trees) and 5 soil/cultivation conditions (i.e., only one plant species, plant consociation, redox cycle, compost or ammonium thiosulfate addition) with the appropriate unplanted controls. After 18months of biostimulation the overall reduction of total PCBs varied between 14 and 20%. Microbial analysis revealed a shift in the microbial community structure over time and showed that all the planted treatments significantly enhanced microbial hydrolytic activity and the abundance of bacterial populations, including potential PCB degraders, in the soil surrounding plant roots. The plant species most effective in reducing the contaminant concentrations were Festuca arundinacea cultivated adding compost or in consociation with Cucurbita pepo ssp. pepo and Medicago sativa cultivated with Rhizobium spp. and mycorrhizal fungi; they reduced total PCB concentrations of about 20% and showed the significant depletion of a high number of PCB congeners (29, 37 and 23, respectively, out of the 79 measured). Our results suggest that these plant species are particularly efficient in increasing soil PCB bioavailability and in stimulating microbial degradation. They could be used in field rhizoremediation strategies to enhance the natural attenuation process and reduce PCB levels in historically contaminated sites.

Novel PCB-degrading Rhodococcus strains able to promote plant growth for assisted rhizoremediation of historically polluted soils

Extended soil contamination by polychlorinated biphenyls (PCBs) represents a global environmental issue that can hardly be addressed with the conventional remediation treatments. Rhizoremediation is a sustainable alternative, exploiting plants to stimulate in situ the degradative bacterial communities naturally occurring in historically polluted areas. This approach can be enhanced by the use of bacterial strains that combine PCB degradation potential with the ability to promote plant and root development. With this aim, we established a collection of aerobic bacteria isolated from the soil of the highly PCB-polluted site “SIN Brescia-Caffaro” (Italy) biostimulated by the plant Phalaris arundinacea. The strains, selected on biphenyl and plant secondary metabolites provided as unique carbon source, were largely dominated by Actinobacteria and a significant number showed traits of interest for remediation, harbouring genes homologous to bphA, involved in the PCB oxidation pathway, and displaying 2,3-catechol dioxygenase activity and emulsification properties. Several strains also showed the potential to alleviate plant stress through 1-aminocyclopropane-1-carboxylate deaminase activity. In particular, we identified three Rhodococcus strains able to degrade in vitro several PCB congeners and to promote lateral root emergence in the model plant Arabidopsis thaliana in vivo. In addition, these strains showed the capacity to colonize the root system and to increase the plant biomass in PCB contaminated soil, making them ideal candidates to sustain microbial-assisted PCB rhizoremediation through a bioaugmentation approach.

Recombinant production and characterization of a novel esterase from a hypersaline lake, Acıgöl, by metagenomic approach

The aim of this study was to isolate a novel esterase from a hypersaline lake by sequence-based metagenomics. The metagenomic DNA was isolated from the enriched hypersaline lake sediment. Degenerate primers targeting the conserved regions of lipolytic enzymes of halophilic microorganisms were used for polymerase chain reaction (PCR) and a whole gene was identified by genome walking. The gene was composed of 783 bp, which corresponds to 260 amino acids with a molecular weight of 28.2 kDa. The deduced amino acid sequence best matched with the esterase from Halomonas gudaonensis with an identity of 91%. Recombinantly expressed enzyme exhibited maximum activity towards pNP-hexanoate with a k_cat value of 12.30 s^-1. The optimum pH and temperature of the enzyme were found as 9 and 30 °C, respectively. The effects of NaCl, solvents, metal ions, detergents and enzyme inhibitors were also studied. In conclusion, a novel enzyme, named as hypersaline lake "Acıgöl" esterase (hAGEst), was identified by sequence-based metagenomics. The high expression level, the ability to maintain activity at cold temperatures and tolerance to DMSO and metal ions are the most outstanding properties of the hAGEst.

pahE, a Functional Marker Gene for Polycyclic Aromatic Hydrocarbon-Degrading Bacteria

