Pedobacter deserti sp. nov., a novel species isolated from desert soil.

An aerobic, Gram-stain-negative bacterium, designated as SYSU D00382T, was sourced from soil of Gurbantunggut Desert, PR China. The strain was short-rod-shaped, oxidase-positive and catalase-negative, with yellow-colored, convex, round, and smooth colonies on TSA plate. Growth and proliferation occurred at 4-37 °C (optimal: 28-30 °C), pH 5.0-8.0 (optimal: pH 6.0-7.0) and NaCl concentration of 0-2.5% (optimal: 0-0.5%). The 16S rRNA gene based phylogenetic assessment showed that SYSU D00382T belonged to the genus Pedobacter, and was most closely related to Pedobacter ginsengisoli Gsoil 104T with similarity of 97.7%. The genomic DNA G+C content of SYSU D00382T was 46.4%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU D00382T and P. ginsengisoli Gsoil 104T were 75.7% and 17.5%, respectively. The main polar lipid was phosphatidylethanolamine. The major fatty acids (> 5%) were iso-C15:0, iso-C17:0 3-OH, summed features 3 and 9. The sole respiratory quinone identified was MK-7. The phylogeny based on 16S rRNA gene and whole-genome sequences revealed that SYSU D00382T formed a robust lineage with P. ginsengisoli Gsoil 104T. Based on phenotypic, phylogenetic and genotypic data, a novel specie named Pedobacter deserti sp. nov. is proposed. The type strain is SYSU D00382T (= CGMCC 1.18627T = MCCC 1K04972T = KCTC 82279T).

Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx.

Strain ELA7T, a novel Gram-negative, non-motile bacterium with a white pigment and rod-shaped morphology, was isolated from the faeces of an eland at Seoul Grand Park, a zoo in the Republic of Korea. The novel bacterial strain grew optimally in R2A medium under the following conditions: 0 % (w/v) NaCl, pH 8.0, and 34 °C. Based on phylogenetic analyses using 16S rRNA gene sequencing, strain ELA7T was found to have the closest relatedness to Pedobacter ginsengisoli Gsoil 104T (97.8 %), P. frigoris RP-3-15T (97.2 %), P. humi THG S15-2T (97.0 %), P. seoulensis THG-G12T (97.0 %), and P. foliorum LMG 31463T (96.9 %). The genome size and genomic DNA G+C content of strain ELA7T were 3.63 Mbp and 46.5 %, respectively. A whole genome-level comparison of strain ELA7T with P. ginsengisoli Gsoil 104T, P. frigoris RP-3-15T, P. africanus DSM 12126T, and P. psychroterrae RP-1-14T revealed average nucleotide identity values of 72.0, 71.8, 71.9, and 71.6 %, respectively. The major fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and MK-7 was the predominant respiratory quinone. The major polar lipids of strain ELA7T were phosphatidylethanolamine, sphingolipid, unidentified aminolipid, unidentified phosphoglycolipid, unidentified glycolipid, and eight unidentified lipids. Considering our chemotaxonomic, genotypic, and phenotypic findings, strain ELA7T (=KACC 23137T=JCM 36003T) is identified as representing a novel species within the genus Pedobacter, for which the name Pedobacter faecalis sp. nov. is proposed.

Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov., isolated from desert soil, and reclassification of Pedobacter xinjiangensis as Desertivirga xinjiangensis comb. nov. and Pedobacter mongoliensis as Paradesertivirga mongoliensis gen.nov., comb. nov.

