A novel dichloromethane-degrading Lysinibacillus sphaericus strain wh22 and its degradative plasmid

Study of the effects of mineral salts on the biofilm formation on polypropylene fibers using three quantification methods

The microbial biofilms are ubiquitous in nature and represent important biological entities that affect various aspects of human life. As such, they attracted considerable attention during last decades, with the factors affecting the biofilm development being among the frequently studied topics. In our work, the biofilm was cultivated on the surface of polypropylene fibers in a nutrient medium inoculated by the suspension of two unsterile soils. The effects of ionic strength and valence of salt on the amount of the produced biofilm and on composition of biofilm microbial communities were investigated. The effect of valence was significant in some OTUs: Arthrobacter/Pseudarthrobacter/Paenarthrobacter and Bacillus with positive response to monovalent salt (KCl) and Streptomyces, Lysinibacillus, Pseudomonas, and Ensifer with positive response to divalent salt (MgSO₄). The significant preference for a certain concentration of salts was observed in the case of OTUs Agrobacterium, Bacillus (both 100 mM), and Brevundimonas (30 mM). A new quantification method based on measuring of oxidizable organic carbon in biofilm biomass, based on dichromate oxidation, was used. We compared the results obtained using this method with results of crystal violet destaining and measuring of extracted DNA concentration as proxies of the biofilm biomass. The dichromate oxidation is simple, inexpensive, and fast, and our results show that it may be more sensitive than crystal violet destaining. The highest biomass values tended to associate with high concentrations of the divalent salt. This trend was not observed in treatments where the monovalent salt was added. Our data confirm the importance of inorganic ions for biofilm composition and biomass accumulation.

Insights into Advancements and Electrons Transfer Mechanisms of Electrogens in Benthic Microbial Fuel Cells

Benthic microbial fuel cells (BMFCs) are a kind of microbial fuel cell (MFC), distinguished by the absence of a membrane. BMFCs are an ecofriendly technology with a prominent role in renewable energy harvesting and the bioremediation of organic pollutants through electrogens. Electrogens act as catalysts to increase the rate of reaction in the anodic chamber, acting in electrons transfer to the cathode. This electron transfer towards the anode can either be direct or indirect using exoelectrogens by oxidizing organic matter. The performance of a BMFC also varies with the types of substrates used, which may be sugar molasses, sucrose, rice paddy, etc. This review presents insights into the use of BMFCs for the bioremediation of pollutants and for renewable energy production via different electron pathways.

Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability

Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.

Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

Production of Biosurfactant Produced from Used Cooking Oil by Bacillus sp. HIP3 for Heavy Metals Removal

Heavy metals from industrial effluents and sewage contribute to serious water pollution in most developing countries. The constant penetration and contamination of heavy metals into natural water sources may substantially raise the chances of human exposure to these metals through ingestion, inhalation, or skin contact, which could lead to liver damage, cancer, and other severe conditions in the long term. Biosurfactant as an efficient biological surface-active agent may provide an alternative solution for the removal of heavy metals from industrial wastes. Biosurfactants exhibit the properties of reducing surface and interfacial tension, stabilizing emulsions, promoting foaming, high selectivity, and specific activity at extreme temperatures, pH, and salinity, and the ability to be synthesized from renewable resources. This study aimed to produce biosurfactant from renewable feedstock, which is used cooking oil (UCO), by a local isolate, namely Bacillus sp. HIP3 for heavy metals removal. Bacillus sp. HIP3 is a Gram-positive isolate that gave the highest oil displacement area with the lowest surface tension, of 38 mN/m, after 7 days of culturing in mineral salt medium and 2% (v/v) UCO at a temperature of 30 °C and under agitation at 200 rpm. An extraction method, using chloroform:methanol (2:1) as the solvents, gave the highest biosurfactant yield, which was 9.5 g/L. High performance liquid chromatography (HPLC) analysis confirmed that the biosurfactant produced by Bacillus sp. HIP3 consists of a lipopeptide similar to standard surfactin. The biosurfactant was capable of removing 13.57%, 12.71%, 2.91%, 1.68%, and 0.7% of copper, lead, zinc, chromium, and cadmium, respectively, from artificially contaminated water, highlighting its potential for bioremediation.

