Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil.

The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.

Aerobic degradation of 2,4,6-trinitrophenol by Proteus sp. strain OSES2 obtained from an explosive contaminated tropical soil.

A 2,4,6-trinitrophenol (TNP) degrading bacterial strain isolated from a site polluted with explosives was identified as Proteus sp. strain OSES2 via 16S rRNA gene sequencing. Metabolic investigation showed that the organism grew exponentially on 100 mg l-1 of TNP as a source of carbon, nitrogen, and energy. In addition, the growth of the organism was sustainable on 3-nitrotoluene, 2,4-dinitrotoluene, 2,4,6-trinitrotoluene, 4-nitrophenol, methyl-3-nitrobenzoate, 4-nitroaniline, aniline and nitrobenzene. Strain OSES2 was able to utilize TNP within a concentration range of 100 mg l-1 to 500 mg l-1. The specific growth rate and degradation rates on TNP were 0.01043 h-1 and 0.01766 mg l-1 h-1 respectively. Effective degradation of TNP in a chemically defined medium was evident with a gradual reduction in the concentration of TNP concomitant with an increase in cell density as well as the substantial release of ammonium (NH4+), nitrite (NO2-), and nitrate (NO3-) as metabolites in 96 h. Degradation competence of the organism was enhanced in the presence of starch and acetate. On starch-supplemented TNP, the highest specific growth rate and degradation rates were 0.02634 h-1 and 0.04458 mg l-1 h-1, respectively, while the corresponding values on acetate were 0.02341 h-1 and 0.02811 mg l-1 h-1. However, amendment with nitrogen sources yielded no substantial improvement in degradation. TNP was utilized optimally at pH 7 to 9 and within the temperature range of 30 °C to 37 °C. The enzyme hydride transferase II [HTII], encoded by the npdI gene which is the first step involved in the TNP degradation pathway, was readily expressed by the isolate thus suggesting that substrate was utilized through the classical metabolic pathway.

Aerobic degradation of 2,4-dinitrotoluene: Effect of raw organic wastes and nitrogen fortification.

2,4-Dinitrotoluene (2,4-DNT), a principal derivative generated in the synthesis of 2,4,6-trinitrotoluene, is widely used as a waterproofer, plasticizer, and gelatinizer in propellants and explosives. This compound has been documented as a priority pollutant because of its toxicity. Therefore, its removal from contaminated systems is a major focus of research and environmental attention. The presence of 2,4-DNT bacterial-degrading strains that could utilize 2,4-DNT as growth substrate in polluted sites in Ibadan, Nigeria, was determined using continual enrichment techniques on nitroaromatic mixtures. Proteus sp. strain OSES2 isolated in this study was characterized by phenotypic typing and 16S ribosomal RNA gene sequencing. Growth of the strain on 2,4-DNT resulted in an exponential increase in biomass and complete substrate utilization within 72 h, accompanied by NO3 - elimination. Degradation competence was enhanced in the presence of corn steep liquor, molasses, and Tween 80 compared with incubation without amendment. Conversely, amendment with nitrogen sources yielded no significant improvement in degradation. Use of these organic wastes as candidates in a bioremediation strategy should be exploited. This would provide a less-expensive organic source supplement for cleanup purposes, with the ultimate aim of reducing the cost of bioremediation while reducing wastes intended for landfill.

Biodegradation of anthracene by a novel actinomycete, Microbacterium sp. isolated from tropical hydrocarbon-contaminated soil.

A novel anthracene-degrading Gram-positive actinomycete, Microbacterium sp. strain SL10 was isolated from a hydrocarbon-contaminated soil at a mechanical engineering workshop in Lagos, Nigeria. The polluted soil had an unusually high total hydrocarbon content of 157 g/kg and presence of various heavy metals. The isolate tolerated salt concentration of more than 4%. It resisted cefotaxime, streptomycin and ciprofloxacin, but susceptible to meropenem, linezolid and vancomycin. The isolate exhibited growth rate and doubling time of 0.82 days(-1) and 0.84 days, respectively on anthracene. It degraded 57.5 and 90.12% of anthracene within 12 and 21 days, respectively while the rate of anthracene utilization by the isolate was 4.79 mg l(-1) d(-1). To the best of our knowledge, this is the first report of isolation and characterization of anthracene-degrading Microbacterium sp.