Two novel bacterial strains, designated as SYSU D00823T and SYSU D00873T, were isolated from sandy soil of the Gurbantunggut Desert in Xinjiang, north-west China. SYSU D00823T and SYSU D00873T shared 99.0 % 16S rRNA gene sequence identity, and were both most closely related to Pedobacter xinjiangensis 12157T with 96.1 % and 96.0 % similarities, respectively. Phylogenetic and phylogenomic analyses revealed that the two isolates and P. xinjiangensis 12157T formed a separate distinct cluster in a stable subclade with the nearby species Pedobacter mongoliensis 1-32T, as well as the genera Pararcticibacter and Arcticibacter. Furthermore, P. mongoliensis 1-32T formed a separate deep-branching lineage and did not form a cluster with members of the genus Pedobacter. The average nucleotide identity and digital DNA-DNA hybridization values between SYSU D00823T and SYSU D00873T and related species were well below the thresholds for species delineation (<81.0 % and <24.0 %, respectively). The genomes of SYSU D00823T and SYSU D00873T were 6.19 and 6.43 Mbp in size with 40.4 % and 40.5 % DNA G+C contents, respectively. The predominant fatty acids (>10 %) of SYSU D00823T and SYSU D00873T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). Menaquinone-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine, glycosphingolipid, aminoglycolipid/glycolipid, aminophospholipid and three or four unidentified polar lipids. These data indicated that strains SYSU D00823T and SYSU D00873T should be assigned to two novel species of a new genus within the family Sphingobacteriaceae, for which the names Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov. are proposed. The type strains are SYSU D00823T (=CGMCC 1.18630T=MCCC 1K04973T=KCTC 82278T) and SYSU D00873T (=CGMCC 1.18629T=MCCC 1K04974T=KCTC 82281T), respectively. Accordingly, the reclassification of P. xinjiangensis as Desertivirga xinjiangensis comb. nov., and P. mongoliensis as Paradesertivirga mongoliensis gen. nov., comb. nov. are also proposed.

Biochemical characterization of a novel ß-galactosidase from Pedobacter sp. with strong transglycosylation activity at low lactose concentration.

A novel ß-galactosidase gene (PbBgal35A) from Pedobacter sp. CAUYN2 was cloned and expressed in Escherichia coli. The gene had an open reading frame of 1917 bp, encoding 638 amino acids with a predicted molecular mass of 62.3 kDa. The deduced amino acid sequence of the gene shared the highest identity of 41% with a glycoside hydrolase family 35 ß-galactosidase from Xanthomonas campestris pv. campestris (AAP86763.1). The recombinant ß-galactosidase (PbBgal35A) was purified to homogeneity with a specific activity of 65.9 U/mg. PbBgal35A was optimally active at pH 5.0 and 50 °C, respectively, and it was stable within pH 4.5‒7.0 and up to 45 °C. PbBgal35A efficiently synthesized galacto-oligosaccharides from lactose with a conversion ratio of 32% (w/w) and fructosyl-galacto-oligosaccharides from lactulose with a conversion ratio of 21.9% (w/w). Moreover, the enzyme catalyzed the synthesis of galacto-oligosaccharides from low-content lactose in fresh milk, and the GOS conversion ratios of 17.1% (w/w) and 7.8% (w/w) were obtained when the reactions were performed at 45 and 4 °C, respectively. These properties make PbBgal35A an ideal candidate for commercial use in the manufacturing of GOS-enriched dairy products.

Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil.

Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11T and HCMS5-2 T, were isolated from soil in South Korea. The growth of strain SJ11T was observed from 15℃ to 35℃ (optimum, 30℃), from pH 6.0 to 11.0 (optimum, pH 6.0-7.0) and with NaCl 0-1% (w/v) (optimum, 0%) and that of strain HCMS5-2 T was observed from 4℃ to 40℃ (optimum, 25℃), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0-5% (w/v) (optimum, 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3T (98.5%) and strain HCMS5-2 T had the highest similarities with Pedobacter nototheniae 36B243T (98.7%). The digital DNA-DNA hybridization value of strain SJ11T with Pedobacter jejuensis THG-DR3T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 T with Pedobacter nototheniae 36B243T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11T and HCMS5-2 T were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3-OH. The genome size of strain SJ11T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11T and HCMS5-2 T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11T and HCMS5-2 T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11T (= KACC 22884 T = TBRC 16597 T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 T (= KACC 22863 T = TBRC 16598 T) were respectively proposed.

Draft genome sequences of 21 Pedobacter strains isolated from amphibian specimens.

The genomes of 21 Pedobacter strains isolated from the European salamander Salamandra salamandra and different Madagascan frog species were sequenced using Illumina sequencing. Here, we report their draft genome sequences (~4.7-7.2 Mbp in size) to allow comparative genomics and taxonomic assignment of these strains.

Pedobacter montanisoli sp. nov., isolated from soil.

