Pusillimonas maritima sp. nov., isolated from surface seawater

Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance

A novel Gram-stain-negative, aerobic rod-shaped bacterial strain, which was catalase- and oxidase-positive, designated as DMV24BSW_DT, was isolated from the estuarine waters of the Bhavnagar (India) coast of the Arabian Sea. Its 16S rRNA gene exhibited 99.52% similarity with Neopusillimonas maritima 17-4AT, followed by 97.95% similarity with the Pusillimonas caeni strain EBR-8-1 and 97.4% similarity with the P. noertemannii strain BN9T. Phylogenomic analysis using BPGA (14,332 aa) and UBCG (90,261 bp) tools revealed a unique phylogenetic position within the genus Neopusillimonas. The genome exhibited a G + C content of 53.25%. In comparison with N. maritima 17-4AT, the strain demonstrated an average nucleotide identity (ANIb) of 94.47% and a digital DNA-DNA hybridization (dDDH) value of 60.1%, indicating distinct genomic divergence. The genome of DMV24BSW_DT contains several unique metabolic genes that facilitate efficient electron transfer during aerobic respiration. Additionally, it harbours one intact prophage and four defective prophages, indicating ongoing viral interactions. The genome encodes a complete pathway for ectoine biosynthesis and transportation. Strain DMV24BSW_DT tested positive for gelatin hydrolysis and demonstrated the ability to utilize a wide range of carbohydrates, including α-D-glucose, D-melibiose, D-fructose, L-rhamnose, and various organic acids, such as methyl pyruvate and propionic acid, along with tolerance to fluctuating pH (5 to 10) and salinity (0-4% NaCl). The major polar lipids included phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine, while fatty acid analysis revealed C12:0, C16:0, C17:0 cyclo, and summed feature 2 (C12:0 aldehyde/unknown) as major components. The respiratory quinones identified were MK-7 and MK-8. These comprehensive phenotypic, chemotaxonomic, and genomic characteristics support the unique taxonomic position of DMV24BSW_DT within the genus Neopusillimonas and the proposal of a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aestuarii sp. nov. (Type strain DMV24BSW_DT = MCC 2506 T = KCTC 72453 T = JCM 34508 T) is proposed.

Novel 4-chlorophenoxyacetate dioxygenase-mediated phenoxyalkanoic acid herbicides initial catabolism in Cupriavidus sp. DL-D2

Microbial metabolism is an important driving force for the elimination of 4-chlorophenoxyacetic acid residues in the environment. The α-Ketoglutarate-dependent dioxygenase (TfdA) or 2,4-D oxygenase (CadAB) catalyzes the cleavage of the aryl ether bond of 4-chlorophenoxyacetic acid to 4-chlorophenol, which is one of the important pathways for the initial metabolism of 4-chlorophenoxyacetic acid by microorganisms. However, strain Cupriavidus sp. DL-D2 could utilize 4-chlorophenoxyacetic acid but not 4-chlorophenol for growth. This scarcely studied degradation pathway may involve novel enzymes that has not yet been characterized. Here, a gene cluster (designated cpd) responsible for the catabolism of 4-chlorophenoxyacetic acid in strain DL-D2 was cloned and identified, and the dioxygenase CpdA/CpdB responsible for the initial degradation of 4-chlorophenoxyacetic acid was successfully expressed, which could catalyze the conversion of 4-chlorphenoxyacetic acid to 4-chlorocatechol. Then, an aromatic cleavage enzyme CpdC further converts 4-chlorocatechol into 3-chloromuconate. The results of substrate degradation experiments showed that CpdA/CpdB could also degrade 3-chlorophenoxyacetic acid and phenoxyacetic acid, and homologous cpd gene clusters were widely discovered in microbial genomes. Our findings revealed a novel degradation mechanism of 4-chlorophenoxyacetic acid at the molecular level.

