Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties

A comparative analysis of the rhizosphere microbial communities among three species of the Salix genus

Rhizosphere microorganisms exert a significant influence in counteracting diverse external stresses and facilitating plant nutrient uptake. While certain rhizosphere microorganisms associated with Salix species have been investigated, numerous rhizosphere microorganisms from various Salix species remain underexplored. In this study, we employed high-throughput sequencing to examine the rhizosphere bacterial and fungal communities composition and diversity of three Salix species: Salix zangica (SZ), Salix myrtilllacea (SM), and Salix cheilophila (SC). Furthermore, the BugBase and FUNGuild were utilized to predict the functional roles of bacterial and fungal microorganisms. The findings revealed notable variations in the alpha and beta diversities of bacterial and fungal communities among the three Salix species exhibited significant differences (p < 0.05). The relative abundance of Flavobacterium was highest in the SZ samples, while Microvirga exhibited significant enrichment in the SM samples. Microvirga and Vishniacozyma demonstrate the highest number of nodes within their respective bacterial and fungal community network structures. The functions of bacterial microorganisms, including Gram-positive, potentially pathogenic, Gram-negative, and stress-tolerant types, exhibited significant variation among the three Salix species (p < 0.05). Furthermore, for the function of fungal microbe, the ectomycorrhizal guild had the highest abundance of symbiotic modes. This results demonstrated the critical role of ectomycorrhizal fungi in enhancing nutrient absorption and metabolism during the growth of Salix plants. Additionally, this findings also suggested that S. zangica plant was better well-suited for cultivation in stressful environments. These findings guide future questions about plant-microbe interactions, greatly enhancing our understanding of microbial communities for the healthy development of Salix plants.

Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils

Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.

Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil

The bacterial strain WB46 was isolated from the rhizosphere of willow plants (Salix purpurea L.) growing in soil contaminated with petroleum hydrocarbons. The strain was subjected to whole-genome shotgun sequencing using Illumina HiSeq. Its draft genome is 7.15 Mb, with a 69.55% GC content, containing 6387 protein-coding genes and 51 tRNA and 15 rRNA sequences. The quality and reliability of the genome were assessed using CheckM, attaining an estimated genome completeness of 98.75% and an estimated contamination of 1.68%. These results indicate a high-quality genome (>95%) and low contamination (<5%). Many of these genes are responsible for petroleum hydrocarbon degradation, such as alkane 1-monooxygenase (alkB) and naphthalene dioxygenase (ndo). 16S rRNA gene analysis, including in silico DNA-DNA hybridization (DDH) and average nucleotide identity (ANI), showed that strain WB46 belongs to the genus Nocardia, and the most closely related species is Nocardia asteroides. The strain WB46 showed a distance of 63.4% and sequence identity of 88.63%, respectively. These values fall below the threshold levels of 70% and 95%, respectively, suggesting that the strain WB46 is a new species. We propose the name of Nocardia canadensis sp. nov. for this new species. Interestingly, the sequence divergence of the 16S rRNA gene showed that the divergence only occurred in the V2 region. Therefore, the conventional V3-V4, V5-V7, or V8-V9 targeting metabarcoding, among others, would not be able to assess the diversity related to this new species.

Converging alfalfa (Medicago sativa L.) and petroleum hydrocarbon acclimated ACC-deaminase containing bacteria for phytoremediation of petroleum hydrocarbon contaminated soil

Plant assisted bioremediation of petroleum hydrocarbon contaminated soil is considered an effective green technology whereby accelerated degradation occurs due to converged effect of microorganisms and plants. However, survival and growth of microbes and plants under stress conditions is challenging task for success of the technology. In this study, plant growth promoting bacteria containing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase activity and tolerance to petroleum hydrocarbon contamination were used in association with alfalfa for bioremediation of petroleum hydrocarbon contaminated soil. Eight pre-isolated bacterial isolates from soil having previous history of petroleum contamination were used in convergence with alfalfa on sand soil which was artificially contaminated (10 g crude oil per kg^-1 of coarse textured soil). Combined effect of bacteria and plants on the degradation of petroleum hydrocarbons under controlled conditions of light and temperature was observed for a period of 60 days. The results of the study revealed that four bacterial isolates Bacillus subtilis strain PM32Y, Bacillus cereus strain WZ3S1, Bacillus sp. strain SM73 and Bacillus sp. strain WZ3S3 in association with alfalfa significantly degraded petroleum hydrocarbons. The most significant biodegradation (47%) of petroleum hydrocarbons was recorded in the experimental unit receiving PM32Y inoculation in association with alfalfa. Biodegradation of petroleum hydrocarbons was 33% with alone inoculation (without alfalfa) of PM32Y. The study revealed that combined use of bacteria and alfalfa plant is more efficient than alone application of either bacteria or plants for degradation of petroleum hydrocarbons.

In-Depth Characterization of Plant Growth Promotion Potentials of Selected Alkanes-Degrading Plant Growth-Promoting Bacterial Isolates

The use of plant growth-promoting rhizobacteria (PGPR) as a bioremediation enhancer in plant-assisted phytoremediation requires several steps, consisting of the screening, selection, and characterization of isolates. A subset of 50 bacterial isolates representing a wide phylogenetic range were selected from 438 morphologically different bacteria that were originally isolated from a petroleum hydrocarbon (PHC)-polluted site of a former petrochemical plant. Selected candidate bacteria were screened using six conventional plant growth-promoting (PGP) traits, complemented with the genetic characterization of genes involved in alkane degradation, as well as other pertinent functions. Finally, the bacterial isolates were subjected to plant growth promotion tests using a gnotobiotic approach under normal and stressed conditions. Our results indicated that 35 bacterial isolates (70%) possessed at least four PGP traits. Twenty-nine isolates (58%) were able to utilize n-hexadecane as a sole carbon source, whereas 43 isolates (86%) were able to utilize diesel as the sole carbon source. The presence of catabolic genes related to hydrocarbon degradation was assessed using endpoint PCR, with the alkane monooxygenase (alkB) gene found in 34 isolates, the cytochrome P450 hydroxylase (CYP153) gene found in 24 isolates, and the naphthalene dioxygenase (nah1) gene found to be present in 33 isolates. Thirty-six strains (72%) promoted canola root elongation in the growth pouch assay. After several rounds of screening, seven bacterial candidates (individually or combined in a consortium) were tested for canola root and shoot growth promotion in substrates amended by different concentrations of n-hexadecane (0%, 1%, 2%, and 3%) under gnotobiotic conditions. Our results showed that Nocardia sp. (WB46), Pseudomonas plecoglossicida (ET27), Stenotrophomonas pavanii (EB31), and Gordonia amicalis (WT12) significantly increased the root length of canola grown in 3% n-hexadecane compared with the control treatment, whereas Nocardia sp. (WB46) and Bacillus megaterium (WT10) significantly increased shoot length compared to control treatment at the same concentration of n-hexadecane. The consortium had a significant enhancement effect on root length compared to all isolates inoculated individually or to the control. This study demonstrates that the combination of PGPR traits and the PHC degradation potential of bacteria can result in an enhanced beneficial effect in phytoremediation management, which could lead to the development of innovative bacterial inoculants for plants to remediate PHC-contaminated soils.