Complete Genome of the Chitin-Degrading Bacterium, Paenibacillus xylanilyticus W4

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.

Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

The genus Lentzea is a rare group of actinobacteria having potential for the exploration of bioactive compounds. Despite its proven ability to produce compounds with medical relevance, Lentzea genome analysis remains unexplored. Here we show a detailed understanding of the genetic features, biosynthetic gene clusters (BGCs), and genetic clusters for carbohydrate-active enzymes present in the Lentzea genome. Our analysis determines the genes for core proteins, non-ribosomal peptide synthetase condensation domain, and polyketide synthases-ketide synthase domain. The antiSMASH-based sequence analysis identifies 692 BGCs among which 8% are identical to the BGCs that produce geosmin, citrulassin, achromosin (lassopeptide), vancosamine, anabaenopeptin NZ857/nostamide A, alkylresorcinol, BE-54017, and bezastatin. The remaining BGCs code for advanced category antimicrobials like calcium-dependent, glycosylated, terpenoids, lipopeptides, thiopeptide, lanthipeptide, lassopeptide, lingual antimicrobial peptide and lantibiotics together with antiviral, antibacterial, antifungal, antiparasitic, anticancer agents. About 28% of the BGCs, that codes for bioactive secondary metabolites, are exclusive in Lentzea and could lead to new compound discoveries. We also find 7121 genes that code for carbohydrate-degrading enzymes which could essentially convert a wide range of polymeric carbohydrates. Genome mining of such genus is very much useful to give scientific leads for experimental validation in the discovery of new-generation bioactive molecules of biotechnological importance.

Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans

The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.

Identification of Chitinolytic Enzymes in Chitinolyticbacter meiyuanensis and Mechanism of Efficiently Hydrolyzing Chitin to N-Acetyl Glucosamine

Chitinolyticbacter meiyuanensis SYBC-H1, a bacterium capable of hydrolyzing chitin and shrimp shell to N-acetyl glucosamine (GlcNAc) as the only product, was isolated previously. Here, the hydrolysis mechanism of this novel strain toward chitin was investigated. Sequencing and analysis of the complete genome of SYBC-H1 showed that it encodes 32 putatively chitinolytic enzymes including 30 chitinases affiliated with the glycoside hydrolase (GH) families 18 (26) and 19 (4), one GH family 20 β-N-acetylglucosaminidase (NAGase), and one Auxiliary Activities (AA) family 10 lytic polysaccharide monooxygenase (LPMO). However, only eight GH18 chitinases, one AA10 LPMO, and one GH20 NAGase were detected in the culture broth of the strain, according to peptide mass fingerprinting (PMF). Of these, genes encoding chitinolytic enzymes including five GH18 chitinases (Cm711, Cm3636, Cm3638, Cm3639, and Cm3769) and one GH20 NAGase (Cm3245) were successfully expressed in active form in Escherichia coli. The hydrolysis of chitinous substrates showed that Cm711, Cm3636, Cm3638, and Cm3769 were endo-chitinases and Cm3639 was exo-chitinase. Moreover, Cm3639 and Cm3769 can convert the GlcNAc dimer and colloidal chitin (CC) into GlcNAc, which showed that they also possess NAGase activity. In addition, NAGase Cm3245 possesses a very high exo-acting activity of hydrolyzing GlcNAc dimer. These results suggest that chitinases and NAGase from SYBC-H1 both play important roles in conversion of N-acetyl chitooligosaccharides to GlcNAc, resulting in the accumulation of the final product GlcNAc. To our knowledge, this is the first report of the complete genome sequence and chitinolytic enzyme genes discovery of this strain.

Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain

A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10^T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 lipase-positive strain. It is aerobic, respiratory and has a fermentative metabolism using oxygen as an electron acceptor, produces acids from glucose and can fix nitrogen. Phylogenetic analysis of the 16S rRNA gene sequence, multilocus sequence analysis (MLSA) of 16S rRNA, gyrB, recA and rpoB, as well as phylogenomic analyses indicate that strain N10^T is a novel species of the genus Paenibacillus, with the highest 16S rRNA sequence similarity (95.4%) to P. chitinolyticus LMG 18047^T and <95% similarity to other species of the genus Paenibacillus. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANIb) were 21.1% and <75%, respectively. Its major cellular fatty acids were anteiso-C_15:0, C_16:0, and iso-C_15:0. G + C content ranged between 45%–50%. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with chemotaxonomic and phenotypic data, we demonstrate that type strain N10^T (= CECT 9541^T =LMG 30535^T) is a novel species of genus Paenibacillus and the name Paenibacillus lutrae sp. nov. is proposed.