The Impact of Bioaugmentation on Metal Cyanide Degradation and Soil Bacteria Community Structure

Enantioselective effects of cyflumetofen on microbial community and related nitrogen cycle gene function in acid-soil

Cyflumetofen (CYF) is a novel chiral acaricide widely used in commercial crops to control mites. The environmental risks exposed by CYF in the soil, especially at the enantiomer level, remain unclear. We found that the (+)-CYF enantiomer was preferentially degraded in acid-soil, resulting in (-)-CYF enrichment. 16S rRNA and qPCR analysis indicated that decreased bacterial abundance by 12.79-61.80% and 2.52-52.48% in (-)-CYF treatment and (+)-CYF treatment, respectively. Diversity was also decreased with (-)-CYF treatment. Interestingly, several beneficial bacteria, for instance, Alphaproteobacteria (class), Sphingomonadaceae (family), and Arthrobacter (specise) were more enriched following (-)-CYF. The abundance of N₂-fixing bacteria showed a sustained reduction with time, and the decrease was 3.24-72.94% with (-)-CYF and 25.37-73.11% with (+)-CYF treatment. Compared with the (+)-CYF treatment could positively promote nitrification, while the treatment (-)-CYF significantly reduced the abundance of amoA gene; namely it significantly negatively affected the nitrification in the nitrogen cycle. Through our further research, we found that Actinobacteria, Alphaproteobacteria, Lysobacter; Sphingomonas, Patescibacteria, Saccharimonadia, and Saccharimonadales showed synergistic effects with the nitrogen cycling-related genes nifH and amoA. These results contribute to a comprehensive environmental risk assessment of CYF in acid-soil at the enantiomer level.

The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil

The chiral herbicide imazethapyr (IM) is frequently used to control weeds in soybean fields in northeast China. However, the impact of IM enantiomers on microbial communities in soil is still unknown. Genetic markers (16S rRNA V3-V4 regions) were used to characterize and evaluate the variation of the bacterial communities potentially effected by IM enantiomers. Globally, the bacterial community structure based on the OTU profiles in (-)-R-IM-treated soils was significantly different from those in (+)-S-IM-treated soils, and the differences were enlarged with the treatment dose increasing. Interestingly, the Rhizobiaceae family and several other beneficial bacteria, including Bradyrhizobium, Methylobacterium, and Paenibacillus, were strongly enriched in (-)-R-IM treatment compared to (+)-S-IM treatment. In contrast, the pathogenic bacteria, including Erwinia, Pseudomonas, Burkholderia, Streptomyces, and Agrobacterium, were suppressed in the presence of (-)-R-IM compared to (+)-S-IM. Furthermore, we also observed that the bacterial community structure in (-)-R-IM-treated soils was more quickly restored to its original state compared with those in (+)-S-IM-treated soils. These findings unveil a new role of chiral herbicide in the development of soil microbial ecology and provide theoretical support for the application of low-persistence, high-efficiency, and eco-friendly optical rotatory (-)-R-IM.

Effect of abandonment on diversity and abundance of free-living nitrogen-fixing bacteria and total bacteria in the cropland soils of Hulun Buir, Inner Mongolia

In Inner Mongolia, steppe grasslands face desertification or degradation because of human over activity. One of the reasons for this condition is that croplands have been abandoned after inappropriate agricultural management. The soils in these croplands present heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, we assessed the molecular ecology of total and free-living nitrogen-fixing bacterial communities in soils from steppe grasslands and croplands that were abandoned for different periods (1, 5, and 25 years) and compared the degree of recovery. The abandoned croplands included in the study were natural restoration areas without human activity. Denaturing gradient gel electrophoresis and quantitative PCR (qPCR) were used to analyze the nifH and 16S rRNA genes to study free-living diazotrophs and the total bacterial community, respectively. The diversities of free-living nitrogen fixers and total bacteria were significantly different between each site (P<0.001). Neither the total bacteria nor nifH gene community structure of a cropland abandoned for 25 years was significantly different from those of steppe grasslands. In contrast, results of qPCR analysis of free-living nitrogen fixers and total bacteria showed significantly high abundance levels in steppe grassland (P<0.01 and P<0.03, respectively). In this study, the microbial communities and their gene abundances were assessed in croplands that had been abandoned for different periods. An understanding of how environmental factors and changes in microbial communities affect abandoned croplands could aid in appropriate soil management to optimize the structures of soil microorganisms.