The characterization of native polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is significant for understanding the PAH degradation process in the natural environment and developing effective remediation technologies. Most previous investigations of PAH-degrading bacteria in environmental samples employ pahAc, which encodes the α-subunit of PAH ring-hydroxylating dioxygenase, as a functional marker gene. However, the poor phylogenetic resolution and nonspecificity of pahAc result in a misestimation of PAH-degrading bacteria. Here, we propose a PAH hydratase-aldolase-encoding gene, pahE, as a superior biomarker for PAH-degrading bacteria. Comparative phylogenetic analysis of the key enzymes involved in the upper pathway of PAH degradation indicated that pahE evolved dependently from a common ancestor. A phylogenetic tree constructed based on PahE is largely congruent with PahAc-based phylogenies, except for the dispersion of several clades of other non-PAH-degrading aromatic hydrocarbon dioxygenases present in the PahAc tree. Analysis of pure strains by PCR confirmed that pahE can specifically distinguish PAH-degrading bacteria, while pahAc cannot. Illumina sequencing of pahE and pahAc amplicons showed more genotypes and higher specificity and resolution for pahE Novel reads were also discovered among the pahE amplicons, suggesting the presence of novel PAH-degrading populations. These results suggest that pahE is a more powerful biomarker for exploring the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution and environmental microbial ecology.IMPORTANCE PAH contamination has become a worldwide environmental issue because of the potential toxic effects on natural ecosystems and human health. Biotransformation and biodegradation are considered the main natural elimination forms of PAHs from contaminated sites. Therefore, the knowledge of the degradation potential of the microbial community in contaminated sites is crucial for PAH pollution bioremediation. However, the nonspecificity of pahAc as a functional marker of PAH-degrading bacteria has resulted neither in a reliable prediction of PAH degradation potential nor an accurate assessment of degradation. Here, we introduced pahE encoding the PAH hydratase-aldolase as a new and better functional marker gene of PAH-degrading bacteria. This study provides a powerful molecular tool to more effectively explore the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution.

Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics

PAH ring-hydroxylating dioxygenases (PAH-RHDα) gene, a useful biomarker for PAH-degrading bacteria, has been widely used to examine PAH-degrading bacterial community in different contaminated sites. However, the distribution of PAH-RHDα genes in oilfield soils and mangrove sediments and their relationship with environmental factors still remain largely unclear. In this study, gene-targeted metagenomics was first used to investigate the diversity of PAH-degrading bacterial communities in oilfield soils and mangrove sediments. The results showed that higher diversity of PAH-degrading bacteria in the studied samples was revealed by gene-targeted metagenomics than traditional clone library analysis. Pseudomonas, Burkholderia, Ralstonia, Polymorphum gilvum, Mycobacterium, Sciscionella marina, Rhodococcus, and potential new degraders were prevailed in the oilfield area. For mangrove sediments, novel PAH degraders and Mycobacterium were predominated. The spatial distribution of PAH-RHDα gene was dependent on geographical location and regulated by local environmental variables. PAH content played a key role in shaping PAH-degrading bacterial communities in the studied samples, which would enrich PAH-degrading bacterial population and decrease PAH-degrading bacterial diversity. This work brings a more comprehensive and some new insights into the distribution and biodegradation potential of PAH-degrading bacteria in soil and sediments ecosystems.

High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu

OBJECTIVE

To explore the diversity of glycoside hydrolase family 10 xylanase genes in the sediment of soda lake Dabusu by using high-throughput amplicon sequencing based on the Illumina HiSeq2500 platform.

RESULTS

A total of 227,420 clean reads, representing approximately 49.5 M bp, were obtained. Operational taxonomic unit (OTU) classification, with a 95% sequence identity cut-off, resulted in 467 OTUs with 392 annotated as GH10 xylanase, exhibiting 35-99% protein sequence identity with their closest-related xylanases in GenBank. Above 75% of the total OTUs demonstrated less than 80% identity with known xylanases. In addition, xylanases derived from the sediment were found to be affiliated to 12 different phyla, with Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and Basidiomycota being the dominant phyla. Moreover, barcode sequence had a major effect on abundance with only a minor effect on diversity.

CONCLUSIONS

High-throughput amplicon sequencing offers insight into xylanase gene diversity at a substantially higher resolution and lesser cost than library cloning and Sanger sequencing, facilitating a more thorough understanding of xylanase distribution and ecology.

