A polysaccharide utilization locus from Chitinophaga pinensis simultaneously targets chitin and β-glucans found in fungal cell walls

In nature, complex carbohydrates are rarely found as pure isolated polysaccharides. Instead, bacteria in competitive environments are presented with glycans embedded in heterogeneous matrices such as plant or microbial cell walls. Members of the Bacteroidota phylum thrive in such ecosystems because they are efficient at extracting nutrients from complex substrates, secreting consortia of synergistic enzymes to release metabolizable sugars. Carbohydrate-binding modules (CBMs) are used to target enzymes to substrates, enhancing reaction rate and product release. Additionally, genome organizational tools like polysaccharide utilization loci (PULs) ensure that the appropriate set of enzymes is produced when needed. In this study, we show that the soil bacterium Chitinophaga pinensis uses a PUL and several CBMs to coordinate the activities of enzymes targeting two distinct polysaccharides found in fungal cell walls. We describe the enzymatic activities and carbohydrate-binding behaviors of components of the fungal cell wall utilization locus (FCWUL), which uses multiple chitinases and one β-1,3-glucanase to hydrolyze two different substrates. Unusually, one of the chitinases is appended to a β-glucan-binding CBM, implying targeting to a bulk cell wall substrate rather than to the specific polysaccharide being hydrolyzed. Based on our characterization of the PUL's outer membrane sensor protein, we suggest that the FCWUL is activated by β-1,3-glucans, even though most of its enzymes are chitin-degrading. Our data showcase the complexity of polysaccharide deconstruction in nature and highlight an elegant solution for how multiple different glycans can be accessed using one enzymatic cascade. IMPORTANCE We report that the genome of the soil bacterium Chitinophaga pinensis encodes three multi-modular carbohydrate-active enzymes that work together to hydrolyze the major polysaccharide components found in fungal cell walls (FCWs). The enzymes are all encoded by one polysaccharide utilization locus and are co-expressed, potentially induced in the presence of β-1,3-glucans. We present biochemical characterization of each enzyme, including the appended carbohydrate-binding modules that likely tether the enzymes to a FCW substrate. Finally, we propose a model for how this so-called fungal cell wall utilization locus might enable C. pinensis to metabolize both chitin and β-1,3-glucans found in complex biomass in the soil.

strain R-73072-mediated alkannin/shikonin biosynthesis in Lithospermum officinale

Plants are colonized by a wide range of bacteria, several of which are known to confer benefits to their hosts such as enhancing plant growth and the biosynthesis of secondary metabolites (SMs). Recently, it has been shown that Chitinophaga sp. strain R-73072 enhances the production of alkannin/shikonin, SMs of pharmaceutical and ecological importance. However, the mechanisms by which this bacterial strain increases these SMs in plants are not yet understood. To gain insight into these mechanisms, we analyzed the molecular responses of Lithospermum officinale, an alkannin/shikonin producing member of Boraginaceae, to inoculation with R-73072 in a gnotobiotic system using comparative transcriptomics and targeted metabolite profiling of root samples. We found that R-73072 modulated the expression of 1,328 genes, of which the majority appeared to be involved in plant defense and SMs biosynthesis including alkannin/shikonin derivatives. Importantly, bacterial inoculation induced the expression of genes that predominately participate in jasmonate and ethylene biosynthesis and signaling, suggesting an important role of these phytohormones in R-73072-mediated alkannin/shikonin biosynthesis. A detached leaf bioassay further showed that R-73072 confers systemic protection against Botrytis cinerea. Finally, R-73072-mediated coregulation of genes involved in plant defense and the enhanced production of alkannin/shikonin esters further suggest that these SMs could be important components of the plant defense machinery in alkannin/shikonin producing species.

Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops

Despite growing evidence that plant growth-promoting bacteria can be used to improve crop vigor, a comparison of the different methods of delivery to determine which is optimal has not been published. An optimal inoculation method ensures that the inoculant colonizes the host plant so that its potential for plant growth-promotion is fully evaluated. The objective of this study was to compare the efficacy of three seed coating methods, seedling priming, and soil drench for delivering three bacterial inoculants to the sorghum rhizosphere and root endosphere. The methods were compared across multiple time points under axenic conditions and colonization efficiency was determined by quantitative polymerase chain reaction (qPCR). Two seed coating methods were also assessed in the field to test the reproducibility of the greenhouse results under non-sterile conditions. In the greenhouse seed coating methods were more successful in delivering the Gram-positive inoculant (Terrabacter sp.) while better colonization from the Gram-negative bacteria (Chitinophaga pinensis and Caulobacter rhizosphaerae) was observed with seedling priming and soil drench. This suggested that Gram-positive bacteria may be more suitable for the seed coating methods possibly because of their thick peptidoglycan cell wall. We also demonstrated that prolonged seed coating for 12 h could effectively enhance the colonization of C. pinensis, an endophytic bacterium, but not the rhizosphere colonizing C. rhizosphaerae. In the field only a small amount of inoculant was detected in the rhizosphere. This comparison demonstrates the importance of using the appropriate inoculation method for testing different types of bacteria for their plant growth-promotion potential.

nov., isolated from rhizosphere soil of banana

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as strain B61^T, was isolated from rhizosphere soil of banana collected from Dongguan, Guangdong Province, PR China. Growth occurred at 15-40 °C, within a pH range of pH 6.0-9.0. Results of 16S rRNA gene sequence similarity and phylogenetic analyses showed that strain B61^T was most closely related to 'Chitinophaga agri' KACC 21303 (98.9 %) and Chitinophaga pinensis DSM 2588^T (98.8 %). The genome size was 7.6 Mb with a G+C content of 45.2 mol%. The genome-inferred average nucleotide identity values between strain B61^T and two closely related strains were 79.2 and 79.3 %, respectively, with corresponding digital DNA-DNA hybridization values of 22.3 and 22.6 %. The major fatty acids of the novel strain were iso-C_15:0, C_16:1 ω5c and iso-C_17:0 3-OH and the sole respiratory quinone was menaquinone 7 (MK-7). The polar lipids consisted of phosphatidylethanolamine, five unidentified aminolipids, four unidentified glycolipids and six unidentified lipids. The phenotypic and phylogenetic results clearly supported that strain B61^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga rhizophila, sp. nov. is proposed, with the type strain B61^T (=GDMCC 1.2608^T=KCTC 82856^T).

Novel Glycerophospholipid, Lipo- and N-acyl Amino Acids from Bacteroidetes: Isolation, Structure Elucidation and Bioactivity

The 'core' metabolome of the Bacteroidetes genus Chitinophaga was recently discovered to consist of only seven metabolites. A structural relationship in terms of shared lipid moieties among four of them was postulated. Here, structure elucidation and characterization via ultra-high resolution mass spectrometry (UHR-MS) and nuclear magnetic resonance (NMR) spectroscopy of those four lipids (two lipoamino acids (LAAs), two lysophosphatidylethanolamines (LPEs)), as well as several other undescribed LAAs and N-acyl amino acids (NAAAs), identified during isolation were carried out. The LAAs represent closely related analogs of the literature-known LAAs, such as the glycine-serine dipeptide lipids 430 (2) and 654. Most of the here characterized LAAs (1, 5-11) are members of a so far undescribed glycine-serine-ornithine tripeptide lipid family. Moreover, this study reports three novel NAAAs (N-(5-methyl)hexanoyl tyrosine (14) and N-(7-methyl)octanoyl tyrosine (15) or phenylalanine (16)) from Olivibacter sp. FHG000416, another Bacteroidetes strain initially selected as best in-house producer for isolation of lipid 430. Antimicrobial profiling revealed most isolated LAAs (1-3) and the two LPE 'core' metabolites (12, 13) active against the Gram-negative pathogen M. catarrhalis ATCC 25238 and the Gram-positive bacterium M. luteus DSM 20030. For LAA 1, additional growth inhibition activity against B. subtilis DSM 10 was observed.

nov., an epiphytic bacterium isolated from rice root surfaces

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303^T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16-37 °C (optimum, 30 °C), pH 5.0-10.0 (optimum, pH 7.0) and 0-2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga. Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729^T, Chitinophaga qingshengii JN246^T, Chitinophaga varians 10-7 W-9003^T and Chitinophaga fulva G-6-1-13^T. When the genomic sequences of strains 1303^T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA-DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C_15 : 0, C_16 : 1  ω5c, iso-C_17 : 0 3-OH and summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303^T and 1310 represent members of a novel species of the genus Chitinophaga, for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303^T (=KACC 22075^T=TBRC 12926^T).