Biodegradation of cyanide by a new isolated strain under alkaline conditions and optimization by response surface methodology (RSM)

BACKGROUND

Biodegradation of free cyanide from industrial wastewaters has been proven as a viable and robust method for treatment of wastewaters containing cyanide.

RESULTS

Cyanide degrading bacteria were isolated from a wastewater treatment plant for coke-oven-gas condensate by enrichment culture technique. Five strains were able to use cyanide as the sole nitrogen source under alkaline conditions and among them; one strain (C2) was selected for further studies on the basis of the higher efficiency of cyanide degradation. The bacterium was able to tolerate free cyanide at concentrations of up to 500 ppm which makes it a good potentially candidate for the biological treatment of cyanide contaminated residues. Cyanide degradation corresponded with growth and reached a maximum level 96% during the exponential phase. The highest growth rate (1.23 × 10(8)) was obtained on day 4 of the incubation time. Both glucose and fructose were suitable carbon sources for cyanotrophic growth. No growth was detected in media with cyanide as the sole carbon source. Four control factors including, pH, temperature, agitation speed and glucose concentration were optimized according to central composite design in response surface method. Cyanide degradation was optimum at 34.2°C, pH 10.3 and glucose concentration 0.44 (g/l).

CONCLUSIONS

Bacterial species degrade cyanide into less toxic products as they are able to use the cyanide as a nitrogen source, forming ammonia and carbon dioxide as end products. Alkaliphilic bacterial strains screened in this study evidentially showed the potential to possess degradative activities that can be harnessed to remediate cyanide wastes.

Review on Cyanogenic Bacteria for Gold Recovery from E-Waste

Electronic waste (E-waste) is recognized as a new emerging and fast-growing waste stream, and may be considered as a secondary ore for the recovery of some precious metals (such as gold). A number of control technologies have been conducted for gold recovery, and in which, cyanidation is widely used. In recent years, an alternate approach to the gold cyanidation process is being considered, in which the aim is to replace with the microorganism, specifically cyanogenic bacteria such asChromobacterium violaceum,Pseudomonas fluorescens,Pseudomonas aeruginosaandEscherichia coli.All these species can produce cyanide ions and dissolve gold in their metabolic processes. The mechanism is a combination of chemical knowledge (interaction of metals and cyanide) with microbiological principles (biological cyanide formation) regarding metal solubilization from waste printed circuit boards and the formation of water-soluble cyanide complexes. And the activity of cyanogenic bacteria is affected by many factors, such as pH, dissolved oxygen pulp density and nutriment, especially several metal ions, which can serve as the catalyst in the metabolism. Now researchers are devoting themselves to looking for the proper conditions, not only from the bacteria themselves, but also the combination of many methods, which can reinforce the cyanide generation and improve gold leaching efficiency. At present the reported leaching efficiency of gold with cyanogenic is approximately 70%. As the continuous optimization of conditions, the industrial application can be expected soon.

Metals bioleaching from electronic waste by Chromobacterium violaceum and Pseudomonads sp

These days, electronic waste needs to be taken into consideration due to its materials content, but due to the heterogeneity of the metals present, reprocessing of electronic waste is quite limited. The bioleaching of metals from electronic waste was investigated by using cyanogenic bacterial strains (Chromobacterium violaceum, Pseudomonas aeruginosa and Pseudomonas fluorescens). A two-step bioleaching process was followed under cyanide-forming conditions for maximum metals mobilization. Both single and mixed cultures of cyanogenic bacteria were able to mobilize metals from electronic waste with different efficiencies. In all the flasks in which high metal mobilizations were observed, the consequent biomass productions were also high. Pseudomonas aeruginosa was applied in the bioleaching process for the first time and this achieved its bioleaching ability of mobilization of metals from electronic waste. Chromobacterium violaceum as a single culture and a mixture of C. violaceum and P. aeruginosa exhibited maximum metal mobilization. Chromobacterium violaceum was capable of leaching more than 79, 69, 46, 9 and 7% of Cu, Au, Zn, Fe and Ag, respectively at an electronic waste concentration of 1% w/v. Moreover, the mixture of C. violaceum and P. aeruginosa exhibited metals leaching of more than 83, 73, 49, 13 and 8% of total Cu, Au, Zn, Fe, and Ag, respectively. Precious metals were mobilized through bioleaching which might be considered as an industrial application for recycling of electronic waste in the near future.

Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils

Agricultural soils are heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, the molecular ecology of the total bacterial and free-living nitrogen-fixing communities in soils from the Nafferton Factorial Systems Comparison (NFSC) study in northeast England were examined. The field experiment was factorial in design, with organic versus conventional crop rotation, crop protection, and fertility management factors. Soils were sampled on three dates (March, June, and September) in 2007. Total RNA was extracted from all soil samples and reverse transcribed. Denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were used to analyze nifH and 16S rRNA genes in order to study free-living diazotrophs and the total bacterial community, respectively. Crop rotation was shown to have a significant effect on total bacterial diversity (and that of free-living N fixers) (P ≤ 0.001). On all three dates, nifH activity was higher in the conventional crop rotation. In contrast, qPCR analysis of free-living N fixers indicated significantly higher levels of activity in conventionally fertilized plots in June (P = 0.0324) and in plots with organic crop protection in September (P = 0.0143). To our knowledge, the effects of organic and conventional farming systems on free-living diazotrophs have never been studied. An increased understanding of the impacts of management practices on free-living N fixers could allow modifications in soil management practices to optimize the activity of these organisms.

Assessment of sample handling practices on microbial activity in sputum samples from patients with cystic fibrosis

AIM

The aim of this study was to quantitatively and qualitatively assess the effect of sample storage on the metabolically active microbial community found in sputum samples from patients with cystic fibrosis (CF).

METHODS

Sputum samples were collected and split in two equal aliquots one of which was immersed in RNAlater and refrigerated immediately, the second stored at room temperature for 24 h and RNAlater was subsequently added. mRNA was extracted, and RT-PCR-DGGE and qPCR analysis of the bacterial and fungal communities was carried out.

RESULTS

Significant differences in the bacterial communities between the two protocols were observed but there were no significant difference seen in the fungal community analyses. Analysis by qPCR demonstrated that room temperature storage gave statistically significant increases in eubacteria and Pseudomonas spp. and a statistically significant decrease in those of Haemophilus influenzae.

CONCLUSIONS

The analysis of metabolically active microbial communities from CF sputum using molecular techniques indicated that samples should be stored at 4 degrees C upon addition of RNAlater to obtain an accurate depiction of the CF lung microbiota. Also, storing respiratory samples at room temperature may cause an over representation of Pseudomonas aeruginosa and mask the presence of other clinically significant organisms.

Monitoring thiocyanate-degrading microbial community in relation to changes in process performance in mixed culture systems near washout

Changes in microbial community structure, associated with changes in process performance, were investigated with respect to the sludge retention time (SRT) in bioreactors treating thiocyanate. Among the seven reactors operated at 0.8-3.0 d SRTs, respectively, the reactor at 2.0 d SRT displayed the maximal thiocyanate removal rate of 240.2mg/L/d. However, the thiocyanate removal efficiency suddenly decreased from 96.1% to 43.1% when the SRT was reduced from 2.0 to 1.8d, corresponding to a 50.1% drop in the removal rate. Microbial communities in the reactors operated at short SRTs, near washout, were analyzed by denaturing gradient gel electrophoresis (DGGE) based on bacterial 16S rRNA genes. All band sequences recovered were assigned to two phyla, Proteobacteria and Bacteriodetes. A Thiobacillus-like microorganism was commonly detected in all the reactors and is suggested to be the main organism responsible for thiocyanate decomposition. Several DGGE band sequences were closely related to the environmental clones detected in environments rich in sulfur and/or nitrogen compounds. Statistical analysis of the DGGE profiles demonstrated that the structure of thiocyanate-degrading communities, as well as the process performance, changed with change in SRT. The microbial community profiles were not always more closely related to those at similar SRT than those at less similar SRT on the non-metric multidimensional scaling (NMDS) map. This was also supported by clustering analysis. These results were contrary to the general notion that the community structures in continuous systems will be controlled by the washout of microbial populations. Our experimental results suggest that the structure of a microbial thiocyanate-degrading community at a given SRT would not be determined only by the washout effect.