A white-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated CYS-01T, was obtained from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 28 °C. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain CYS-01T formed a lineage within the family Sphingobacteriaceae and clustered with members of the genus Pedobacter. The closest relatives were Pedobacter xixiisoli CGMCC 1.12803T (95.70 % sequence similarity), Pedobacter ureilyticus THG-T11T (95.35 %), Pedobacter helvus P-25T (95.28 %), Pedobacter chitinilyticus CM134L-2T (94.94 %), Pedobacter nanyangensis Q-4T (94.73 %) and Pedobacter zeaxanthinifaciens TDMA-5T (94.07 %). The principal respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid, unidentified lipids and an unidentified glycolipid. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C17 : 0 3-OH. The DNA G+C content was 36.6 mol%. Based on the results of genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain CYS-01T represents novel species in the genus Pedobacter, for which the name Pedobacter montanisoli sp. nov. is proposed. The type strain is CYS-01T (=KACC 22655T=NBRC 115630T).

Genome-based classification of Pedobacter polysacchareus sp. nov., isolated from Antarctic soil producing exopolysaccharide.

A psychrotolerant bacterial strain, designated ZS13-49T, with strong extracellular polysaccharide synthesis ability was isolated from soil collected in Antarctica and subjected to polyphasic taxonomic and comparative genomics. Chemotaxonomic features, including fatty acids, and polar lipid profiles, support the assignment of strain ZS13-49T to the genus Pedobacter. 16S rRNA gene phylogeny demonstrates that strain ZS13-49T forms a well-supported separate branch as a sister clade to Pedobacter gandavensis LMG 31462T and is clearly separated from Pedobacter steynii DSM 19110T and Pedobacter caeni DSM 16990T. Phylogenetic analysis showed strain ZS13-49T shared the highest 16S rRNA gene sequence similarity (99.9%) with P. gandavensis LMG 31462T. However, the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) value and average amino identity (AAI) value between strain ZS13-49T and P. gandavensis LMG 31462T were 26.5%, 83.3%, and 87.5%, respectively. Phylogenomic tree and a comparative genomic analysis indicated distinct characteristics to distinguish strain ZS13-49T from the closely related species. The complete genome sequence of strain ZS13-49T consists of 5 830 353 bp with 40.61% G + C content. Genomic features of strain ZS13-49T adapted to Antarctic environment were also revealed. Based on the phenotypic, chemotaxonomic, and genomic data, strain ZS13-49T could be assigned to a novel species within the genus Pedobacter for which the name Pedobacter polysacchareus sp. nov. is proposed. The type strain is ZS13-49T ( = CCTCC AB 2019394T = KCTC 72824T).

Synthesis of 2'-fucosyllactose from apple pomace-derived xyloglucan oligosaccharides by an α-L-fucosidase from Pedobacter sp. CAU209.

2'-Fucosyllactose (2'-FL) is known for its ability to provide various health benefits to infants, such as gut maturation, pathogen resistance, improved immunity, and nervous system development. However, the production of 2'-FL using α-L-fucosidases is hindered by the lack of low-cost natural fucosyl donors and high-efficiency α-L-fucosidases. In this work, a recombinant xyloglucanase from Rhizomucor miehei (RmXEG12A) was applied to produce xyloglucan-oligosaccharide (XyG-oligos) from apple pomace. Then, an α-L-fucosidase gene (PbFucB) was screened from the genomic DNA of Pedobacter sp. CAU209 and expressed in Escherichia coli. The capability of purified PbFucB to catalyze XyG-oligos and lactose to synthesize 2'-FL was further evaluated. The deduced amino acid sequence of PbFucB shared the highest identity (38.4%) with that of other reported α-L-fucosidases. PbFucB showed the highest activity at pH 5.5 and 35 °C. It catalyzed the hydrolysis of 4-nitrophenyl-α-L-fucopyranoside (pNP-Fuc, 20.3 U mg-1), 2'-FL (8.06 U mg-1), and XyG-oligos (0.43 U mg-1). Furthermore, PbFucB demonstrated a high enzymatic conversion rate in 2'-FL synthesis with pNP-Fuc or apple pomace-derived XyG-oligos as donors and lactose as acceptor. Under the optimized conditions, PbFucB converted 50% of pNP-Fuc or 31% of the L-fucosyl residue in XyG-oligos into 2'-FL. This work elucidated an α-L-fucosidase that mediates the fucosylation of lactose and provided an efficient enzymatic strategy to synthesize 2'-FL either from artificial pNP-Fuc or natural apple pomace-derived XyG-oligos. KEY POINTS: • Xyloglucan-oligosaccharide (XyG-oligos) was produced from apple pomace by a xyloglucanase from Rhizomucor miehei. • An α-L-fucosidase (PbFucB) from Pedobacter sp. CAU209 shared the highest identity (38.4%) with reported α-L-fucosidases. •PbFucB synthesized 2'-FL using apple pomace-derived XyG-oligos and lactose with a conversion ratio of 31%.