nov., isolated from soil

A Gram-stain-negative, non-motile, yellow-pigmented and non-spore forming rod-shaped bacterium, designated strain BN140078^T, was isolated from farmland soil, Chungbuk, Republic of Korea. It was able to grow aerobically at 10-40 °C (optimum 28 °C), pH 5.5-7.5 (optimum pH 7.0) and with 0-2.0% (w/v) NaCl concentration (optimum 1.0%) on Reasoner's 2A (R2A) agar medium. Comparative 16S rRNA gene sequence analysis showed that the strain BN140078^T had 96.9%, 96.5% and 96.1% 16S rRNA gene similarities with Chitinophaga ginsengihumi KACC 17604^T, Chitinophaga rupis KACC 14521^T and Chitinophaga japonensis KACC 12057^T, respectively. The predominant respiratory quinone was menaquinone MK-7 and the major fatty acids (≥ 5%) were C_16:1 ω5c, iso-C_15:0, iso-C_17:0 3-OH and Summed Feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The polar lipids were composed of phosphatidylethanolamine, four unidentified amino lipids and six unidentified lipids. The genomic DNA G+C content was 49.5 mol%. The genome of strain BN140078^T comprises a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide products. The polyphasic taxonomic study clearly distinguished this strain from its closest phylogenetic neighbors. Thus, we propose that the BN140078^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga agrisoli sp. nov. was proposed. The type strain is BN140078^T (=KCTC 62555^T = CCTCC AB 2018162^T).

nov., a bacterium isolated from soil of reclaimed land

A Gram-negative, aerobic, and long rod-shaped bacterium, designated as H33E-04^T, was isolated from the soil of reclaimed land, Republic of Korea. The strain grew at a temperature range of 15-40 °C, pH 5.0-10.0, and 0-2% NaCl (w/v). The phylogenetic analysis based on 16S rRNA gene sequences showed that strain H33E-04^T was in the same clade with Chitinophaga pinensis DSM 2588^T, Chitinophaga filiformis IFO 15056^T, and Chitinophaga ginsengisoli Gsoil 052^T with 98.4%, 97.9%, and 97.8% sequence similarities, respectively. The de novo genome assembly revealed that the DNA G + C content of the strain was 46.2 mol%. Comparative genome analysis between strain H33E-04^T and C. pinensis DSM 2588 ^T showed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 79.9% and 23.4%, respectively. The major respiratory quinone was menaquinone-7 (MK-7) and the predominant cellular fatty acids were iso-C_15:0 (31.7%), C_16:1 ω5c (31.2%), and iso-C_17:0 3-OH (11.8%), supporting the affiliation of strain H33E-04^T with the genus Chitinophaga. Based on phylogenetic, physiological, and chemotaxonomic characteristics, strain H33E-04^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga agri sp. nov. is proposed. The type strain of Chitinophaga agri is H33E-04^T (= KACC 21303^T = NBRC114512^T).

nov., a multi-drug resistant bacterium infecting humans

We describe a new multidrug resistant Chitinophaga species that was isolated from patients with type 2 diabetes in Vietnam. Strain BD 01^T was cultivated in 2017 from a blood sample of a patient suffering from bacteremia. Strain VP 7442 was isolated in 2018 from a pleural fluid sample of a patient who had presented with lung abscess and pleural effusion. Both strains are aerobic, Gram-negative, non-motile and non-spore-forming. The 16S rRNA gene sequences of both strains are 100 % similar and share a highest 16S sequence identity with Chitinophaga polysaccharea MRP-15^T of 97.42 %. Their predominant fatty acid is iso-C_15 : 0 (73.8 % for strain BD 01^T and 79.8 % for strain VP 7442). The draft genome sizes of strains BD 01^T and VP 7442 are 6 308 408 and 6 308 579 bp, respectively. They are resistant to beta-lactams, aminoglycosides, fluoroquinolones, metronidazole, fosfomycin, vancomycin and macrolides, and exhibit 20 and 18 antimicrobial resistance-related genes, respectively. Using the multiphasic taxonogenomic approach, we propose that strains BD 01^T (=CSUR P9622=VTCC 70981) and VP 7442 (=CSUR P9623=VTCC 70982) represent a new species, for which we propose the name Chitinophaga vietnamensis sp. nov. Strain BD 01^T was chosen as type strain of C. vietnamensis sp. nov.

