Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera

The evolutionary relationships among species of the family Pseudomonadaceae were examined based on 255 available genomes representing >85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus Pseudomonas grouped within one large cluster which also included members of the genera Azotobacter and Azomonas. Within this large cluster 18-30 clades/subclades of species of the genus Pseudomonas consisting of between 1 and 36 species, were observed. However, a number of species of the genus Pseudomonas branched outside of this main cluster and were interspersed among other genera of the family Pseudomonadaceae. This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family Pseudomonadaceae is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus Pseudomonas also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. Pseudomonas caeni also branches outside of the main cluster and groups reliably with Oblitimonas alkaliphila and Thiopseudomonas denitrificans. Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus Thiopseudomonas, which has priority over the name Oblitimonas. We are also proposing transfer of the deep-branching Pseudomonas hussainii, for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species Pseudomonas cissicola and Pseudomonas geniculata are misclassified into the genus Pseudomonas and that they are specifically related to the genera Xanthomonas and Stenotrophomonas, respectively. In addition, we are also reclassifying 'Pseudomonas acidophila' as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).

Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera

Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.

Pseudomonas nanhaiensis sp. nov., a lipase-producing bacterium isolated from deep-sea sediment of the South China Sea

A bacterial lipase producing bacterium, designated SCS 2-3, was isolated from deep-sea sediment of the South China Sea. Phylogenetic analysis based on the 16S rRNA sequence revealed that strain SCS2-3 belonged to the genus Pseudomonas and had 98.56% similarity to P. xinjiangensis NRRL B-51270^T as the closest relative strain. MLSA using four protein-coding genes (dnaK, gyrA, recA, and rpoB) showed strain SCS 2-3 to form a separate branch. ANI and in silico DDH values between strain SCS 2-3 and related type strains of Pseudomonas were less than 81.51% and 23.80%, respectively. Genome comparison showed that strain SCS 2-3 shared 1875 core gene families with other eight closely related type strains in Pseudomonas, and the number of strain-unique genes was 263. Through gene annotations, genes related to lipase were found in the genome. Furthermore, a combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SCS 2-3 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas nanhaiensis sp. nov. is proposed. The type strain is SCS 2-3^T (= GDMCC 1.2219^T = JCM 34440^T).

Pseudomonas pratensis sp. nov., Isolated from Grassland Soil from Inner Mongolia, China

A novel bacterial strain, designated MHJ-10J^T, was isolated from a soil sample obtained from a grassland in Inner Mongolia, China. MHJ-10J^T strain could grow at 4-37 °C (optimum: 30 °C) and pH 4-9 (optimum: pH 6), as well as in the presence of 0-6% NaCl (optimum: 1%). Cells of strain MHJ-10J^T are Gram-negative, rod-shaped, and motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MHJ-10J^T was most closely related to Pseudomonas lutea OK2^T (98.5% 16S rRNA gene sequence similarity). The values of the average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) between strain MHJ-10J^T and its related species were all below 80.5% and 24.4%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The genomic G + C content of the MHJ-10J^T strain is 64.8 mol%. Based on the phenotypic, genotypic, chemotaxonomic, and phylogenetic analyses, strain MHJ-10J^T can be assigned to the genus Pseudomonas. In this study, we propose that strain MHJ-10J^T be classified as a novel species belonging to the genus Pseudomonas with the species name Pseudomonas pratensis sp. nov. The type strain of the proposed novel species is MHJ-10J^T (= KCTC 82206^T = CGMCC 17322^T).

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods

Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.

Pseudomonas laoshanensis sp. nov., isolated from peanut field soil

A novel Gram-stain-negative, aerobic strain, designated Y22^T, was isolated from peanut field soil in Laoshan Mountain in China. Cells of strain Y22^T were rod-shaped and motile by a single flagellum. The strain was found to be oxidase- and catalase-positive. 16S rRNA gene sequence based on phylogenetic analysis indicated that strain Y22^T belonged to the genus Pseudomonas, and showed the highest 16S rRNA gene sequence similarity of 99.0% to Pseudomonas pelagia JCM 15562^T, followed by Pseudomonas salina JCM 19469^T (98.4%), Pseudomonas sabulinigri JCM 14963^T (97.9%), Pseudomonas bauzanensis CGMCC 1.9095^T (97.6%) and Pseudomonas litoralis KCTC23093^T (97.5%). The phylogenetic analysis based on multilocus sequence analyses with concatenated 16S rRNA, gyrB, rpoD and rpoB genes indicated that strain Y22^T belonged to Pseudomonas pertucinogena lineage. The average nucleotide identity scores between strain Y22^T and closely related species were 74.6-82.8%, and the Genome-to-Genome Distance Calculator scores were 16.4-44.9%. The predominant cellular fatty acids of strain Y22^T were C_18:1ω7c (29.6%), C_17:0 cyclo (17.5%) and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) (17.4%). The genomic DNA G+C content was 57.9 mol%. On the basis of phenotypic characteristics, phylogenetic analyses and in silico DNA-DNA relatedness, a novel species, Pseudomonas laoshanensis sp. nov. is proposed. The type strain is Y22^T (= JCM 32580^T = KCTC 62385^T = CGMCC 1.16552^T).

Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions

In the current study, we aimed to elucidate the plant growth-promoting characteristics of Pseudomonas psychrotolerans CS51 under heavy metal stress conditions (Zn, Cu, and Cd) and determine the genetic makeup of the CS51 genome using the single-molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that inoculation with CS51 induced endogenous indole-3-acetic acid (IAA) and gibberellins (GAs), which significantly enhanced cucumber growth (root shoot length) and increased the heavy metal tolerance of cucumber plants. Moreover, genomic analysis revealed that the CS51 genome consisted of a circular chromosome of 5,364,174 base pairs with an average G+C content of 64.71%. There were around 4774 predicted protein-coding sequences (CDSs) in 4859 genes, 15 rRNA genes, and 67 tRNA genes. Around 3950 protein-coding genes with function prediction and 733 genes without function prediction were identified. Furthermore, functional analyses predicted that the CS51 genome could encode genes required for auxin biosynthesis, nitrate and nitrite ammonification, the phosphate-specific transport system, and the sulfate transport system, which are beneficial for plant growth promotion. The heavy metal resistance of CS51 was confirmed by the presence of genes responsible for cobalt-zinc-cadmium resistance, nickel transport, and copper homeostasis in the CS51 genome. The extrapolation of the curve showed that the core genome contained a minimum of 2122 genes (95% confidence interval = 2034.24 to 2080.215). Our findings indicated that the genome sequence of CS51 may be used as an eco-friendly bioresource to promote plant growth in heavy metal-contaminated areas.

The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena

Marine habitats represent a prolific source for molecules of biotechnological interest. In particular, marine bacteria have attracted attention and were successfully exploited for industrial applications. Recently, a group of Pseudomonas species isolated from extreme habitats or living in association with algae or sponges were clustered in the newly established Pseudomonas pertucinogena lineage. Remarkably for the predominantly terrestrial genus Pseudomonas, more than half (9) of currently 16 species within this lineage were isolated from marine or saline habitats. Unlike other Pseudomonas species, they seem to have in common a highly specialized metabolism. Furthermore, the marine members apparently possess the capacity to produce biomolecules of biotechnological interest (e.g. dehalogenases, polyester hydrolases, transaminases). Here, we summarize the knowledge regarding the enzymatic endowment of the marine Pseudomonas pertucinogena bacteria and report on a genomic analysis focusing on the presence of genes encoding esterases, dehalogenases, transaminases and secondary metabolites including carbon storage compounds.

Pseudomonas nitrititolerans sp. nov., a nitrite-tolerant denitrifying bacterium isolated from a nitrification/denitrification bioreactor

A nitrite-tolerant denitrifying bacterium, strain GL14^T, was isolated from the nitrification/denitrification bioreactor in our laboratory. Strain GL14^T was Gram-stain-negative, rod-shaped, non-spore-forming, facultatively anaerobic and motile by means of a single polar flagellum. Phylogenetic analyses based on 16S rRNA gene sequences indicated that it was assigned to the genus Pseudomonas with highest 16S rRNA gene sequence similarity (98.77 %) to Pseudomonas xanthomarina DSM 18231^T and Pseudomonassongnenensis NEAU-ST5-5^T, followed by Pseudomonasstutzeri ATCC 17588^T (98.42 %), Pseudomonaskunmingensis HL22-2^T (98.29 %) and Pseudomonaszhaodongensis NEAU-ST5-21^T (98.22 %). Phylogenetic analysis based on both concatenated sequences of the 16S rRNA gene and two housekeeping genes (gyrB and rpoD) and genome sequences further clarified the intrageneric phylogenetic position of strain GL14^T. The DNA G+C content of GL14^T was 63.1 mol%. The results of digital DNA-DNA hybridization (highest 24.2 % of DNA-DNA relatedness) based on the Genome-to-Genome Distance Calculator and average nucleotide identity analyses (highest 80.23 %) confirmed that the strain was distinctly delineated from known species of the genus Pseudomonas. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C17 : 0cyclo and C12 : 0. The respiratory quinone was ubiquinone Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the phylogenetic, genomic, phenotypic and chemotaxonomic analyses, it was concluded that strain GL14^T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas nitrititolerans sp. nov. is proposed. The type strain is GL14^T (=CGMCC 1.13874^T=NBRC 113853^T).

