Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Strategies to Name Metallo-β-Lactamases and Number Their Amino Acid Residues

Metallo-β-lactamases (MBLs), also known as class B β-lactamases (BBLs), are Zn(II)-containing enzymes able to inactivate a broad range of β-lactams, the most commonly used antibiotics, including life-saving carbapenems. They have been known for about six decades, yet they have only gained much attention as a clinical problem for about three decades. The naming conventions of these enzymes have changed over time and followed various strategies, sometimes leading to confusion. We are summarizing the naming strategies of the currently known MBLs. These enzymes are quite diverse on the amino acid sequence level but structurally similar. Problems trying to describe conserved residues, such as Zn(II) ligands and other catalytically important residues, which have different numbers in different sequences, have led to the establishment of a standard numbering scheme for BBLs. While well intended, the standard numbering scheme is not trivial and has not been applied consistently. We revisit this standard numbering scheme and suggest some strategies for how its implementation could be made more accessible to researchers. Standard numbering facilitates the comparison of different enzymes as well as their interaction with novel antibiotics and BBL inhibitors.

Seasonal activities of the phyllosphere microbiome of perennial crops

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

Pontibacter qinzhouensis sp. nov., isolated from rhizosphere soil of a mangrove plant Rhizophora stylosa

A novel bacterium of the genus Pontibacter, designated GY10130^T, was isolated from rhizosphere soil of a mangrove plant Rhizophora stylosa collected from Guangxi province, China. Strain GY10130^T was Gram-stain negative, positive for oxidase activities, aerobic, short rod-shaped cells without flagella. Growth was observed at 10-40 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, 7.0) and NaCl concentrations of 0-4% (optimum, 1%). Strain GY10130^T is closely related to members of the genus Pontibacter, namely P. beigongshangensis CGMCC 1.17104^T (97.8%) and P. amylolyticus CGMCC 1.12749^T (95.0%), P. humi SWU8^T (94.7%), and less than 94.0% with other currently described type strains of Pontibacter. The strain GY10130^T showed an ANI value of 80.6% and dDDH value of 23.2% with P. beigongshangensis CGMCC 1.17104^T, followed by P. amylolyticus CGMCC 1.12749^T with ANI and dDDH values of 72.9 and 13.8%, respectively. Strain GY10130^T contains carotenoid-like pigments, but flexirubin-type pigments were absent. The cellular fatty acids (> 10%) consist of summed feature 4 (17:1 iso I/anteiso B) and iso-C_15:0. The predominant menaquinone is MK-7. The polar lipids comprise phosphatidylethanolamine, two unidentified glycolipids, two unidentified aminolipids and six unidentified phospholipids. The genome length of strain GY10130^T was 6.2 Mbp with a DNA G + C content of 47.1 mol% and 4727 protein-coding genes. The result of polyphasic taxonomic study show strain GY10130^T represents one novel species of Pontibacter, Pontibacter qinzhouensis sp. nov., with the type strain GY10130^T (=NBRC 113901^T  = CGMCC 1.16772^T).

Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water

A Gram-stain-negative, rod-shaped, non-motile, red-pink bacterium designated SD6^T was isolated from coastal marine water at Sadong Beach, Ulleung Island, South Korea. Cells of SD6^T grew at 10-42 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, pH 6.0-7.0) and at 0-8.0 % (w/v) NaCl (optimum, 0-3 %). Moreover, 16S rRNA gene sequence analysis indicated that strain SD6^T was a member of the genus Pontibacter, sharing similarities to Pontibacter aydingkolensis XAAS-1^T (98.0 %), Pontibacter amylolyticus 9-2^T (97.3 %), Pontibacter korlensis X14-1^T (97.2 %) and Pontibacter soli HYL7-26^T (96.8 %). The predominant fatty acids of strain SD6^T were identified as iso-C_15 : 0 and summed feature 4 (comprising anteiso-C_17 : 1 B and/or iso-C_17 : 1 I) and the sole respiratory quinone was identified as MK-7 (menaquinone 7). Major polar lipids included phosphatidylethanolamine, one unidentified phosphoglycolipid, two unidentified glycolipids and one unidentified lipid. The average nucleotide identity and in silico DNA-DNA hybridization values of strain SD6^T with its closely related strains were 72.8-79.8 % and 19.2-22.6 %, respectively. The genomic DNA G+C content was 45.4 mol%. In accordance with the results of phenotypic, chemotaxonomic and phylogenetic data, strain SD6^T represents a novel species of the genus Pontibacter, for which the name Pontibacter cellulosilyticus sp. nov. is proposed. The type strain is SD6^T (=KACC 21543^T=NBRC 114313^T=JCM 31022^T).

Characterization of a Glycoside Hydrolase Family 27 α-Galactosidase from Pontibacter Reveals Its Novel Salt-Protease Tolerance and Transglycosylation Activity

α-Galactosidases are of great interest in various applications. A glycoside hydrolase family 27 α-galactosidase was cloned from Pontibacter sp. harbored in a saline soil and expressed in Escherichia coli. The purified recombinant enzyme (rAgaAHJ8) was little or not affected by 3.5-30.0% (w/v) NaCl, 10.0-100.0 mM Pb(CH3COO)2, 10.0-60.0 mM ZnSO4, or 8.3-100.0 mg mL(-1) trypsin and by most metal ions and chemical reagents at 1.0 and 10.0 mM concentrations. The degree of synergy on enzymatic degradation of locust bean gum and guar gum by an endomannanase and rAgaAHJ8 was 1.22-1.54. In the presence of trypsin, the amount of reducing sugars released from soybean milk treated by rAgaAHJ8 was approximately 3.8-fold compared with that treated by a commercial α-galactosidase. rAgaAHJ8 showed transglycosylation activity when using sucrose, raffinose, and 3-methyl-1-butanol as the acceptors. Furthermore, potential factors for salt adaptation of the enzyme were presumed.