The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil

The potential of ferrihydrite-synthetic humic-like acid composite as a soil amendment for metal-contaminated agricultural soil: Immobilization mechanisms by combining abiotic and biotic perspectives

In-situ passivation technique has attracted increasing attention for metal-contaminated agricultural soil remediation. However, metal immobilization mechanisms are mostly illustrated based on metal speciation changes and alterations in soil physicochemical properties from a macroscopic and abiotic perspective. In this study, a ferrihydrite-synthetic humic-like acid composite (FH-SHLA) was fabricated and applied as a passivator for a 90-day soil incubation. The heavy metals immobilization mechanisms of FH-SHLA were investigated by combining both abiotic and biotic perspectives. Effects of FH-SHLA application on soil micro-ecology were also evaluated. The results showed that the 5%FH-SHLA treatment significantly decreased the DTPA-extractable Pb, Cd and Zn by 80.75%, 46.82% and 63.63% after 90 days of incubation (P < 0.05), respectively. Besides, 5% FH-SHLA addition significantly increased soil pH, soil organic matter content and cation exchange capacity (P < 0.05). The SEM, FTIR, and XPS characterizations revealed that the abiotic metal immobilization mechanisms by FH-SHLA included surface complexation, precipitation, electrostatic attraction, and cation-π interactions. For biotic perspective, in-situ microorganisms synergistically participated in the immobilization process via sulfide precipitation and Fe mineral production. FH-SHLA significantly altered the diversity and composition of the soil microbial community, and enhanced the intensity and complexity of the microbial co-occurrence network. Both metal bioavailability and soil physiochemical parameters played a vital role in shaping microbial communities, while the former contributed more. Overall, this study provides new insight into the heavy metal passivation mechanism and demonstrates that FH-SHLA is a promising and environmentally friendly amendment for metal-contaminated soil remediation.

Genomic insights revealed the environmental adaptability of Planococcus halotolerans Y50 isolated from petroleum-contaminated soil on the Qinghai-Tibet Plateau

The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C₁₁-C₂₃, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 10³ J/m² UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.

Cold-adaptive traits identified by comparative genomic analysis of a lipase-producing Pseudomonas sp. HS6 isolated from snow-covered soil of Sikkim Himalaya and molecular simulation of lipase for wide substrate specificity

The genomic analysis of industrially important bacteria can help in understanding their capability to withstand extreme environments and shed light on their metabolic capabilities. The whole genome of a previously reported broad temperature active lipase-producing Pseudomonas sp. HS6, isolated from snow-covered soil of the Sikkim Himalayan Region, was analyzed to understand the capability of the bacterium to withstand cold temperatures and study its lipolytic nature. Pseudomonas sp. HS6 was found to be psychrotolerant with an optimal growth temperature ranging between 25 and 30 °C, with the ability to grow at 5 °C. The genome harbours various cold-adaptation genes, such as cold-shock proteins, fatty acid alteration, and cold stress-tolerance genes, supporting the psychrotolerant nature of the organism. The comparative analysis of Pseudomonas sp. HS6 genome showed the presence of amino acid substitutions in genes that favor efficient functioning and flexibility at cold temperatures. Genome mining revealed the presence of four triacylglycerol lipases, among which the putative lipase 3 was highly similar to the broad temperature-active lipase purified and characterized in our previous study. In silico studies of putative lipase 3 revealed broad substrate specificity with partial and no inhibition of the enzyme activity in the presence of PMSF and orlistat. The presence of genes associated with cold adaptations and true lipases with activity at broad temperature and substrate specificity in the genome of Pseudomonas sp. HS6 makes this bacterium a suitable candidate for industrial applications.

Pollution Indicators and HAB-Associated Halophilic Bacteria Alongside Harmful Cyanobacteria in the Largest Mussel Cultivation Area in Greece

Taking into consideration the essential contribution of Mytilus galloprovincialis farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples from aquaculture zones from the point of view of both the organism and public health. In the present study, we investigated the bacterial community existing in water samples from six Mytilus galloprovincialis aquaculture areas in the Thermaikos gulf, northern Greece, that may provoke toxicity in aquatic organisms and humans and may indicate environmental pollution in mussel production as well as algal blooms. Bacterial species were identified molecularly by sequencing of a partial 16s rRNA segment and were analyzed phylogenetically for the confirmation of the bacterial taxonomy. The results obtained revealed the presence of four bacterial genera (Halomonas sp., Planococcus sp., Sulfitobacter sp., and Synechocystis sp.). Members of the Halomonas and Sulfitobacter genera have been isolated from highly polluted sites, Planococcus bacteria have been identified in samples derived directly from plastic debris, and Synechocystis bacteria are in line with microcystin detection. In this context, the monitoring of the bacteria community in mussel aquaculture water samples from the Thermaikos gulf, the largest mussel cultivation area in Greece, represents an indicator of water pollution, microplastics presence, algal blooms, and toxin presence.