Isolation of a fluoroglycofen-degrading KS-1 strain and cloning of a novel esterase gene fluE

The bacterium KS-1, capable of degrading fluoroglycofen, was isolated from sludge collected at a herbicide factory. The isolate was identified as Lysinibacillus sp. according to its phenotypic features and 16S rDNA phylogeny. KS-1 degraded 85.25% of the fluoroglycofen (50 mg L-1) within 3 days of incubation. The optimum temperature and pH for fluoroglycofen degradation were 30°C and 7.0, respectively. Furthermore, Zn2+ and Cu2+ could significantly decrease the degradation rate. Three degradation products, which appeared during KS-1-mediated fluoroglycofen metabolism, were identified as deethyl-fluoroglycofen, acifluorfen and decarboxylate-acifluorfen. The fluE gene, which encodes a novel esterase that catalyzes the cleavage of carboxyl ester bonds of fluoroglycofen, was cloned from the KS-1 strain. Sequence alignment reveals that FluE shares 30%-40% amino acid sequence identity with members of the hormone sensitive lipase family. FluE was expressed in Escherichia coli BL21 and purified by Ni-NTA affinity chromatography. Purified FluE could efficiently hydrolyze fluoroglycofen and short-chain p-nitrophenol esters. However, no lipolytic activity was observed with esters containing acyl chains longer than 10 carbon atoms, thereby indicating that this enzyme is an esterase.

Acetoclastic methane formation from Eucalyptus detritus in pristine hydrocarbon-rich river sediments by Methanosarcinales

Pristine hydrocarbon-rich river sediments in the Greater Blue Mountains World Heritage Area (Australia) release substantial amounts of methane. The present study aimed to unravel for the first time the active methanogens mediating methane formation and exploiting the bacterial diversity potentially involved in the trophic network. Quantitative PCR of 16S rRNA gene and functional genes as well as 454 pyrosequencing were used to address the unknown microbial diversity and abundance. Methane-releasing sediment cores derived from three different river sites of the Tootie River. Highest methane production rates of 10.8 ± 0.5 μg g(-1)(wet weight) day(-1) were detected in 40 cm sediment depth being in congruence with the detection of the highest abundances of the archaeal 16S rRNA gene and the methyl-coenzyme M reductase (mcrA) genes. Stable carbon and hydrogen isotopic signatures of the produced methane indicated an acetoclastic origin. Long-term enrichment cultures amended with either acetate or H2/CO2 revealed acetoclastic methanogenesis as key methane-formation process mediated by members of the order Methanosarcinales. Conditions prevailing in the river sediments might be suitable for hydrocarbon-degrading bacteria observed in the river sediments that were previously unclassified or closely related to the Bacteroidetes/Chlorobi group, the Firmicutes and the Chloroflexi group fuelling acetoclastic methanogensis in pristine river sediments.

Degradation of dichloromethane by an isolated strain Pandoraea pnomenusa and its performance in a biotrickling filter

A strain Pandoraea pnomenusa LX-1 that uses dichloromethane (DCM) as sole carbon and energy source has been isolated and identified in our laboratory. The optimum aerobic biodegradation of DCM in batch culture was evaluated by response surface methodology. Maximum biodegradation (5.35 mg/(L·hr)) was achieved under cultivation at 32.8°C, pH 7.3, and 0.66% NaCl. The growth and biodegradation processes were well fitted by Haldane's kinetic model, yielding maximum specific growth and degradation rates of 0.133 hr(-1) and 0.856 hr(-1), respectively. The microorganism efficiently degraded a mixture of DCM and coexisting components (benzene, toluene and chlorobenzene). The carbon recovery (52.80%-94.59%) indicated that the targets were predominantly mineralized and incorporated into cell materials. Electron acceptors increased the DCM biodegradation rate in the following order: mixed > oxygen > iron > sulfate > nitrate. The highest dechlorination rate was 0.365 mg Cl(-)/(hr·mg biomass), obtained in the presence of mixed electron acceptors. Removal was achieved in a continuous biotrickling filter at 56%-85% efficiency, with a mineralization rate of 75.2%. Molecular biology techniques revealed the predominant strain as P. pnomenusa LX-1. These results clearly demonstrated the effectiveness of strain LX-1 in treating DCM-containing industrial effluents. As such, the strain is a strong candidate for remediation of DCM coexisting with other organic compounds.

Isolation, identification and cyfluthrin-degrading potential of a novel Lysinibacillus sphaericus strain, FLQ-11-1

