The potential of enhanced phytoremediation to clean up multi-contaminated soil - insights from metatranscriptomics.

This study aimed to (i) investigate the potential for enhanced phytoremediation to remove contaminants from soil historically co-contaminated with petroleum hydrocarbons (PHs) and heavy metals (HMs) and (ii) analyze the expression of crucial bacterial genes and whole metatranscriptomics profiles for better understanding of soil processes during applied treatment. Phytoremediation was performed using Zea mays and supported by the Pseudomonas qingdaonensis ZCR6 strain and a natural biofertilizer: meat and bone meal (MBM). In previous investigations, mechanisms supporting plant growth and PH degradation were described in the ZCR6 strain. Here, ZCR6 survived in the soil throughout the experiment, but the efficacy of PH removal from all soils fertilized with MBM reached 32 % regardless of the bacterial inoculation. All experimental groups contained 2 % (w/w) MBM. The toxic effect of this amendment on plants was detected 30 days after germination, irrespective of ZCR6 inoculation. Among the 17 genes tested using the qPCR method, only expression of the acdS gene, encoding 1-aminocyclopropane-1-carboxylic acid deaminase, and the CYP153 gene, encoding cytochrome P450-type alkane hydroxylase, was detected in soils. Metatranscriptomic analysis of soils indicated increased expression of methane particulated ammonia monooxygenase subunit A (pmoA-amoA) by Nitrosomonadales bacteria in all soils enriched with MBM compared to the non-fertilized control. We suggest that the addition of 2 % (w/w) MBM caused the toxic effect on plants via the rapid release of ammonia, and this led to high pmoA-amoA expression. In parallel, due to its wide substrate specificity, enhanced bacterial hydrocarbon removal in MBM-treated soils was observed. The metatranscriptomic results indicate that MBM application should be considered to improve bioremediation of soils polluted with PHs rather than phytoremediation. However, lower concentrations of MBM could be considered for phytoremediation enhancement. From a broader perspective, these results indicated the superior capability of metatranscriptomics to investigate the microbial mechanisms driving various bioremediation techniques.

Draft genome of a clinical Pseudomonas qingdaonensis isolate from a hospitalized patient at Kenyatta National Hospital, Kenya.

The first draft genome of Pseudomonas qingdaonensis, a gram-negative bacteria isolated from hospitalized patients in Kenya, is presented in this study. The genome was assembled using nanopore MinION readings, yielding an assembly of 8,857,650 base pairs made up of 5(five) contigs. The genome sequence of Pseudomonas qingdaonensis will help researchers better grasp its genetics. Furthermore, the data can be a valuable resource for comparative genomics and future research in this novel species.

Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits.

The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca3(PO4)2, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg-1 h-1). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.

Pseudomonas qingdaonensis sp. nov., an aflatoxin-degrading bacterium, isolated from peanut rhizospheric soil.

A Gram-stain-negative, aerobic, mobile, and rod-shaped bacterium, designated JJ3T, was isolated from peanut rhizospheric soil in Qingdao, Shandong Province, China, and was characterized using a polyphasic approach. Strain JJ3T grew at 4-40 °C, at pH 5.0-9.0 and 0-4% NaCl. The strain was positive for both catalase and oxidase tests, and was able to degrade aflatoxin B1. According to the 16S rRNA gene sequence comparisons, the strain JJ3T was identified as a member of the genus Pseudomonas and was most closely related to Pseudomonas japonica JCM 21532T and Pseudomonas alkylphenolica JCM 16553T with sequence similarity of 99.0% and 98.9%, respectively. A multilocus sequence analysis (MLSA) of concatenating 16S rRNA, gyrB and rpoD gene sequences showed that strain JJ3T belonged to the Pseudomonas putida subcluster. Genomic comparison of strain JJ3T with its closest phylogenetic type strain using average nucleotide index (ANI) and digital DNA-DNA relatedness revealed 76.7-82.9% and 20.2-37.1%, respectively. All values were distinctly lower than the thresholds established for species differentiation. The predominant cellular fatty acids of strain JJ3T were C17:0 cyclo (24.0%), C16:0 (21.4%), summed features 3 (C16:1ω7c and/or C16:1ω6c) (11.5%) and summed features 8 (C18:1ω7c and/or C18:1ω6c) (10.5%). The major polar lipids of strain JJ3T were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The physiological, biochemical, and genetic characteristics support the assignment of JJ3T to the genus Pseudomonas, but are different to those of phylogenetically neighboring species to represent a novel species. The name Pseudomonas qingdaonensis sp. nov. is proposed, with JJ3T (= JCM 32579T = KCTC 62384T = CGMCC 1.16493T) as the type strain.