The degradation of the herbicide bromoxynil and its impact on bacterial diversity in a top soil

AIMS

To study how repeated applications of an herbicide bromoxynil to a soil, mimicking the regime used in the field, affected the degradation of the compound and whether such affects were reflected by changes in the indigenous bacterial community present.

METHODS AND RESULTS

Bromoxynil degradation was monitored in soil microcosms using HPLC. Its impact on the bacterial community was determined using denaturing gradient gel electrophoresis (DGGE) and quantitative PCR of five bacterial taxa (Pseudomonads, Actinobacteria, alpha-Proteobacteria, Acidobacteria and nitrifying bacteria). Three applications of 10 mg kg(-1) of bromoxynil at 28-day intervals resulted in rapid degradation, the time for removal of 50% of the compound decreasing from 6.4 days on the first application to 4.9 days by the third. Bacterial population profiles showed significant similarity throughout the experiment. With the addition of 50 mg kg(-1) bromoxynil to soil, the degradation was preceded by a lag phase and the time for 50% of the compound to be degraded increased from 7 days to 28 days by the third application. The bacterial population showed significant differences 7 days after the final application of bromoxynil that correlated with an inhibition of degradation during the same period.

CONCLUSIONS

These analyses highlighted that the addition of bromoxynil gave rise to significant shifts in the community diversity and its structure as measured by four abundant taxa, when compared with the control microcosm. These changes persisted even after bromoxynil had been degraded.

SIGNIFICANCE AND IMPACT OF THE STUDY

Here we show that bromoxynil can exert an inhibitory effect on the bacterial population that results in decreased rates of degradation and increased persistence of the compound. In addition, we demonstrate that molecular approaches can identify statistically significant changes in microbial communities that occur in conjunction with changes in the rate of degradation of the compound in the soil.

The application of the herbicide bromoxynil to a model soil-derived bacterial community: impact on degradation and community structure

AIMS

Bromoxynil degradation by soil micro-organisms has been shown to be co-oxidative in character. In this study, we investigate both the impact of the application of increasing bromoxynil concentrations on soil-derived bacterial communities and how these changes are reflected in the degradation of the compound. Our aim was to test the hypothesis that the addition of bromoxynil to a soil-derived bacterial community, and the availability of a readily utilizable carbon source would have an impact on bromoxynil degradation, and that would be reflected in the bacteria present in the soil community.

METHODS AND RESULTS

Degradation of bromoxynil was observed in soil-derived communities containing 15 mg l(-1), but not 50 mg l(-1) of the compound, unless glucose was added. This suggests that the addition of carbon stimulates co-oxidative bromoxynil degradation by the members of the bacterial community. Measurable changes in the bacterial community indicated that the addition of bromoxynil led to deterministic selection on the bacterial population, i.e. the communities observed arise through the selection of specific micro-organisms that are best adapted to the conditions in the soil. The addition of bromoxynil was also shown to have a negative impact on the presence of alpha and gamma-proteobacteria in the soil community.

CONCLUSION

Bromoxynil degradation is significantly inhibited in bacterial soil communities in the absence of readily accessible carbon. The application of bromoxynil appears to exert deterministic selection on the bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the effects of increasing bromoxynil concentrations on a model bacterial population derived from soil. Soil communities show qualitative and quantitative differences to bromoxynil application depending on the availability of organic carbon. These findings might have implications for the persistence of bromoxynil in agricultural soils.

The impact of acrylonitrile and bioaugmentation on the biodegradation activity and bacterial community structure of a topsoil

The analysis of the bacterial community within the soil using DGGE showed acrylonitrile (ACN) could lead to the selection of significantly similar communities. Moreover, Rhodococcus sp. AJ270 was successfully established in the soil community. High GC G+-bacteria also responded positively to ACN addition. Bioaugmentation or carbon addition had no impact on the rate or degree of ACN degradation. ACN could be readily degraded by the soil bacteria, however, the community structure was significantly affected by its addition as well as by the addition of carbon or Rhodococcus sp. AJ270. The bioaugmentation of the soil with this strain was successful, in that the organism became established within the community. ACN addition to a soil produces statistically significant changes in the bacterial community.