Strain FLQ-11-1, isolated from sewage sludge, was able to degrade cyfluthrin and was identified as Lysinibacillus sphaericus based on its morphology, 16S rRNA sequence and fatty acid methyl ester (FAME) analyses. This strain could use cyfluthrin as its carbon or nitrogen source. Response surface methodology (RSM) analysis showed that the optimum conditions for degradation were at pH 7.0 and 35 °C, using an inoculum amount with an OD600nm value of 1.6. Under these conditions, approximately 80.4% of cyfluthrin (50 mgl(-1)) was degraded within five days (d) of incubation. Four metabolic compounds were detected during cyfluthrin degradation and identified as methyl-3-(2,2-dichlorovinyl)-2,2-dimethyl-(1-cyclopropane)-carboxylate, 4-fluoro-3-phenoxy-benzoic acid methyl ester, methyl-3-phenoxybenzoate, 3-phenoxy-benzaldehyde by gas chromatography-mass spectrometry (GC-MS) and tandem mass spectrum (MS/MS) analysis and no cyfluthrin was detected after seven days of incubation. A possible degradation pathway was proposed, and our data showed that cyfluthrin could be efficiently degraded by FLQ-11-1, indicating that this strain could potentially be used to eliminate the contamination of pyrethroid herbicides.

Plasmid-mediated bioaugmentation for the degradation of chlorpyrifos in soil

To overcome the poor survival and low activity of the bacteria used for bioremediation, a plasmid-mediated bioaugmentation method was investigated, which could result in a persistent capacity for the degradation of chlorpyrifos in soil. The results indicate that the pDOC plasmid could transfer into soil bacteria, including members of the Pseudomonas and Staphylococcus genera. The soil bacteria acquired the ability to degrade chlorpyrifos within 5 days of the transfer of pDOC. The efficiency of the pDOC transfer in the soil, as measured by the chlorpyrifos degradation efficiency and the most probable number (MPN) of chlorpyrifos degraders, was influenced by the soil temperature, moisture level and type. The best performance for the transfer of pDOC was observed under conditions of 30°C and 60% water-holding capacity (WHC). The results presented in this paper show that the transfer of pDOC can enhance the degradation of chlorpyrifos in various soils, although the degradation efficiency did vary with the soil type. It may be concluded that the introduction of plasmids encoding enzymes that can degrade xenobiotics or donor strains harboring these plasmids is an alternative approach in bioaugmentation.

Isolation and molecular identification of landfill bacteria capable of growing on di-(2-ethylhexyl) phthalate and deteriorating PVC materials

Waste materials containing Di-(2-ethylhexyl) phthalate (DEHP), a suspected endocrine disruptor and reasonably anticipated human carcinogen, are typically disposed of in landfills. Despite this, very few studies had been conducted to isolate and identify DEHP-degrading bacteria in landfill leachate. Therefore, this study was conducted to isolate and characterize bacteria in landfill leachate growing on DEHP as the sole carbon source and deteriorating PVC materials. Four strains LHM1, LHM2, LHM3 and LHM4, not previously reported as DEHP-degraders, were identified via 16S rRNA gene sequence. Gram-positive strains LHM1 and LHM2 had a greater than 97% similarity with Chryseomicrobium imtechense MW 10(T) and Lysinibacillus fusiformis NBRC 15717(T), respectively. Gram-negative strains LHM3 and LHM4 were related to Acinetobacter calcoaceticus DSM 30006(T) (90.7% similarity) and Stenotrophomonas pavanii ICB 89(T) (96.0% similarity), respectively. Phylogenetic analysis also corroborated these similarities of strains LHM1 and LHM2 to the corresponding bacteria species. Strains LHM2 and LHM4 grew faster than strains LHM1 and LHM3 in the enrichment where DEHP was the sole carbon source. When augmented to the reactors with PVC shower curtains containing DEHP, strains LHM1 and LHM2 developed greater optical densities in the solution phase and thicker biofilm on the surfaces of the shower curtains.

Biodegradation of fomesafen by strain Lysinibacillus sp. ZB-1 isolated from soil

The fomesafen degrading bacterium ZB-1 was isolated from contaminated agricultural soil, and identified as Lysinibacillus sp. based on the comparative analysis of 16S rRNA gene. The strain could utilize fomesafen as the sole carbon source for growth, and the total degradation rate was 81.32% after 7 d of inoculation in mineral salts medium. Strain ZB-1 could also degrade other diphenyl ethers including lactofen and fluoroglycofen. The optimum temperature for fomesafen degradation by strain ZB-1 was 30 degrees C. The effect of fomesafen concentration on degradation was also examined. Cell-free extract of strain ZB-1 was able to degrade fomesafen and other diphenyl ethers. Metabolism of fomesafen was accompanied by a transient accumulation of a metabolite identified as [N-[4-{4-(trifluoromethyl)phenoxy}-2-methanamidephenyl]acetamide] using liquid chromatography-mass spectrometry, thus indicating a metabolic pathway involving reduction, acetylation of nitro groups and dechlorination. The inoculation of strain ZB-1 to soil treated with fomesafen resulted in a higher degradation rate than in noninoculated soil regardless of the soil sterilized or nonsterilized.