nov., isolated from arsenic-contaminated soil

A yellow-coloured bacterial strain, designated ZY74^T, was isolated from arsenic contaminated soil (34 mg kg^-1) sample collected in Longkou, Hubei Province, PR China. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. Strain ZY74^T produced round, yellow-pigmented, smooth and opaque colonies. Based on the results of 16S rRNA gene sequence analysis, strain ZY74^T was found to be affiliated with members of the genus Chitinophaga. Its closest members were Chitinophagabarathri YLT18^T (97.72 %) and Chitinophaganiabensis JS13-10^T (97.17 %). The genome size of strain ZY74^T was 6.61 Mb, containing 5351 predicted protein-coding genes, with a DNA G+C content of 55.0 mol%. The average nucleotide identity values of strain ZY74^T with C. barathri YLT18^T and C. niabensis DSM 24787^T were 76.12 and 73.32 %, respectively. The digital DNA-DNA hybridization values of strain ZY74^T with C. barathri YLT18^T and C. niabensis JS13-10^T were 20.60 and 19.40 %, respectively. The major respiratory quinone was menaquinone 7 and the predominant fatty acids (>5 %) were iso-C15:0, C16 : 1ω5c and iso-C17 : 03-OH. On the basis of phylogenetic, genotypic, phenotypic and chemotaxonomic characterization, strain ZY74^T represents a novel species in the genus Chitinophaga, for which the name Chitinophagalutea sp. nov. is proposed. The type strain is ZY74^T (=CCTCC AB2018369^T=KCTC 72039^T).

nov., isolated from monsoon evergreen broad-leaved forest soil

A Gram-stain-negative, aerobic, non-motile strain, K3CV102501^T, was isolated from a soil sample collected from the monsoon evergreen broad-leaved forest of Dinghushan Biosphere Reserve located in Guangdong Province, PR China. The primal colony of strain K3CV102501^T was very similar to the fruiting body of myxobacteria on the original isolation plates. Young cultures of strain K3CV102501^T contained long (2-4×0.4-0.5 µm) filamentous cells and divided into rod shapes (0.7-1.0×0.6-0.8 µm) after 4 days of incubation at 28 °C. Strain K3CV102501^T grew at pH 6.0-9.5 (optimum, pH 6.5-7.5) and 7-42 °C (optimum, 28-35 °C). Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain K3CV102501^T belonged to the genus Chitinophagaand showed the highest similarity to C.hitinophaga jiangningensis JCM 19354^T (96.9 %). The DNA G+C content of the type strain was 46.6 mol%. The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and an unidentified aminolipid. Menaquinone-7 was the predominant quinone. The phenotypic, chemotaxonomic and phylogenetic data clearly showed that strain K3CV102501^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga flava sp. nov. is proposed. The type strain is K3CV102501^T (=KCTC 62435^T=GDMCC 1.1325^T).

nov., isolated from forest soil

A Gram-stain-negative, rod-shaped and aerobic bacterium, designated K20C18050901^T, was isolated from forest soil collected on 11 September 2017 from Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10' 24'' N; 112° 32' 10'' E). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain K20C18050901^T belongs to the genus Chitinophaga, and showed the highest similarities to Chitinophaga sancti NBRC 15057^T (98.6 %) and Chitinophaga oryziterrae JCM 16595^T (96.9 %). The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-7. The major polar lipid was phosphatidylethanolamine. The draft genome size of strain K20C18050901^T was 8.36 Mb with a DNA G+C content of 44.7 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain K20C18050901^T and C. sancti NBRC 15057^T were 31.40 and 85.82 %, respectively. On the basis of phenotypic, genotypic and phylogenetic analysis, strain K20C18050901^T represents a novel species of the genus Chitinophaga, for which the name Chitinophagasilvisoli sp. nov. is proposed. The type strain is K20C18050901^T (=GDMCC 1.1411^T=KCTC 62860^T).