Bacteria with dual resistance to elevated concentrations of heavy metals and antibiotics in Nigerian contaminated systems.

Samples of soil, water, and sediments from industrial estates in Lagos were collected and analyzed for heavy metals and physicochemical composition. Bacteria that are resistant to elevated concentrations of metals (Cd(2+), Co(2+), Ni(2+), Cr(6+), and Hg(2+)) were isolated from the samples, and they were further screened for antibiotic sensitivity. The minimum tolerance concentrations (MTCs) of the isolates with dual resistance to the metals were determined. The physicochemistry of all the samples indicated were heavily polluted. Twenty-two of the 270 bacterial strains isolated showed dual resistances to antibiotics and heavy metals. The MTCs of isolates to the metals were 14 mM for Cd(2+), 15 mM for Co(2+) and Ni(2+), 17 mM for Cr(6+), and 10 mM for Hg(2+). Five strains (Pseudomonas aeruginosa, Actinomyces turicensis, Acinetobacter junni, Nocardia sp., and Micrococcus sp.) resisted all the 18 antibiotics tested. Whereas Rhodococcus sp. and Micrococcus sp. resisted 15 mM Ni(2+), P. aeruginosa resisted 10 mM Co(2+). To our knowledge, there has not been any report of bacterial strains resisting such high doses of metals coupled with wide range of antibiotics. Therefore, dual expressions of antibiotics and heavy-metal resistance make the isolates, potential seeds for decommissioning of sites polluted with industrial effluents rich in heavy metals, since the bacteria will be able to withstand in situ antibiosis that may prevail in such ecosystems.

Effects of corn steep liquor on growth rate and pyrene degradation by Pseudomonas strains.

The growth rates and pyrene degradation rates of Pseudomonas sp. LP1 and Pseudomonas aeruginosa LP5 were increased in corn steep liquor (CSL) supplemented. On pyrene alone the highest specific growth rate of LP1 was 0.018 h(-1), while on CSL-supplemented pyrene MSM, the value was 0.026 h(-)1. For LP5 the highest growth rate on CSL-supplemented pyrene-MSM was 0.034 h(-1). Conversely, on pyrene alone the highest rate was 0.024 h(-1). CSL led to marked reduction in residual pyrene. In the case of Pseudomonas sp. LP1 values of residual pyrene were 58.54 and 45.47%, respectively, for the unsupplemented and supplemented broth cultures, showing a difference of 13.09%. For LP5 the corresponding values were 64.01 and 26.96%, respectively, showing a difference of 37.05%. The rate of pyrene utilization by LP1 were 0.08 and 0.11 mg l(-1) h(-1) on unsupplemented and supplemented media, respectively. The corresponding values for LP5 were 0.07 and 0.015 mg l(-1) h(-1), respectively. These results suggest that CSL, a cheap and readily available waste product, could be very useful in the bioremediation of environments contaminated with pyrene.

Differential degradation of crude oil (Bonny Light) by four Pseudomonas strains.

Four hydrocarbon degraders isolated from enriched oil- and asphalt-contaminated soils in Lagos, Nigeria, were tested for their petroleum degradation potentials. All the isolates were identified as species of Pseudomonas. Pseudomonas putida P11 demonstrated a strong ability to degrade kerosene, gasoline, diesel, engine oil and crude oil while P. aeruginosa BB3 exhibited fair degradative ability on crude oil, gasoline, engine oil, anthracene and pyrene but weak on kerosene, diesel and dibenzothiophene. Pseudomonas putida WL2 and P. aeruginosa MVL1 grew on crude oil and all its cuts tested with the latter possessing similar polycyclic aromatic potentials as P11. All the strains grew logarithmically with 1-2 orders of magnitude and with generation time ranging significantly between 3.07 and 8.55 d at 0.05 level of confidence. Strains WL2 and MVL1 utilized the oil substrate best with more than 70% in 6 d experimental period, whereas the same feat was achieved by P11 in 12 d period. BB3 on the other hand degraded only 46% within 6 d. Interestingly, data obtained from gas chromatographic analysis of oil recovered from the culture fluids of MVL1 confirmed near-disappearance of major peaks (including aliphatics and aromatics) in the hydrocarbon mixture.