Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov

Degradation of polyethylene by three bacteria isolated from coastal beach

Polyethylene accumulates due to high production and slow degradation. Microbial degradation offers a promising solution for PE waste treatment. In this study, three bacterial strains, Alloalcanivorax sp. C16-1, Alloalcanivorax sp. C16-2, and Gordonia sp. R-1, were isolated from coastal plastic debris, each capable of utilizing polyethylene powder as the carbon source. After 30 days at 30 °C, low density polyethylene films showed modifications, including bacterial colonization, cracks, and holes as revealed by scanning electron microscopy. The water contact angle decreased, indicating increased hydrophilicity, while attenuated total reflection fourier transform infrared analysis confirmed surface oxidation with the formation of hydroxyl and carbonyl groups. High-temperature gel permeation chromatography showed decreases in the weight-average molecular weight of the films, indicating depolymerization. Nanoscale secondary ion mass spectrometry imaging demonstrated 13C assimilation from PE by the three strains at the single-cell level. Genomic analysis revealed that C16-1 and C16-2 were novel Alloalcanivorax species, with genes encoding potential PE-degrading enzymes, such as laccase and alkane hydroxylase, in all three isolates. These strains are widely distributed in marine environments, particularly in plastic accumulation hotspots, offering promising candidates for PE biodegradation research.

Isoalcanivorax beigongshangi sp. nov., isolated from the fermented grains of Chinese baijiu

A bacterial strain, REN37T, was isolated from fermented grains of Baijiu samples collected from Sichuan, PR China. The cells of strain REN37T was Gram-negative and aerobic. The cellular morphology exhibited rod-shaped cells without flagellum, displaying non-motility. The optimal growth condition was at 32-37 °C, pH 6.0-7.0, and with a NaCl concentration of 1-2% (w/v). Based on the analysis of 16S rRNA gene sequence, strain REN37T was identified to belong to the genus of Isoalcanivorax. Its closest species was Isoalcanivorax pacificus W11-5 T (96.1%). The polar lipids were identified to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, unidentified glycolipid, two unidentified phospholipids. The predominant menaquinone was MK-12. The predominant fatty acids were C15:0 anteiso (49.4%), C16:0 iso (18.1%), C17:0 anteiso (16.5%) and C15:0 iso (9.5%). The digital DNA-DNA hybridization (dDDH), average nucleotide identity (OrthoANI) and average amino acid identify (AAI) values between strain REN37T and its most similar species were 19.2%, 74.0% and 78.0%, respectively. The DNA G + C content of the strain REN37T was 63.0 mol%. Three alkane 1-monooxygenase (alkB1) genes (1152 bp, 1149 bp, 1179 bp) were identified in the genome, indicating that strain REN37T may be associated with efficient oil-degradation capabilities. Based on the results, REN37T represents a novel specie, and the name Isoalcanivorax beigongshangi sp. nov. was proposed. The type strain is REN37T (= GDMCC 1.3120 T = JCM 35319 T).

Phylogenomic analyses of the Listeriaceae family support species reclassification and proposal of a new family and new genera

The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72-73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health.

Microbial response to a port fuel spill: Community dynamics and potential for bioremediation

Following a fuel leakage inside a Portuguese maritime port, we conducted parallel 30-day experiments using contaminated seawater and fuel, sampled five days after the incident. This study aimed to (i)survey the native microbial community response to the spilled fuel and (ii)evaluate the efficacy of bioremediation, both biostimulation and bioaugmentation with a lyophilized bacterial consortium (Rhodococcus erythropolis, Pseudomonas sp.), in accelerating hydrocarbon degradation. Metabarcoding analysis revealed a shift in microbial communities, with increased abundance of hydrocarbon-degraders (e.g. Alcanivorax, Thalassospira). Ninety-five hydrocarbonoclastic bacteria were isolated, including key groups from the enriched communities. The lyophilized bacteria added in bioaugmentation, enhanced the abundance of hydrocarbon-degraders over time and were recovered throughout time. Bioremediation treatments favoured biodegradation, achieving over 60 % removal of total petroleum hydrocarbons after 15 days, contrasting with natural attenuation where almost no TPH was removed. This work highlights the potential of bioremediation technologies to accelerate hydrocarbon-degrading activity, for oil spills inside ports.

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.

Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea

Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.