nov., isolated from forest soil

A Gram-stain-negative, aerobic, non-motile bacterium, designated strain 10-7W-9003^T, was isolated from the forest soil of Limushan National Forest Park, south-east China (19° 10' 42″ N, 109° 44' 45″ E). Strain 10-7W-9003^T showed a shape change during the course of culture from long filamentous cells (5-10×0.4-0.5 µm) at 5-36 h, to rod shaped (1.0-1.5×0.5-0.7 µm) with inoculation after 2 days. It grew optimally at 28-30 °C and pH 6.5-7.5. On the basis of 16S rRNA gene sequence analysis, it belongs to the genus Chitinophaga and is most closely related to Chitinophaga eiseniae KACC 13774^T and Chitinophaga qingshengii JCM 30026^T, with 16S rRNA gene sequences similarities of 98.8 and 98.3 %, respectively. However, the DNA-DNA hybridization study showed that strain 10-7W-9003^T shared relatively low relatedness values with KACC 13774^T (21.8 %) and JCM 30026^T (20.4 %), respectively. The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The genomic DNA G+C content was 50.7 mol%. It contained MK-7 as the major quinone. The phenotypic, chemotaxonomic and phylogenetic data clearly showed that strain 10-7W-9003^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga varians sp. nov. is proposed. The type strain is 10-7W-9003^T (=GDMCC 1.1252^T=KACC 19415^T=KCTC 52926^T).

Bacterial diversity indicates dietary overlap among bats of different feeding habits

Bats are among the most conspicuous mammals with extraordinary adaptations. They play a key role in the ecosystem. Frugivorous bats are important seed dispersing agents that help in maintaining forest tree diversity, while insectivorous bats are natural insect pest control agents. Several previous reports suggest that bats are reservoir of viruses; nonetheless their bacterial counterparts are relatively less explored. The present study describes the microbial diversity associated with the intestine of bats from different regions of India. Our observations stipulate that there is substantial sharing of bacterial communities between the insectivorous and frugivorous bats, which signifies fairly large dietary overlap. We also observed the presence of higher abundance of Mycoplasma in Cynopterus species of bats, indicating possible Mycoplasma infection. Considering the scarcity of literature related to microbial communities of bat intestinal tract, this study can direct future microbial diversity studies in bats with reference to their dietary habits, host-bacteria interaction and zoonosis.

Microbial dynamics and properties of aerobic granules developed in a laboratory-scale sequencing batch reactor with an intermediate filamentous bulking stage

Aerobic granules offer enhanced biological nutrient removal and are compact and dense structures resulting in efficient settling properties. Granule instability, however, is still a challenge as understanding of the drivers of instability is poorly understood. In this study, transient instability of aerobic granules, associated with filamentous outgrowth, was observed in laboratory-scale sequencing batch reactors (SBRs). The transient phase was followed by the formation of stable granules. Loosely bound, dispersed, and pinpoint seed flocs gradually turned into granular flocs within 60 days of SBR operation. In stage 1, the granular flocs were compact in structure and typically 0.2 mm in diameter, with excellent settling properties. Filaments appeared and dominated by stage 2, resulting in poor settleability. By stage 3, the SBRs were selected for larger granules and better settling structures, which included filaments that became enmeshed within the granule, eventually forming structures 2-5 mm in diameter. Corresponding changes in sludge volume index were observed that reflected changes in settleability. The protein-to-polysaccharide ratio in the extracted extracellular polymeric substance (EPS) from stage 1 and stage 3 granules was higher (2.8 and 5.7, respectively), as compared to stage 2 filamentous bulking (1.5). Confocal laser scanning microscopic (CLSM) imaging of the biomass samples, coupled with molecule-specific fluorescent staining, confirmed that protein was predominant in stage 1 and stage 3 granules. During stage 2 bulking, there was a decrease in live cells; dead cells predominated. Denaturing gradient gel electrophoresis (DGGE) fingerprint results indicated a shift in bacterial community composition during granulation, which was confirmed by 16S rRNA gene sequencing. In particular, Janthinobacterium (known denitrifier and producer of antimicrobial pigment) and Auxenochlorella protothecoides (mixotrophic green algae) were predominant during stage 2 bulking. The chitinolytic activity of Chitinophaga is likely antagonistic towards Auxenochlorella and may have contributed to stage 3 stable granule formation. Rhodanobacter, known to support complete denitrification, were predominant in stage 1 and stage 3 granules. The relative abundance of Rhodanobacter coincided with high protein concentrations in EPS, suggesting a role in microbial aggregation and granule formation.