Revisiting Polymorphic Diversity of Aminoglycoside N-Acetyltransferase AAC(6')-Ib Based on Bacterial Genomes of Human, Animal, and Environmental Origins

The prevalence of aac(6')-Ib variants has been demonstrated in numerous epidemiological studies. We revisited the polymorphic diversity of aminoglycoside 6'-N-acetyltransferase gene [aac(6')-Ib] in the bacterial genome databases based on One Health perspectives. aac(6')-Ib was searched against bacterial complete and draft genome databases of NCBI. Based on the major polymorphic residues 102, 117, and 179, taxonomy, ecology, and temporal emergence of bacterial isolates harboring variants of aac(6')-Ib gene were evaluated using whole-genome sequences available in the databases. A total of 3,964 aac(6')-Ib sequences were found to be present in the genomes of 34 bacterial genera, mostly found in Gammaproteobacteria. Among these, aac(6')-Ib-cr variant, known to confer fluoroquinolone resistance, were increasingly detected in bacterial genomes and most abundant in the genera Klebsiella and Escherichia, thereby suggesting that these genera were the major reservoirs of the plasmid-mediated quinolone resistance (PMQR) determinant. The proportions of the cr variant were higher in animal and environmental isolates than in human isolates, among which the variant was dominant (>50%) in the genomes of intestinal, rectal, and fecal origins. In addition, our study suggested that the prevalence of the cr variant was associated with the occurrence of a variant with the mutation L117 (IbL). An integrated surveillance system for antimicrobial resistance in human, animal, and environmental sectors, based on whole-genome sequencing, would provide a better insight into the evolution, ecology, and epidemiology of antimicrobial-resistant bacteria.

The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil

Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.

Thermophilic bacteria are potential sources of novel Rieske non-heme iron oxygenases

Rieske non-heme iron oxygenases, which have a Rieske-type [2Fe-2S] cluster and a non-heme catalytic iron center, are an important family of oxidoreductases involved mainly in regio- and stereoselective transformation of a wide array of aromatic hydrocarbons. Though present in all domains of life, the most widely studied Rieske non-heme iron oxygenases are found in mesophilic bacteria. The present study explores the potential for isolating novel Rieske non-heme iron oxygenases from thermophilic sources. Browsing the entire bacterial genome database led to the identification of 45 homologs from thermophilic bacteria distributed mainly among Chloroflexi, Deinococcus-Thermus and Firmicutes. Thermostability, measured according to the aliphatic index, showed higher values for certain homologs compared with their mesophilic relatives. Prediction of substrate preferences indicated that a wide array of aromatic hydrocarbons could be transformed by most of the identified oxygenase homologs. Further identification of putative genes encoding components of a functional oxygenase system opens up the possibility of reconstituting functional thermophilic Rieske non-heme iron oxygenase systems with novel properties.

Polymorphism of antibiotic-inactivating enzyme driven by ecology expands the environmental resistome

The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment. Furthermore, ecologically dominant polymorphic variants of AAC(6')-Ib were characterized and found to display different substrate specificities for quinolones and aminoglycosides, conferring the altered resistance spectra. Interestingly, a novel variant with the D179Y substitution showed an extended resistance spectrum to the recently developed fluoroquinolone gemifloxacin. Our results suggest that soil and animal microbiomes could be major reservoirs of antibiotic resistance; polymorphic diversity expands the antibiotic resistome in the environment, resulting in the potential emergence of novel resistance.

Genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome

Catechol 1,2-dioxygenase is the key enzyme that catalyzes the cleavage of the aromatic ring of catechol. We explored the genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome by PCR with degenerate primers. A total of 35 gene fragments of C12O were retrieved from microbial DNA in the feces of pygmy loris. Based on phylogenetic analysis, most sequences were closely related to C12O sequences from Acinetobacter. A full-length C12O gene was directly cloned, heterologously expressed in Escherichia coli, and biochemically characterized. Purified catPL12 had optimum pH and temperature pH 8.0 and 25 °C and retained 31 and 50% of its maximum activity when assayed at 0 and 35 °C, respectively. The enzyme was stable at 25 and 37 °C, retaining 100% activity after pre-incubation for 1 h. The kinetic parameters of catPL12 were determined. The enzyme had apparent K_m of 67 µM, V_max of 7.3 U/mg, and k_cat of 4.2 s^-1 for catechol, and the cleavage activities for 3-methylcatechol, 4-methylcatechol, and 4-chlorocatechol were much less than for catechol, and no activity with hydroquinone or protocatechuate was detected. This study is the first to report the molecular and biochemical characterizations of a cold-adapted catechol 1,2-dioxygenase from a fecal microbial metagenome.

Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation

The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates according to in vitro assays. PGP tested in vivo on tomato plants using eleven selected bacterial isolates, confirmed the promotion and protection potential of the rhizosphere bacteria. Different spontaneous plant species naturally selected in a historical chronically polluted site showed to determine the enrichment of peculiar bacterial communities in the soil fractions associated to the roots. All the rhizosphere communities, nevertheless, hosted bacteria with degradation/detoxification and PGP potential, putatively sustaining the natural attenuation process.

Degradation of crude oil in a contaminated tidal flat area and the resilience of bacterial community

Crude oil spills, Hebei Spirit in South Korea, is considered as one of the worst environmental disasters of the region. Our understanding on activation of oil-degrading bacteria and resilience of microbial community in oil contaminated sites are limited due to scarcity of such event. In the present study, tidal flat sediment contaminated by the oil spill were investigated for duration of 13months to identify temporal change in microbial community and functional genes responsible for PAH-degradation. The results showed predominance of previously known oil-degrading genera, such as Cycloclasticus, Alcanivorax, and Thalassolituus, displaying significant increase within first four months of the accident. The disturbance caused by the oil spill altered the microbial community and its functional structures, but they were almost restored to the original state after 13months. Present study demonstrated high detoxification capacity of indigenous bacterial populations in the tidal flat sediments and its resilience of microbial community.

Phyto-rhizoremediation of polychlorinated biphenyl contaminated soils: An outlook on plant-microbe beneficial interactions

Polychlorinated biphenyls (PCBs) are toxic chemicals, recalcitrant to degradation, bioaccumulative and persistent in the environment, causing adverse effects on ecosystems and human health. For this reason, the remediation of PCB-contaminated soils is a primary issue to be addressed. Phytoremediation represents a promising tool for in situ soil remediation, since the available physico-chemical technologies have strong environmental and economic impacts. Plants can extract and metabolize several xenobiotics present in the soil, but their ability to uptake and mineralize PCBs is limited due to the recalcitrance and low bioavailability of these molecules that in turn impedes an efficient remediation of PCB-contaminated soils. Besides plant degradation ability, rhizoremediation takes into account the capability of soil microbes to uptake, attack and degrade pollutants, so it can be seen as the most suitable strategy to clean-up PCB-contaminated soils. Microbes are in fact the key players of PCB degradation, performed under both aerobic and anaerobic conditions. In the rhizosphere, microbes and plants positively interact. Microorganisms can promote plant growth under stressed conditions typical of polluted soils. Moreover, in this specific niche, root exudates play a pivotal role by promoting the biphenyl catabolic pathway, responsible for microbial oxidative PCB metabolism, and by improving the overall PCB degradation performance. Besides rhizospheric microbial community, also the endophytic bacteria are involved in pollutant degradation and represent a reservoir of microbial resources to be exploited for bioremediation purposes. Here, focusing on plant-microbe beneficial interactions, we propose a review of the available results on PCB removal from soil obtained combining different plant and microbial species, mainly under simplified conditions like greenhouse experiments. Furthermore, we discuss the potentiality of "omics" approaches to identify PCB-degrading microbes, an aspect of paramount importance to design rhizoremediation strategies working efficiently under different environmental conditions, pointing out the urgency to expand research investigations to field scale.

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.

Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants

Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.

Mining of Ruminant Microbial Phytase (RPHY1) from Metagenomic Data of Mehsani Buffalo Breed: Identification, Gene Cloning, and Characterization