Linking Pedobacter lusitanus NL19 volatile exometabolome with growth medium composition: what can we learn using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry?

Microbial metabolomics allows understanding and to comprehensively analyse metabolites, and their related cellular and metabolic processes, that are produced and released to the extracellular environment under specific conditions. In that regard, the main objective of this research is to understand the impact of culture media changes in the metabolic profile of Pedobacter lusitanus NL19 (NL19) and Pedobacter himalayensis MTCC 6384 (MTCC6384) and respective influence on the production of biotechnologically relevant compounds. Solid-phase microextraction combined with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry with time-of-flight analyser (GC × GC-ToFMS) was applied to comprehensively study the metabolites produced by NL19 and MTCC6384 both in tryptic soy broth 100% (TSB100) and tryptic soy broth with 25% casein peptone (PC25). A total of 320 metabolites were putatively identified, which belong to different chemical families: alcohols, aldehydes, esters, ethers, hydrocarbons, ketones, nitrogen compounds, sulphur compounds, monoterpenes, and sesquiterpenes. Metabolites that were statistically different from the control (sterile medium) were selected allowing for the construction of the metabolic profile of both strains. A set of 80 metabolites was tentatively associated to the metabolic pathways such as the metabolism of fatty acids, branched-chain aminoacids, phenylalanine, methionine, aromatic compounds, and monoterpene and sesquiterpene biosynthesis. This study allowed to better understand how slight changes of the culture media and thus the composition of nutrients impair the metabolic profile of bacteria, which may be further explored for metabolomics pipeline construction or biotechnological applications.

Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovénbreen, Arctic.

A rod-shaped, Gram-stain-negative, non-motile and aerobic bacterium, designated Q8-18T, was isolated from soil of glacier foreland in Austre Lovénbreen, Arctic, and subjected to a polyphasic taxonomic study. Strain Q8-18T grew optimally at 20 °C, pH 5.0-8.0 and in the presence of 0-1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q8-18T belonged to the family Sphingobacteriaceae. Strain Q8-18T showed the highest sequence similarity to Pedobacter mendelii CCM 8685T (96.8%), Pedobacter lithocola CCM 8691T (96.8%), Pedobacter roseus CL-GP80T (96.7%), Pedobacter changchengzhani E01020T (96.7%), Pedobacter alluvionis DSM 19624T (96.6%), Pedobacter jejuensis THG-DR3T (96.3%), Pedobacter ginsengiterrae DCY49T (95.9%) and Pedobacter jamesrossensis CCM 8689T (95.9%). A whole genome-level comparison of strain Q8-18T with P. roseus CL-GP80T, P. changchengzhani E01020T, P. alluvionis DSM 19624T and Pedobacter heparinus LMG 10339T revealed average nucleotide identity values of 77.0, 76.0, 77.0 and 70.4%, respectively. The only respiratory isoprenoid quinone was menaquinone-7. The polar lipid profile of strain Q8-18T was found to contain one phosphatidylethanolamine, eight unidentified aminolipids, one aminophospholipids and five unidentified lipids. The G+C content of the genomic DNA was determined to be 35.4 mol%. The main fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 and anteiso-C15 : 0. On the basis of the evidence presented in this study, a novel species of the genus Pedobacter, Pedobacter mucosus sp. nov., is proposed, with the type strain Q8-18T (=CCTCC AB 2020009T=KCTC 82636T).

Production and characterization of a new detergent-stable keratinase expressed by Pedobacter sp. 3.14.7, a novel Antarctic psychrotolerant keratin-degrading bacterium.