Neopusillimonas aromaticivorans sp. nov. isolated from poultry manure

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST667T, isolated from poultry manure sampled in Taiwan. The cells were observed to be aerobic, motile and non-spore-forming rods, displaying positive reactions for oxidase. Optimal growth of CC-YST667T was observed at 25 °C, pH 8.0 and with 1 % (w/v) NaCl. The polar lipid profile consisted of phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and multiple unidentified polar lipids. The major polyamine was spermidine. The major cellular fatty acids (>5 %) included C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c and C14 : 0 3OH/iso-C16 : 1 I. On the basis of the results of analysis of 16S rRNA gene sequences, this isolate showed the closest phylogenetic relationship with 'Neopusillimonas minor' (with 98.2 % similarity) and Paralcaligenes ureilyticus (with 97.3 % similarity) of the family Alcaligenaceae. The draft genome, (3.3 Mb) with a DNA G+C content of 57.2 mol%, harboured various genes involved in the biodegradation of aromatic hydrocarbons. CC-YST667T shared highest orthologous average nucleotide identity (OrthoANI) with the type strains of species of of the genera Neopusillimonas (72.4‒77.9 %, n=2), Pusillimonas (72.8‒73.0 %, n=2) and Pollutimonas (71.7‒73.0 %, n=5). On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with the results of comparative 16S rRNA gene sequencing, OrthoANI, digital DNA-DNA hybridization (DDH) and the phylogenomic placement, strain CC-YST667T is considered to represent a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aromaticivorans sp. nov. is proposed. The type strain is CC-YST667T (=BCRC 81321T =JCM 34761T).

Impact of petroleum refinery on aquatic ecosystem of Skikda Bay (Algeria): Diversity and abundance of viable bacterial strains

This paper reports a study on the impact of petroleum refinery effluents on the bacterial load and diversity of the aquatic ecosystem in Skikda Bay (Algeria). The results showed a large spatiotemporal variation in the isolated bacterial species. This difference between stations and seasons could be attributed to environmental factors and to the pollution rate at the different sampling sites. Statistical analysis results showed that physicochemical parameters such as pH, electrical conductivity and salinity have a very significant effect on the microbial load (p < 0.001), while hydrocarbon pollution has a significant effect on the diversity of bacterial species (p < 0.05). In total 75 bacteria were isolated from six sampling sites during the four seasons. A significant spatiotemporal richness and diversity was observed in water samples. A total of 42 strains belonging to 18 bacterial genera were identified. Most of these genera belong to the class of Proteobacteria.

Genome analysis of Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., isolated from nitrate- and radionuclide-contaminated groundwater, and transfer of several Pusillimonas species into three new genera Allopusillimonas, Neopusillimonas, and Mesopusillimonas

Two facultatively anaerobic, chemoorganoheterotrophic bacterial strains, designated JR1/69-2-13^T and JR1/69-3-13^T, were isolated from nitrate- and radionuclide-contaminated groundwater (Ozyorsk town, South Urals, Russia). Both strains were found to be motile, Gram-stain negative rod-shaped neutrophilic, psychrotolerant bacteria that grow within the temperature range from 5-10 to 33 °C at 0-3 (0-5)% NaCl (w/v). The major cellular fatty acids were identified as C_16:0, C_16:1 ω7c, C_18:1 ω7c and C_17:0 cyclo. The major polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and unidentified aminophospholipids. The genomic G + C content of strains JR1/69-2-13^T and JR1/69-3-13^T was determined to be 57.2 and 57.9%, respectively. The 16S rRNA gene sequences of the strains showed high similarity between each other (98.6%) and to members of the genera Pusillimonas (96.8-98.4%) and Candidimonas (97.1-98.0%). The average nucleotide identity and digital DNA-DNA hybridization (dDDH) values among genomes of the new isolates and Pusillimonas and Candidimonas genomes were below 84.5 and 28.8%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic and chemotaxonomic characterisation, we propose assignment of strains JR1/69-3-13^T (= VKM B-3223^T = KCTC 62615^T) and JR1/69-2-13^T (= VKM B-3222^T = KCTC 62614^T) to a new genus Pollutimonas as the type strains of two new species, Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., respectively. As a result of the taxonomic revision of the genus Pusillimonas, three novel genera, Allopusillimonas, Neopusillimonas, and Mesopusillimonas are also proposed; and Candidimonas bauzanensis is reclassified as Pollutimonas bauzanensis comb. nov. Genome analysis of the new isolates suggested molecular mechanisms of their adaptation to an environment highly polluted with nitrate and radionuclides.