Hydrocarbon biodegradation potential of microbial communities from high Arctic beaches in Canada's Northwest Passage

Sea ice loss is opening shipping routes in Canada's Northwest Passage, increasing the risk of an oil spill. Harnessing the capabilities of endemic microorganisms to degrade oil may be an effective remediation strategy for contaminated shorelines; however, limited data exists along Canada's Northwest Passage. In this study, hydrocarbon biodegradation potential of microbial communities from eight high Arctic beaches was assessed. Across high Arctic beaches, community composition was distinct, potential hydrocarbon-degrading genera were detected and microbial communities were able to degrade hydrocarbons (hexadecane, naphthalene, and alkanes) at low temperature (4 °C). Hexadecane and naphthalene biodegradation were stimulated by nutrients, but nutrients had little effect on Ultra Low Sulfur Fuel Oil biodegradation. Oiled microcosms showed a significant enrichment of Pseudomonas and Rhodococcus. Nutrient-amended microcosms showed increased abundances of key hydrocarbon biodegradation genes (alkB and CYP153). Ultimately, this work provides insight into hydrocarbon biodegradation on Arctic shorelines and oil-spill remediation in Canada's Northwest Passage.

Planococcus Species - An Imminent Resource to Explore Biosurfactant and Bioactive Metabolites for Industrial Applications

The marine environment represents a well-off and diverse group of microbes, which offers an enormous natural bioactive compounds of commercial importance. These natural products have expanded rigorous awareness due to their widespread stability and functionality under harsh environmental conditions. The genus Planococcus is a halophilic bacterium known for the production of diverse secondary metabolites such as 2-acetamido-2-deoxy-α-d-glucopyranosyl-(1, 2)-β-d-fructofuranose exhibiting stabilizing effect and methyl glucosyl-3,4-dehydro-apo-8-lycopenoate displaying antioxidant activity. The genus Planococcus is reported generally for hydrocarbon degradation in comparison with biosurfactant/bioemulsifier secretion. Although Planococcus was proposed in 1894, it seized long stretch (till 1970) to get accommodated under the genus Planococcus authentically. Large-scale biosurfactant production from Planococcus was reported in 2014 with partial characterization. For the first time in 2019, we documented genomic and functional analysis of Planococcus sp. along with the physico-chemical properties of its biosurfactant. In 2020, again we screened biosurfactant for pharmacological applications. The present review discusses the comprehensive genomic insights and physical properties of Planococcus-derived biosurfactant. Moreover, we also highlight the prospects and challenges in biosurfactant production from Planococcus sp. Among ∼102 reports on biosurfactant produced by marine bacteria, 43 were of glycolipid and 59 were non-glycolipid type. Under other biosurfactant type, they were identified as lipopeptide (20) like surfactin (5), glycolipoprotein/lipoprotein (12), and other non-glycolipid (22). Planococcus sp. generally produces glycolipid-type biosurfactant (4) and exopolysaccharides (2). The single report documented in the literature is on biosurfactant production (glycolipid +non glycolipid) by diverse marine microbes (39) suggesting their novelty and diversity for biosurfactant secretion.

Planococcus lenghuensis sp. nov., an oil-degrading bacterium isolated from petroleum-contaminated soil

A Gram-staining-positive and aerobic coccus with the ability to degrade petroleum bacterium, designated Y42^T, was isolated from the Lenghu oil field located in the northern margin of the Qaidam Basin. Phylogenetic and signature nucleotides analyses revealed that strain Y42^T belongs to the genus Planococcus. The multiple sequence alignments of 16S rRNA and housekeeping genes showed that strain Y42^T formed a distinct lineage with the other Planococcus clade. The average nucleotide identity (ANI) and DNA-DNA hybridization values (DDH) between strain Y42^T and the reference strains were 69.5-70.1 and 19.4-21.7%, respectively, which values were below the threshold for species delineation. The major fatty acids of strain Y42^T were anteiso-C_15:0. The respiratory quinone was MK-7 (71.8%) as the predominant menaquinone followed the MK-6 (28.2%) and the cell-wall hydrolysates contained LL-diaminopimelic acid. The polar lipid was composed of diphosphatidyl glycerol, phosphatidyl glycerol, phosphoglycolipid, aminophospholipid and four unidentified lipids. The peptidoglycan type was A4α (L-Lys-D-Glu). The strain Y42^T possessed larger genome (approximately 4 MB) and revealed obvious differences for the abundance of the COG categories compared with the other Planococcus bacteria. Also, the strain Y42^T also possessed more unique orthologous proteins. The structural characteristics of the strain Y42^T genome provided a competitive advantage for better survival in petroleum-polluted environments. Combined with the 16S rRNA gene and genome sequence, phenotypic as well as chemotaxonomic characterisations, strain Y42^T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus lenghuensis sp. nov. be proposed. The type strain is Y42^T (= CGMCC 1.15921^T = JCM 32719^T).

Complete Genome Sequence of Acidithiobacillus Ferrooxidans YNTRS-40, a Strain of the Ferrous Iron- and Sulfur-Oxidizing Acidophile

Acidithiobacillus ferrooxidans YNTRS-40 (A. ferrooxidans) is a chemolithoautotrophic aerobic bacterium isolated from Tengchong hot springs, Yunnan Province, China, with a broad growth pH range of 1.0–4.5. This study reports the genome sequence of this strain and the information of genes related to the adaptation of diverse stresses and the oxidation of ferrous iron and sulfur. Results showed that YNTRS-40 possesses chromosomal DNA (3,209,933-bp) and plasmid DNA (47,104-bp). The complete genome of 3,257,037-bp consists of 3,349 CDS genes comprising 6 rRNAs, 52 tRNAs, and 6 ncRNAs. There are many encoded genes associated with diverse stresses adaptation and ferrous iron and sulfur oxidation such as rus operon, res operon, petI, petII, sqr, doxDA, cydAB, and cyoABCD. This work will provide essential information for further application of A. ferrooxidans YNTRS-40 in industry.

Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil

Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.