Isolation and characterization of a crude oil degrading bacteria from formation water: comparative genomic analysis of environmental Ochrobactrum intermedium isolate versus clinical strains

Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool

In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36-48%, end: 27-30%) and Firmicutes (start: 13-33%, end: 12-16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.

Potential of Biosurfactants’ Production on Degrading Heavy Oil by Bacterial Consortia Obtained from Tsunami-Induced Oil-Spilled Beach Areas in Miyagi, Japan

Bioremediation is one of the promising environment-friendly approaches to eliminate oil contamination. However, heavy oil is known to degrade slowly due to its hydrophobicity. Therefore, microorganisms capable of producing biosurfactants are gaining substantial interest because of their potential to alter hydrocarbon properties and thereby speed up the degradation process. In this study, six bacterial consortia were obtained from the oil-spilled beach areas in Miyagi, Japan, and all of which exhibited high potential in degrading heavy oil measured by gas chromatography with flame ionization detector (GC-FID). The polymerase chain reaction—denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) revealed that the diverse microbial community in each consortium changed with subculture and became stable with a few effective microorganisms after 15 generations. The total petroleum hydrocarbons (TPH) degradation ability of the consortia obtained from a former gas station (C1: 81%) and oil refinery company (C6: 79%) was higher than that of the consortia obtained from wastewater treatment plant (WWTP) (C3: 67%, and C5: 73%), indicating that bacteria present in C1 and C6 were historically exposed to petroleum hydrocarbons. Moreover, it was intriguing that the consortium C4, also obtained from WWTP, exhibited high TPH degradation ability (77%). The NGS results revealed that two bacteria, Achromobacter sp. and Ochrobactrum sp., occupied more than 99% of the consortium C4, while no Pseudomonas sp. was found in C4, though this bacterium was observed in other consortia and is also known to be a potential candidate for TPH degradation as reported by previous studies. In addition, the consortium C4 showed high biosurfactant-producing ability among the studied consortia. To date, no study has reported the TPH degradation by the combination of Achromobacter sp. and Ochrobactrum sp.; therefore, the consortium C4 provided an excellent opportunity to study the interaction of and biosurfactant production by these two bacteria during TPH degradation.

Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum

Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a bla_OCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different bla_OCH variants as well as of the bla_OCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.

Taxonomic Organization of the Family Brucellaceae Based on a Phylogenomic Approach

Deciphering the evolutionary history of pathogenic bacteria and their near neighbors may help to understand the genetic or ecological bases which led to their pathogenic behavior. The Brucellaceae family comprises zoonotic pathogenic species belonging to the genus Brucella as well as the environmental genus Ochrobactrum for which some species are considered as opportunistic pathogens. Here, we used a phylogenomic approach including a set of 145 Brucellaceae genomes representative of the family diversity and more than 40 genomes of the order Rhizobiales to infer the taxonomic relationships between the family’s species. Our results clarified some unresolved phylogenetic ambiguities, conducting to the exclusion of Mycoplana spp. out of the family Brucellaceae and the positioning of all Brucella spp. as a single genomic species within the current Ochrobactrum species diversity. Additional analyses also revealed that Ochrobactrum spp. separate into two clades, one comprising mostly environmental species while the other one includes the species considered as pathogens (Brucella spp.) or opportunistic pathogens (mainly O. anthropi, O. intermedium, and O. pseudintermedium). Finally, we show that O. intermedium is undergoing a beginning of genome reduction suggestive of an ongoing ecological niche specialization, and that some lineages of O. intermedium and O. anthropi may shift toward an adaption to the human host.

Lipase and biosurfactant from Ochrobactrum intermedium strain MZV101 isolated by washing powder for detergent application

Background

Alkaline thermostable lipase and biosurfactant producing bacteria are very interested at detergent applications, not only because of their eco-friendly characterize, but alsoproduction lipase and biosurfactant by using cheap materials. Ochrobactrum intermedium strain MZV101 was isolated as washing powder resistant, alkaline thermostable lipase and biosurfactant producing bacterium in order to use at detergent applications.

Methods

O. intermedium strain MZV101 produces was lipase and biosurfactant in the same media with pH 10 and temperature of 60 °C. Washing test and some detergent compatibility character of lipase enzyme and biosurfactant were assayed. The antimicrobial activity evaluated against various bacteria and fungi.

Results

Lipase and biosurfactant produced by O. intermedium strain MZV101 exhibited high stability at pH 10–13 and temperature of 70–90 °C, biosurfactant exhibits good stability at pH 9–13 and thermostability in all range. Both lipase and biosurfactant were found to be stable in the presence of different metal ions, detergents and organic solvents. The lipase enzyme extracted using isopropanol with yield of 69.2% and biosurfactant with ethanol emulsification index value of 70.99% and yield of 9.32 (g/l). The single band protein after through from G-50 Sephadex column on SDS-PAGE was calculated to be 99.42 kDa. Biosurfactant O. intermedium strain MZV101 exhibited good antimicrobial activity against Gram-negative bacteria and against various bacterial pathogens. Based upon washing test biosurfactant and lipase O. intermedium strain MZV101considered being strong oil removal.

Conclusion

The results of this study indicate that isolated lipase and biosurfactant with strong oil removal, antimicrobial activity and good stability could be useful for detergent applications.

Graphical abstract