BACKGROUND: Antarctica is one of the harshest environments in the world. Despite this fact, it has been colonized by microorganisms, which had to develop different adaptations in order to survive. By studying their enzymes, we can harness these adaptations in order to use them in various industrial processes. Keratinases (E.C. 3.4.99.11) are characterized by their robustness in withstanding extreme conditions and, along with other enzymes, are commonly added to laundry detergents, which makes their study of industrial interest. RESULTS: In this work, a novel keratinase producer, Pedobacter sp. 3.14.7 (MF 347939.1), isolated from Antarctic birds' nests, was identified. This psychrotolerant isolate displays a typical psychrotolerant growth pattern, with an optimal temperature of 20 °C (µmax=0.23 h-1). After 238 h, maximum proteolytic (22.00 ± 1.17 U ml-1) and keratinolytic (33.04 ± 1.09 U ml-1) activities were achieved with a feather sample conversion of approximately 85%. The keratinase present in crude extract was characterized as a metalloprotease with a molecular weight of 25 kDa, stable in a wide range of pH, with an optimum pH of 7.5. Optimum temperature was 55 °C. Wash performance at 20 °C using this crude extract could remove completely blood stain from cotton cloth. CONCLUSION: We report a new keratinolytic bacteria from maritime Antarctica. Among its biochemical characteristics, its stability in the presence of different detergents and bleaching agents and its wash performance showed promising results regarding its potential use as a laundry detergent additive.

Pedobacter fastidiosus sp. nov., isolated from glacial habitats of maritime Antarctica.

Strains P8930T and 478 were isolated from Antarctic glaciers located on James Ross Island and King George Island, respectively. They comprised Gram-stain-negative short rod-shaped cells forming pink pigmented colonies and exhibited identical 16S rRNA gene sequences and highly similar MALDI TOF mass spectra, and hence were assigned as representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences assigned both isolates to the genus Pedobacter and showed Pedobacter frigidisoli and Pedobacter terrae to be their closest phylogenetic neighbours, with 97.4 and 97.2 % 16S rRNA gene sequence similarities, respectively. These low similarity values were below the threshold similarity value of 98.7%, confirming the delineation of a new bacterial species. Further genomic characterization included whole-genome sequencing accompanied by average nucleotide identity (ANI) and digital DNA-DNA hybridization calculations, and characterization of the genome features. The ANI values between P8930T and P. frigidisoli RP-3-11T and P. terrae DSM 17933T were 79.7 and 77.6 %, respectively, and the value between P. frigidisoli RP-3-11T and P. terrae DSM 17933T was 77.7 %, clearly demonstrating the phylogenetic distance and the novelty of strain P8930T. Further characterization included analysis of cellular fatty acids, quinones and polar lipids, and comprehensive biotyping. All the obtained results proved the separation of strains P8930T and 478 from the other validly named Pedobacter species, and confirmed that they represent a new species for which the name Pedobacter fastidiosus sp. nov. is proposed. The type strain is P8930T (=CCM 8938T=LMG 32098T).

Production, characteristics and applications of microbial heparinases.

Heparinases are enzymes that selectively cleave heparin and heparan sulfate chains, via cleavage of the glycosidic linkage between hexosamines and uronic acids, producing disaccharide and oligosaccharide products. While heparin is well known as an anti-coagulant drug, heparin and heparan sulfate are also involved in biological processes such as inflammation, cancer and angiogenesis and viral and bacterial infections and are of growing interest for their therapeutic potential. Recently, potential roles of heparin and heparan sulfate in relation to COVID-19 infection have been highlighted. The ability of heparinases to selectively cleave heparin chains has been exploited industrially to produce low molecular weight heparin, which has replaced heparin in several clinical applications. Other applications of heparinases include heparin and heparan sulfate structural analysis, neutralisation of heparin in blood and removal of the inhibitory effect of heparin on various enzymes. Heparinases are known to inhibit neovascularization and heparinase III is of interest for treating cancer and inhibiting tumour cell growth. Heparinase activity, first isolated from Pedobacter heparinus, has since been reported from several other microorganisms. Significant progress has been made in the production, characterisation and improvement of microbial heparinases in response to application demands in terms of heparinase yield and purity, which is likely to extend their usefulness in various applications. This review focuses on recent developments in the identification, characterisation and improvement of microbial heparinases and their established and emerging industrial, clinical and therapeutic applications.

Nitrogen source as a modulator of the metabolic activity of Pedobacter lusitanus NL19: a transcriptomic approach.