Lignin-oxidizing and xylan-hydrolyzing Vibrio involved in the mineralization of plant detritus in the continental slope

A large amount of terrigenous organic matter (TOM) is constantly transported to the deep sea. However, relatively little is known about the microbial mineralization of TOM therein. Our recent in situ enrichment experiments revealed that Vibrio is especially enriched as one of the predominant taxa in the cultures amended with natural plant materials in the deep sea. Yet their role in the mineralization of plant-derived TOM in the deep sea remains largely unknown. Here we isolated Vibrio strains representing dominant members of the enrichments and verified their potential to degrade lignin and xylan. The isolated strains were closely related to Vibrio harveyi, V. alginolyticus, V. diabolicus, and V. parahaemolyticus. Extracellular enzyme assays, and genome and transcriptome analyses revealed diverse peroxidases, including lignin peroxidase (LiP), catalase-peroxidase (KatG), and decolorizing peroxidase (DyP), which played an important role in the depolymerization and oxidation of lignin. Superoxide dismutase was found to likely promote lignin oxidation by supplying H2O2 to LiP, DyP, and KatG. Interestingly, these deep-sea Vibrio strains could oxidize lignin and hydrolyze xylan not only through aerobic pathway, but also through anaerobic pathway. Genome analysis revealed multiple anaerobic respiratory mechanisms, including the reductions of nitrate, arsenate, tetrathionate, and dimethyl sulfoxide. The strains showed the potential to anaerobically reduce sulfite and metal oxides of iron and manganese, in contrast the non-deep-sea Vibrio strains were not retrieved of genes involved in reduction of metal oxides. This is the first report about the lignin oxidation mechanisms in Vibrio and their role in TOM mineralization in anoxic and oxic environments of the marginal sea.

Pusillimonas minor sp. nov., a novel member of the genus Pusillimonas isolated from activated sludge

A novel pale white-pigmented bacterial strain designated YC-7-48^T was isolated from activated sludge in China. Cells of the strain, which grew at 15-37 °C (optimum at 30 °C) and pH 6.0-9.0 (optimum at 7.0), were Gram-stain-negative, rod-shaped and motile. Strain YC-7-48^T had 97.4-97.1% 16S rRNA gene sequence similarity to type strains of eight species in the genera Pusillimonas, Eoetvoesia, Paralcaligenes, Parapusillimonas and Paracandidimonas of the family Alcaligenaceae. Phylogenetic analysis based on 16S rRNA gene sequencing placed the strain on a separate branch in the genus Pusillimonas and showed that it exhibited 97.4, 97.3 and 96.6% similarity to Pusillimonas caeni EBR-8-1^T, Pusillimonas noertemannii BN9^T and Pusillimonas maritima 17-4A^T, respectively. The genome size of strain YC-7-48^T was 3202438 bp, with 54.3 mol% G+C content. According to the genome analysis, YC-7-48^T encodes several heavy metal resistance proteins and enzymes related to the metabolism of nicotine and aromatic compounds. The results of digital DNA-DNA hybridization and average nucleotide identity analyses based on whole genome sequences between strain YC-7-48^T and the closely related strains indicated that the strain represented a new species of the genus Pusillimonas. The chemotaxonomic results identified Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified aminolipids as the major polar lipids, and C_16:0 (27.4 %), C_17:0 cyclo (22.0 %), C_18:0 (11.7 %) and C_19:0 cyclo ω8c (9.5 %) as the major fatty acids. Thus, based on morphological, chemotaxonomic and phylogenetic characterization and genomic data, we proposed that the isolate is a representative of a novel species named Pusillimonas minor sp. nov., with the type strain YC-7-48^T (=CGMCC 1.17466^T=KACC 21349^T).