A thiotrophic microbial community in an acidic brine lake in Northern Chile

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Pseudomonas pharmafabricae sp. nov., Isolated From Pharmaceutical Wastewater

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated ZYSR67-Z^T, was isolated from a pharmaceutical wastewater sample collected from a chemical factory in Zhejiang, China. The strain was motile by a single polar flagellum and grew at 4-42 °C (optimum, 35 °C), pH 5.0-9.0 (optimum, 6.0) and 0-5.0% (w/v) NaCl (optimum, 2.0%). Based on multilocus sequence analysis using 16S rRNA, gyrB, rpoB and rpoD, the strain ZYSR67-Z^T formed a distinct phylogenetic group in the genus Pseudomonas. The average nucleotide identity values between strain ZYSR67-Z^T and the closely related 10 type strains of the Pseudomonas species were 75.8-78.6%. The in silico DNA-DNA hybridization values indicated that strain ZYSR67-Z^T and the type strains of the Pseudomonas shared 21.4-23.1% DNA relatedness. The predominant isoprenoid quinone system was ubiquinone-9 while ubiquinone-8 was present in trace amounts. The major fatty acids (> 10%) identified were C_12:0, C_16:0, C_18:1 ω7c and summed features 3 (C_16:1 ω7c and/or iso-C_15:0 2OH). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 62.6 mol%. On the basis of morphological, physiological and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain ZYSR67-Z^T was proposed to represent a novel species of the genus Pseudomonas, named Pseudomonas pharmafabricae sp. nov.. The type strain is ZYSR67-Z^T (= CGMCC 1.15498^T = JCM 31306^T).

Pseudomonas profundi sp. nov., isolated from deep-sea water

A Gram-stain-negative, aerobic bacterium, strain M5^T, was isolated from a seawater sample collected from the western Pacific Ocean at a depth of 1000 m and characterized by using polyphasic taxonomy. Cells of the strain were rod-shaped and motile by a single polar flagellum. Cells grew at 4-40 °C (optimum, 25 °C), at pH 7-10 (optimum, 9) and with 0-10 % NaCl (optimum, 1-2 %). Phylogenetic trees based on 16S rRNA gene sequences showed that strain M5^T was associated with the genus Pseudomonas, and showed highest similarities to Pseudomonas pelagia CL-AP6^T (97.8 %) and Pseudomonas salina XCD-X85^T (97.5 %) and Pseudomonas sabulinigri J64^T (96.4 %). The average nucleotide identity scores for strains CL-AP6^T and XCD-X85^T were 74.6 % and 73.7 %, the Genome-to-Genome Distance Calculator scores were 15.8-19.5 % and 15.4-19.7 %, and the species identification scores were 92.3 % and 92.4 %. The major isoprenoid quinone of strain M5^T was ubiquinone (Q-9) and the major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 33.2 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 22.8 %) and C16 : 0 (13 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and some unidentified lipids. The phylogenetic analysis and physiological and biochemical data showed that strain M5^T should be classified as representing a novel species in the genus Pseudomonas, for which the name Pseudomonas profundi sp. nov. is proposed. The type strain is M5^T (=CCTCC AB 2017186^T=KCTC 62119^T=CICC 24308^T).

Induced Salt Tolerance of Perennial Ryegrass by a Novel Bacterium Strain from the Rhizosphere of a Desert Shrub Haloxylon ammodendron

Drought and soil salinity reduce agricultural output worldwide. Plant-growth-promoting rhizobacteria (PGPR) can enhance plant growth and augment plant tolerance to biotic and abiotic stresses. Haloxylon ammodendron, a C4 perennial succulent xerohalophyte shrub with excellent drought and salt tolerance, is naturally distributed in the desert area of northwest China. In our previous work, a bacterium strain numbered as M30-35 was isolated from the rhizosphere of H. ammodendron in Tengger desert, Gansu province, northwest China. In current work, the effects of M30-35 inoculation on salt tolerance of perennial ryegrass were evaluated and its genome was sequenced to identify genes associated with plant growth promotion. Results showed that M30-35 significantly enhanced growth and salt tolerance of perennial ryegrass by increasing shoot fresh and dry weights, chlorophyll content, root volume, root activity, leaf catalase activity, soluble sugar and proline contents that contributed to reduced osmotic potential, tissue K⁺ content and K⁺/Na⁺ ratio, while decreasing malondialdehyde (MDA) content and relative electric conductivity (REC), especially under higher salinity. The genome of M30-35 contains 4421 protein encoding genes, 12 rRNA, 63 tRNA-encoding genes and four rRNA operons. M30-35 was initially classified as a new species in Pseudomonas and named as Pseudomonas sp. M30-35. Thirty-four genes showing homology to genes associated with PGPR traits and abiotic stress tolerance were identified in Pseudomonas sp. M30-35 genome, including 12 related to insoluble phosphorus solubilization, four to auxin biosynthesis, four to other process of growth promotion, seven to oxidative stress alleviation, four to salt and drought tolerance and three to cold and heat tolerance. Further study is needed to clarify the correlation between these genes from M30-35 and the salt stress alleviation of inoculated plants under salt stress. Overall, our research indicated that desert shrubs appear rich in PGPRs that can help important crops tolerate abiotic stress.

The current status on the taxonomy of Pseudomonas revisited: An update

The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.