Physiological and biochemical characterization and genome analysis of Rhodococcus qingshengii strain 7B capable of crude oil degradation and plant stimulation

Bottom-up construction and screening of algae-bacteria consortia for pollutant biodegradation

Microbial communities have been used as important biological tools for a variety of purposes associated with agriculture, the food industry and human health. Artificial engineering of microbial communities is an emerging field of research motivated by finding stable and efficient microbial systems. However, the successful design of microbial communities with desirable functions not only requires profound understanding of microbial activities, but also needs efficient approaches to piece together the known microbial traits to give rise to more complex systems. This study demonstrates the bottom-up integration of environmentally isolated phototrophic microalgae and chemotrophic bacteria as artificial consortia to bio-degrade selected volatile organic compounds (VOCs). A high throughput screening method based on 96-well plate format was developed for discovering consortia with bioremediation potential. Screened exemplar consortia were verified for VOCs degradation performance, among these, certain robust consortia were estimated to have achieved efficiencies of 95.72% and 92.70% and near 100% removal (7 days) of benzene, toluene, and phenol, respectively, with initial concentrations of 100 mg/L. VOCs degradation by consortia was mainly attributed to certain bacteria including Rhodococcus erythropolis, and Cupriavidus metallidurans, and directly contributed to the growth of microalgae Coelastrella terrestris (R = 0.82, p < 0.001). This work revealed the potential of converting VOCs waste into algal biomass by algae-bacteria consortia constructed through a bottom-up approach. The screening method enables rapid shortlisting of consortia combinatorial scenarios without prior knowledge about the individual strains or the need for interpreting complex microbial interactions.

Whole Genome Analysis and Assessment of the Metabolic Potential of Gordonia rubripertincta Strain 112, a Degrader of Aromatic and Aliphatic Compounds

The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this work was to study the potential of G. rubripertincta 112 as a degrader of aromatic and aliphatic compounds and analyze its complete genome in comparison with other known G. rubripertincta strains. The genome had a total length of 5.28 Mb and contained 4861 genes in total, of which 4799 were coding sequences (CDS). The genome contained 62 RNA genes in total, of which 50 were tRNAs, three were ncRNAs, and nine were rRNAs. The strain bears plasmid elements with a total length of 189,570 nucleotides (plasmid p1517). The strain can utilize 10.79 ± 1.17% of hexadecane and 16.14 ± 0.16% of decane over 3 days of cultivation. In the genome of the strain, we have found metabolic pathways of alkane (cytochrome P450 hydroxylases) and catechol (ortho- and meta-pathways) degradation. These results will help us to further approach the fundamental study of the processes occurring in the strain cells and to enrich our knowledge of the catabolic capabilities of G. rubripertincta.

Complete Genome Sequence of Rhodococcus qingshengii Strain PM1, Isolated from a Selenium-Rich Mine in China

Rhodococcus qingshengii PM1 was isolated from selenium-rich carbonaceous mudstones in Enshi, Hubei, China. Here, we report the complete genome sequence of this strain, which was obtained by combining Illumina and Nanopore sequencing.

Microbial community succession during crude oil-degrading bacterial enrichment cultivation and construction of a degrading consortium

Microbial community succession during the enrichment of crude-oil-degrading bacteria was analyzed using Illumina high-throughput sequencing to guide bacterial isolation and construction of a bacterial consortium. Community change occurred in 6 days; the most abundant phylum changed from Proteobacteria to Actinobacteria; the most abundant genera were Dietzia and unspecified_Idiomarinaceae. Two crude oil-degrading strains, Rhodococcus sp. OS62-1 and Dietzia sp. OS33, and one weak-crude-oil-degrading strain, Pseudomonas sp. P35, were isolated. A consortium comprising Rhodococcus sp. OS62-1 and Pseudomonas sp. P35 showed the highest crude-oil-degrading efficiency, reaching 85.72 ± 3.21% within 7 days, over a wide pH range (5–11) and salinity (0–80 g·L−1). Consumption of saturated hydrocarbons, aromatic hydrocarbons, and resins was greater by the consortium than by a single strain, as was degradation of short-chain-alkanes (C13–C17) according to gas-chromatography. The bacterial consortium provides technical support for bioremediation of crude oil pollution.