Secondary metabolites (SMs) are compounds with relevant biological activities. Their production under laboratory conditions, especially in broth, is still challenging. An example is the pedopeptins, which are nonribosomal peptides active against some bacteria listed by the WHO for which new antibiotics are urgently needed. Their biosynthesis is inhibited by high concentrations of peptone from casein (PC) in tryptic soy broth (TSB), and we applied a RNA-seq approach to identify Pedobacter lusitanus NL19 cellular pathways modulated by this condition. Results were validated by qPCR and revealed 261 differentially expressed genes (DEGs), 46.3% of them with a predicted biological function. Specifically, high concentration of PC significantly repressed the de novo biosynthesis of biotin (- 60X) and the production of nonribosomal peptide synthetases (NRPS) of pedopeptins (about - 14X), but no effect was observed on the expression of other NRPS. Transcription of a L-Dap synthesis operon that includes a protein with a σ70-like domain was also reduced (about - 7X). High concentrations of PC led to a significant overexpression of MFS and RND efflux pumps and a ferrous iron uptake system, suggesting the redirection of cell machinery to export compounds such as amino acids, sugars and metal divalent cations, alongside with a slight increase of iron import. KEY POINTS: • Higher concentrations of phosphate sources highly repress many operons • High concentrations of peptone from casein (PC) cause biotin's operon repression • High concentrations of PC downregulate the production of peptides of unknown function.

Microbial diversity of garden snail mucus.

The search for new natural compounds for application in medicine and cosmetics is a trend in biotechnology. One of the sources of such active compounds is the snail mucus. Snail physiology and the biological activity of their fluids (especially the mucus) are still poorly studied. Only a few previous studies explored the relationship between snails and their microbiome. The present study was focused on the biodiversity of the snail mucus used in the creation of cosmetic products, therapeutics, and nutraceuticals. The commonly used cultivation techniques were applied for the determination of the number of major bacterial groups. Fluorescence in situ hybridization for key taxa was performed. The obtained images were subjected to digital image analysis. Sequencing of the 16S rRNA gene was also done. The results showed that the mucus harbors a rich bacterial community (10.78 × 1010 CFU/ml). Among the dominant bacteria, some are known for their ability to metabolize complex polysaccharides or are usually found in soil and plants (Rhizobiaceae, Shewanella, Pedobacter, Acinetobacter, Alcaligenes). The obtained data demonstrated that the snail mucus creates a unique environment for the development of the microbial community that differs from other parts of the animal and which resulted from the combined contribution of the microbiomes derived from the soil, plants, and the snails.

Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water.

A novel bacterial strain designated CJ43T was isolated from fresh water located in Gangwon-do, South Korea, displaying multi-drug resistance. The isolate was Gram-stain-negative, aerobic, orange-pigmented, and rod-shaped. Strain CJ43T grew optimally at 30 °C and pH 7 on R2A agar in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CJ43T belonged to the genus Pedobacter in the family Sphingobacteriaceae and was most closely related to Pedobacter puniceum HX-22-1 T and P. glucosidilyticus 1-2 T (98.3 and 98.1% sequence similarity). The genome size of strain CJ43T was 3.9 Mb in a single contig with DNA G + C content of 34.9%. The genome included 3144 predicted protein-coding genes, as well as 55 tRNA, 9 rRNA and 3 ncRNA genes. The genome also contained 128 putative antibiotic resistance genes, reflecting its phenotypes. The average nucleotide identity values between strain CJ43T and two closely related strains P. puniceum HX-22-1 T and P. glucosidilyticus 1-2 T were 91.0 and 88.7%, respectively. In silico digital DNA-DNA hybridization results between strain CJ43T and the related strains were 42.8 and 38.6%, respectively. The major fatty acids of strain CJ43T were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). Strain CJ43T contained phosphatidylethanolamine as the major polar lipid and menaquinone-7 as the sole respiratory quinone. Based on the polyphasic taxonomy data, strain CJ43T represents a novel species of the genus Pedobacter, for which the name Pedobacter aquae sp. nov. is proposed with the type strain CJ43T (= KACC 21350 T = JCM 33709 T).

A Combination of Structural, Genetic, Phenotypic and Enzymatic Analyses Reveals the Importance of a Predicted Fucosyltransferase to Protein O-Glycosylation in the Bacteroidetes.

