Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes

Genomic Insights into Phosphorus Solubilization of Pseudomonas extremaustralis

Pseudomonas extremaustralis was first isolated from Antarctica and gained interest for its ability to thrive in extreme environmental conditions and degrade recalcitrant compounds. Some strains have been identified as phosphobacteria, which play a significant role in phosphorus (P) cycling by solubilizing or mineralizing insoluble phosphate forms for plant uptake. However, there is limited knowledge about the genomic mechanisms involved in P-cycling in the species P. extremaustralis. In this study, we aimed to evaluate the genomic potential of P. extremautralis as a phosphobacteria species by screening genes related to P-cycling. Two P. extremaustralis strains from pisciculture sludge residues were selected to sequence their complete genomes based on their ability to solubilize inorganic P in vitro, and an in silico analysis with all the P. extremaustralis genomes was performed to identify the presence of phosphorus-cycling-related genes. Genes mainly involved in the metabolic processes of two-component systems and transporters, and genes involved in organic acid production and alkaline phosphatases, were identified. This study helps us to understand the metabolic potential of this species and its role as a solubilizer of phosphates and thus a facilitator of plant-available phosphorus, which could guide the use of this species of phosphobacteria in the development of sustainable agriculture.

Unraveling the effects of polyhydroxyalkanoates accumulation in Pseudomonas extremaustralis growth and survival under different pH conditions

Polyhydroxyalkanoates (PHAs) are intracellular polymers that enhance bacterial fitness against various environmental stressors. Pseudomonas extremaustralis 14-3b is an Antarctic bacterium capable of accumulating, short-chain-length PHAs (sclPHAs), composed of C3-C5 monomers, as well as medium-chain-length PHAs (mclPHAs) containing ≥ C6 monomers. Since pH changes are pivotal in bacterial physiology, influencing microbial growth and metabolic processes, we propose that accumulated PHA increases P. extremaustralis fitness to cope with pH changes. To test this, we analyzed the production of sclPHA and mclPHA at different pH levels and its effect on bacterial survival against pH stress. P. extremaustralis was able to grow and accumulate PHA when the culture media pH ranged from 6.0 to 9.5, showing a marked loss of viability outside this range. Additionally, based on the analysis of different PHA-deficient mutants, we found that when exposed to both acidic and alkaline conditions, sclPHA and mclPHA conferred different protection against pH stress, with sclPHA making the main contribution. These results highlight the importance of PHA in supporting survival in pH-stressful environments.

Complete genome sequence analysis of a biosurfactant-producing bacterium Bacillus velezensis L2D39

Biosurfactants are amphipathic molecules with high industrial values owing to their chemical properties and stability under several environmental conditions. They have become attractive microbial products in the emerging biotechnology industry, offering a potential environmentally-friendly alternative to synthetic surfactants. Nowadays, several types of biosurfactants are commercially available for a wide range of applications in healthcare, agriculture, oil extraction and environmental remediation. In this study, a marine bacterium Bacillus velezensis L2D39 with the capability of producing biosurfactants was successfully isolated and characterized. The complete genome sequence of the bacterium B. velezensis L2D39 was obtained using PacBio Sequel HGAP.4, resulting in a sequence consisting of 4,140,042 base pairs with a 46.2 mol% G + C content and containing 4071 protein-coding genes. The presence of gene clusters associated with biosurfactants was confirmed through antiSMASH detection. The analysis of complete genome sequence will provide insight into the potential applications of this bacterium in biotechnological and natural product biosynthesis.

Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast

By investigating wet and dry age-related ripening of beef, Pseudomonas strains V3/3/4/13T and V3/K/3/5T were isolated. Strain V3/3/4/13T exhibited more than 99 % 16S rRNA gene-based similarity to Pseudomonas fragi and other members of this group, while isolate V3/K/3/5T was very close to Pseudomonas veronii and a number of relatives within the Pseudomonas fluorescens group. Additional comparisons of complete rpoB sequences and draft genomes allowed us to place isolate V3/3/4/13T close to Pseudomonas deceptionensis DSM 26521T. In the case of V3/K/3/5T the closest relative was P. veronii DSM 11331T. Average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values calculated from the draft genomes of V3/3/4/13T and P. deceptionensis DSM 26521T were 88.5 and 39.8 %, respectively. For V3/K/3/5T and its closest relative P. veronii DSM 11331T, the ANIb value was 95.1 % and the dDDH value was 60.7 %. The DNA G+C contents of V3/3/4/13T and V3/K/3/5T were 57.4 and 60.8 mol%, respectively. Predominant fatty acids were C16 : 0, C18 : 1 ω7c, C17 : 0 cyclo and summed feature C16 : 1 ω7ct/C15 : 0 iso 2OH. The main respiratory quinones were Q9, with minor proportions of Q8 and, in the case of V3/K/3/5T, additional Q10. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and, in the case of V3/K/3/5T, additional phosphatidylcholine. Based on the combined data, isolates V3/3/4/13T and V3/K/3/5T should be considered as representatives of two novel Pseudomonas species. The type strain of the newly proposed Pseudomonas kulmbachensis sp. nov. is V3/3/4/13T (=DSM 113654T=LMG 32520T), a second strain belonging to the same species is FLM 004-28 (=DSM 113604=LMG 32521); the type strain for the newly proposed Pseudomonas paraveronii sp. nov. is V3/K/3/5T (=DSM 113573T=LMG 32518T) with a second isolate FLM 11 (=DSM 113572=LMG 32519).

Ecological features of trace elements tolerant microbes isolated from sewage sludge of urban wastewater treatment plant

Worldwide wastewater treatment plants generate enormous amounts of sewage sludge, and their further disposal depends on the treatment technologies applied and spontaneously occurring microbiological processes. From different ages urban sewage sludge, 12 strains of bacteria with simultaneous tolerance to two or more trace elements: Co, Ni, Cu, Zn, Cd and Pb at concentration of 3-5 mmol were isolated and identified by PCR of target genes and Sanger sequencing methods. The isloated metal(loids) tolerant strains belong to the species, i.e., Serratia fonticola, Rhodococcus qingshengii, Pseudomonas fragi, Pseudomonas extremaustralis, Pseudomonas cedrina, Stenotrophomonas maltophilia, Serratia liquefaciens and Citrobacter freundii. The ecological features of the isolated strains were studied. The optimal growth temperatures for most strains was 15-30°C at pH range of 5-9, although some strains grew at 7°C (Pseudomonas fragi SS0-4, Serratia fonticola SS0-9 and Serratia fonticola SS12-11). Satisfactory growth of two strains (Serratia fonticola SS0-1and Citrobacter freundii SS60-12) was noted in an acidic medium at pH 4. Most of the strains grew in the NaCl concentration range of 1-5%. The isolated bacteria resistant to high concentrations of trace elements can be used for the effective mineralization of sewage sludge and for the decontamination of wastewater.

Isolation of Novel Bacterial Strains Pseudomonas extremaustralis CSW01 and Stutzerimonas stutzeri CSW02 from Sewage Sludge for Paracetamol Biodegradation

Paracetamol is one of the most used pharmaceuticals worldwide, but due to its widespread use it is detected in various environmental matrices, such as surface and ground waters, sediments, soils or even plants, where it is introduced mainly from the discharge of wastewater and the use of sewage sludge as fertilizer in agriculture. Its accumulation in certain organisms can induce reproductive, neurotoxic or endocrine disorders, being therefore considered an emerging pollutant. This study reports on the isolation, from sewage sludge produced in wastewater treatment plants (WWTPs), of bacterial strains capable of degrading paracetamol. Up to 17 bacterial strains were isolated, but only two of them, identified as Pseudomonas stutzeri CSW02 and Pseudomonas extremaustralis CSW01, were able to degrade very high concentrations of paracetamol in solution as a sole carbon and energy source, and none of them had been previously described as paracetamol degraders. These bacteria showed the ability to degrade up to 500 mg L^-1 of paracetamol in only 6 and 4 h, respectively, much quicker than any other paracetamol-degrader strain described in the literature. The two main paracetamol metabolites, 4-aminophenol and hydroquinone, which present high toxicity, were detected during the degradation process, although they disappeared very quickly for paracetamol concentrations up to 500 mg L^-1. The IC₅₀ of paracetamol for the growth of these two isolates was also calculated, indicating that P. extremaustralis CSW01 was more tolerant than S. stutzeri CSW02 to high concentrations of paracetamol and/or its metabolites in solution, and this is the reason for the much lower paracetamol degradation by S. stutzeri CSW02 at 2000-3000 mg L^-1. These findings indicate that both bacteria are very promising candidates for their use in paracetamol bioremediation in water and sewage sludge.

Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland

Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.

Small RNAs in the Antarctic bacterium Pseudomonas extremaustralis responsive to oxygen availability and oxidative stress

Bacterial small non-coding RNAs (sRNAs) play key roles as genetic regulators, mediating in the adaptability to changing environmental conditions and stress responses. In this work, we analysed putative sRNAs identified by RNA-seq experiments in different aeration conditions in the extremophile bacterium P. extremaustralis. These analyses allowed the identification of 177 putative sRNAs under aerobiosis (A), microaerobiosis (M) and microaerobiosis after H₂ O₂ exposure (m-OS). The size and transcription profile of eight sRNAs with differential expression were verified by Northern blot. sRNA40, with unknown function but conserved in other Pseudomonas species, was selected to perform overexpression experiments followed by RNA-seq analysis. The overexpression of sRNA40 in P. extremaustralis resulted in significant expression changes of 19 genes with 14 differentially upregulated and five downregulated. Among the upregulated genes, eight transcripts corresponded to components of secretion systems, such as gspH, gspK, and gspM, belonging to the Type II secretion system, and rspO and rspP from Type III secretion system. Our results showed a novel sRNA which expression was triggered by low oxygen levels, and whose overexpression was associated with upregulation of selected components of protein secretion systems.

The potential of Pseudomonas for bioremediation of oxyanions

Non-metal, metal and metalloid oxyanions occur naturally in minerals and rocks of the Earth's crust and are mostly found in low concentrations or confined in specific regions of the planet. However, anthropogenic activities including urban development, mining, agriculture, industrial activities and new technologies have increased the release of oxyanions to the environment, which threatens the sustainability of natural ecosystems, in turn affecting human development. For these reasons, the implementation of new methods that could allow not only the remediation of oxyanion contaminants but also the recovery of valuable elements from oxyanions of the environment is imperative. From this perspective, the use of microorganisms emerges as a strategy complementary to physical, mechanical and chemical methods. In this review, we discuss the opportunities that the Pseudomonas genus offers for the bioremediation of oxyanions, which is derived from its specialized central metabolism and the high number of oxidoreductases present in the genomes of these bacteria. Finally, we review the current knowledge on the transport and metabolism of specific oxyanions in Pseudomonas species. We consider that the Pseudomonas genus is an excellent starting point for the development of biotechnological approaches for the upcycling of oxyanions into added-value metal and metalloid byproducts.

Biopolymer production by halotolerant bacteria isolated from Caatinga biome

Saline environments are extreme habitats with a high diversity of microorganisms source of a myriad of biomolecules. These microorganisms are assigned as extremophiles recognized to be producers of new natural compounds, which can be synthesized by helping to survive under harshness and extreme conditions. In Brazil, in the saline and semi-arid region of Areia Branca (Caatinga biome), halotolerant bacteria (able to growth at high NaCl concentrations) were isolated from rhizosphere of native plants Blutaparon portulacoides and Spergularia sp. and their biopolymer production was studied. A total of 25 bacterial isolates were identified at genus level based on 16S rRNA gene sequence analysis. Isolates were mainly Gram-positive bacteria from Bacillaceae, Staphylococcaceae, Microbacteriaceae, and Bacillales XII incertae sedis families, affiliates to Bacillus, Staphylococcus, Curtobacterium, and Exiguobacterium genera, respectively. One of the Gram-negative isolates was identified as member of the Pseudomonadaceae family, genus Pseudomonas. All the identified strains were halotolerant bacteria with optimum growth at 0.6-2.0 M salt concentrations. Assays for biopolymer production showed that the halotolerant strains are a rich source of compounds as polyhydroxyalkanoates (PHA), biodegradable biopolymer, such as poly(3-hydroxybutyrate) (PHB) produced from low-cost substrates, and exopolysaccharides (EPS), such as hyaluronic acid (HA), metabolite of great interest to the cosmetic and pharmaceutical industry. Also, eight bacterial EPS extracts showed immunostimulatory activity, promising results that can be used in biomedical applications. Overall, our findings demonstrate that these biomolecules can be produced in culture medium with 0.6-2.0 M NaCl concentrations, relevant feature to avoid costly production processes. This is the first report of biopolymer-producing bacteria from a saline region of Caatinga biome that showed important biological activities.