Phytases have been widely used as animal feed supplements to increase the availability of digestible phosphorus, especially in monogastric animals fed cereal grains. The present study describes the identification of a full-length phytase gene of <i>Prevotella</i> species present in Mehsani buffalo rumen. The gene, designated as RPHY1, consists of 1,251 bp and is expressed into protein with 417 amino acids. A homology search of the deduced amino acid sequence of the RPHY1 phytase gene in a nonredundant protein database showed that it shares 92% similarity with the histidine acid phosphatase domain. Subsequently, the RPHY1 gene was expressed using a pET32a expression vector in <i>Escherichia coli </i>BL21 and purified using a His60 Ni-NTA gravity column. The mass of the purified RPHY1 was estimated to be approximately 63 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimal RPHY1 enzyme activity was observed at 55°C (pH 5) and exhibited good stability at 5°C and within the acidic pH range. Significant inhibition of RPHY1 activity was observed for Mg²⁺ and K⁺ metal ions, while Ca²⁺, Mn²⁺, and Na⁺ slightly inhibited enzyme activity. The RPHY1 phytase was susceptible to SDS, and it was highly stimulated in the presence of EDTA. Overall, the observed comparatively high enzyme activity levels and characteristics of the RPHY1 gene mined from rumen prove its promising candidature as a feed supplement enzyme in animal farming.

Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil

Aerobic mineralization of PCBs, which are toxic and persistent organic pollutants, involves the upper (biphenyl, BP) and lower (benzoate, BZ) degradation pathways. The activity of different members of the soil microbial community in performing one or both pathways, and their synergistic interactions during PCB biodegradation, are not well understood. This study investigates BP and BZ biodegradation and subsequent carbon flow through the microbial community in PCB-contaminated soil. DNA stable isotope probing (SIP) was used to identify the bacterial guilds involved in utilizing ¹³C-biphenyl (unchlorinated analogue of PCBs) and/or ¹³C-benzoate (product/intermediate of BP degradation and analogue of chlorobenzoates). By performing SIP with two substrates in parallel, we reveal microbes performing the upper (BP) and/or lower (BZ) degradation pathways, and heterotrophic bacteria involved indirectly in processing carbon derived from these substrates (i.e. through crossfeeding). Substrate mineralization rates and shifts in relative abundance of labeled taxa suggest that BP and BZ biotransformations were performed by microorganisms with different growth strategies: BZ-associated bacteria were fast growing, potentially copiotrophic organisms, while microbes that transform BP were oligotrophic, slower growing, organisms. Our findings provide novel insight into the functional interactions of soil bacteria active in processing biphenyl and related aromatic compounds in soil, revealing how carbon flows through a bacterial community.

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences

Functional gene ecological analyses using amplicon sequencing can be challenging as translated sequences are often burdened with shifted reading frames. The aim of this work was to evaluate several bioinformatics tools designed to correct errors which arise during sequencing in an effort to reduce the number of frameshifts (FS). Genes encoding for alpha subunits of biphenyl (bphA) and benzoate (benA) dioxygenases were used as model sequences. FrameBot, a FS correction tool, was able to reduce the number of detected FS to zero. However, up to 44% of sequences were discarded by FrameBot as non-specific targets. Therefore, we proposed a de novo mode of FrameBot for FS correction, which works on a similar basis as common chimera identifying platforms and is not dependent on reference sequences. By nature of FrameBot de novo design, it is crucial to provide it with data as error free as possible. We tested the ability of several publicly available correction tools to decrease the number of errors in the data sets. The combination of maximum expected error filtering and single linkage pre-clustering proved to be the most efficient read processing approach. Applying FrameBot de novo on the processed data enabled analysis of BphA sequences with minimal losses of potentially functional sequences not homologous to those previously known. This experiment also demonstrated the extensive diversity of dioxygenases in soil. A script which performs FrameBot de novo is presented in the supplementary material to the study or available at https://github.com/strejcem/FBdenovo. The tool was also implemented into FunGene Pipeline available at http://fungene.cme.msu.edu/FunGenePipeline/.

Marine metagenomics as a source for bioprospecting

This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.

Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology

The rapid expansion of new sequencing technologies has enabled large-scale functional exploration of numerous microbial ecosystems, by establishing catalogs of functional genes and by comparing their prevalence in various microbiota. However, sequence similarity does not necessarily reflect functional conservation, since just a few modifications in a gene sequence can have a strong impact on the activity and the specificity of the corresponding enzyme or the recognition for a sensor. Similarly, some microorganisms harbor certain identified functions yet do not have the expected related genes in their genome. Finally, there are simply too many protein families whose function is not yet known, even though they are highly abundant in certain ecosystems. In this context, the discovery of new protein functions, using either sequence-based or activity-based approaches, is of crucial importance for the discovery of new enzymes and for improving the quality of annotation in public databases. This paper lists and explores the latest advances in this field, along with the challenges to be addressed, particularly where microfluidic technologies are concerned.