Diverse members of the Bacteroidetes phylum have general protein O-glycosylation systems that are essential for processes such as host colonization and pathogenesis. Here, we analyzed the function of a putative fucosyltransferase (FucT) family that is widely encoded in Bacteroidetes protein O-glycosylation genetic loci. We studied the FucT orthologs of three Bacteroidetes species-Tannerella forsythia, Bacteroides fragilis, and Pedobacter heparinus. To identify the linkage created by the FucT of B. fragilis, we elucidated the full structure of its nine-sugar O-glycan and found that l-fucose is linked ß1,4 to glucose. Of the two fucose residues in the T. forsythia O-glycan, the fucose linked to the reducing-end galactose was shown by mutational analysis to be l-fucose. Despite the transfer of l-fucose to distinct hexose sugars in the B. fragilis and T. forsythia O-glycans, the FucT orthologs from B. fragilis, T. forsythia, and P. heparinus each cross-complement the B. fragilis ΔBF4306 and T. forsythia ΔTanf_01305 FucT mutants. In vitro enzymatic analyses showed relaxed acceptor specificity of the three enzymes, transferring l-fucose to various pNP-α-hexoses. Further, glycan structural analysis together with fucosidase assays indicated that the T. forsythia FucT links l-fucose α1,6 to galactose. Given the biological importance of fucosylated carbohydrates, these FucTs are promising candidates for synthetic glycobiology.

Pedobacter riviphilus sp. nov., isolated from stream sediment.

A Gram-stain-negative, aerobic, motile by gliding, rod-shaped and pink-coloured bacterium, designated strain SW-16T, was isolated from the sediment of small stream in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SW-16T formed a lineage within the genus Pedobacter of the family Sphingobacteriaceae. Phylogenetic analysis also showed that strain SW-16T was most closely related to Pedobacter soli 15-51T (98.0% 16S rRNA gene sequence similarity), Pedobacter humicola R135T (97.5%), Pedobacter suwonensis 15-52T (97.4%), Pedobacter sandarakinus DS-27T (97.0%) and Pedobacter kyungheensis THG-T17T (97.0%). Growth was observed at 10-37 °C (optimum at 30 °C), pH 6-8 (optimum at pH 7) and with 0-2.0 % NaCl (optimum at 0%). The major fatty acids of the bacterial strain were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The predominant respiratory quinone was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified amino lipids, one unidentified phospholipid and three unidentified lipids. The genome size of strain SW-16T was 5.8 Mbp and the G+C content was 38.5 mol%. Based on the results of phenotypic, genomic and phylogenetic analyses, strain SW-16T represents a novel species of the genus Pedobacter, for which the name Pedobacter riviphilus sp. nov. is proposed. The type strain is SW-16T (=KEMB 1602-396T=KCTC 82079T=JCM 34181T).

Exploration of Social Spreading Reveals That This Behavior Is Prevalent among Pedobacter and Pseudomonas fluorescens Isolates and That There Are Variations in the Induction of the Phenotype.

Within soil, bacteria are found in multispecies communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is critical for investigating community-level functions. We previously showed that cocultured Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading (ISS) on a hard agar surface, a behavior which required close contact and depended on the nutritional environment. Here, we investigate whether social spreading is widespread among P. fluorescens and Pedobacter isolates and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and Pedobacter sp. V48 but is a prevalent behavior found in one clade in the P. fluorescens group and two clades in the Pedobacter genus. We show that the interaction with certain Pedobacter isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As with ISS by Pf0-1+V48, the motility of interacting pairs is influenced by the environment, with no spreading behaviors (or induction of motility) observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs, the high salt influence was variable. The prevalence of motility phenotypes observed here and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities. IMPORTANCE Interspecies social spreading (ISS) is an emergent behavior observed when Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 interact, during which both species move together across a surface. Importantly, this environment does not permit the movement of either individual species. This group behavior suggests that communities of microbes can function in ways not predictable by knowledge of the individual members. Here, we have asked whether ISS is widespread and thus potentially of importance in soil microbial communities. The significance of this research is the demonstration that surface spreading behaviors are not unique to the Pf0-1-V48 interaction but rather is a more widespread phenomenon observed among members of distinct clades of both P. fluorescens and Pedobacter isolates. Furthermore, we identify differences in mechanisms of signaling and nutritional requirements for ISS. Emergent traits resulting from bacterial interactions are widespread, and their characterization is necessary for a complete understanding of microbial community function.