The plant microbiome at work

Plants host distinct microbial communities on and inside their tissues designated the plant microbiota. Microbial community profiling enabled the description of the phylogenetic structure of the plant microbiota to an unprecedented depth, whereas functional insights are largely derived from experiments using individual microorganisms. The binary interplay between isolated members of the plant microbiota and host plants ranges from mutualistic to commensalistic and pathogenic relationships. However, how entire microbial communities capable of executing both growth-promoting and growth-compromising activities interfere with plant fitness remains largely unknown. Ultimately, unravelling the net result of microbial activities encoded in the extended plant genome-the plant microbiome-will be key to understanding and exploiting the full yield potential of a crop plant. In this perspective, we summarize first achievements of plant-microbiome research, we discuss future research directions, and we provide ideas for the translation of basic science to application to capitalize on the plant microbiome at work.

Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques

Society's reliance upon chemicals over the last few decades has led to their increased production, application and release into the environment. Determination of chemical persistence is crucial for risk assessment and management of chemicals. Current established OECD biodegradation guidelines enable testing of chemicals under laboratory conditions but with an incomplete consideration of factors that can impact on chemical persistence in the environment. The suite of OECD biodegradation tests do not characterise microbial inoculum and often provide little insight into pathways of degradation. The present review considers limitations with the current OECD biodegradation tests and highlights novel scientific approaches to chemical fate studies. We demonstrate how the incorporation of molecular microbial ecology methods (i.e., 'omics') may improve the underlying mechanistic understanding of biodegradation processes, and enable better extrapolation of data from laboratory based test systems to the relevant environment, which would potentially improve chemical risk assessment and decision making. We outline future challenges for relevant stakeholders to modernise OECD biodegradation tests and put the 'bio' back into biodegradation.

Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments

We present a method for the physical isolation of endospores from environmental samples allowing the specific targeting of endospore-forming bacteria for sequencing (endospore-enriched community). The efficiency of the method was tested on lake sediment samples. After 16S rRNA gene amplicon sequencing, the composition in the endospore-enriched community was compared with the community from untreated control samples (whole community). In the whole community, Firmicutes had a relative abundance of 8% and 19% in the two different lake sediments. In contrast, in the endospore-enriched community, Firmicutes abundance increased to 90.6% and 83.9%, respectively, confirming the efficiency of the endospore enrichment. The relative abundance of other microbial groups that form spore-like resisting states (i.e. actinobacteria, cyanobacteria and myxococcales) was below 2% in the endospore-enriched community, indicating that the method is adapted to true endospores. Representatives from two out of the three known classes of Firmicutes (Bacilli and Clostridia) were detected and supposedly asporogenic groups (e.g. Ethanoligenes and Trichococcus) could be detected. The method presented here is a leap forward for ecological studies of endospore-forming Firmicutes. It can be applied to other types of samples in order to reveal the diversity and metabolic potential of this bacterial group in the environment.

Efficient PCR-based amplification of diverse alcohol dehydrogenase genes from metagenomes for improving biocatalysis: screening of gene-specific amplicons from metagenomes

Screening of gene-specific amplicons from metagenomes (S-GAM) has tremendous biotechnological potential. We used this approach to isolate alcohol dehydrogenase (adh) genes from metagenomes based on the Leifsonia species adh gene (lsadh), the enzyme product of which can produce various chiral alcohols. A primer combination was synthesized by reference to homologs of lsadh, and PCR was used to amplify nearly full-length adh genes from metagenomic DNAs. All adh preparations were fused with lsadh at the terminal region and used to construct Escherichia coli plasmid libraries. Of the approximately 2,000 colonies obtained, 1,200 clones were identified as adh positive (∼60%). Finally, 40 adh genes, Hladh-001 to Hladh-040 (for homologous Leifsonia adh), were identified from 223 clones with high efficiency, which were randomly sequenced from the 1,200 clones. The Hladh genes obtained via this approach encoded a wide variety of amino acid sequences (8 to 99%). After screening, the enzymes obtained (HLADH-012 and HLADH-021) were confirmed to be superior to LSADH in some respects for the production of anti-Prelog chiral alcohols.