Characterization of a phenanthrene-degrading methanogenic community

Polycyclic aromatic hydrocarbons (PAHs) often occur in oil-contaminated soil, coke wastewater and domestic sludge; however, associated PAH degraders in these environments are not clear. Here we evaluated phenanthrene degradation potential in the mixed samples of above environments, and obtained a methanogenic community with different microbial profile compared to those from sediments. Phenanthrene was efficiently degraded (1.26 mg/L/d) and nonstoichiometric amount of methane was produced simultaneously. 16S rRNA gene sequencing demonstrated that bacterial populations were mainly associated with Comamonadaceae Nocardiaceae and Thermodesulfobiaceae, and that methanogenic archaea groups were dominated by Methanobacterium and Methanothermobacter. Substances such as hexane, hexadecane, benzene and glucose showed the most positive effects on phenanthrene degradation. Substrate utilization tests indicated that this culture could not utilize other PAHs. These analyses could offer us some suggestions on the putative phenanthrene-degrading microbes in such environments, and might help us develop strategies for the removal of PAHs from contaminated soil and sludge.

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Copper pollution decreases the resistance of soil microbial community to subsequent dry–rewetting disturbance

Dry–rewetting(DW) disturbance frequently occurs in soils due to rainfall and irrigation, and the frequency of DW cycles might exert significant influences on soil microbial communities and their mediated functions. However, how microorganisms respond to DW alternations in soils with a history of heavy metal pollution remains largely unknown.Here, soil laboratory microcosms were constructed to explore the impacts of ten DW cycles on the soil microbial communities in two contrasting soils(fluvo-aquic soil and red soil)under three copper concentrations(zero, medium and high). Results showed that the fluctuations of substrate induced respiration(SIR) decreased with repeated cycles of DW alternation. Furthermore, the resistance values of substrate induced respiration(RS-SIR)were highest in non-copper-stressed(zero) soils. Structural equation model(SEM) analysis ascertained that the shifts of bacterial communities determined the changes of RS-SIR in both soils. The rate of bacterial community variance was significantly lower in noncopper-stressed soil compared to the other two copper-stressed(medium and high) soils,which might lead to the higher RS-SIR in the fluvo-aquic soil. As for the red soil, the substantial increase of the dominant group WPS-2 after DW disturbance might result in the low RS-SIR in the high copper-stressed soil. Moreover, in both soils, the bacterial diversity was highest in non-copper-stressed soils. Our results revealed that initial copper stress could decrease the resistance of soil microbial community structure and function to subsequent DW disturbance.     

The dynamic development of bacterial community following long-term weathering of bauxite residue

Bauxite residue is the industrial waste generated from alumina production and commonly deposited in impoundments. These sites are bare of vegetation due to the extreme high salinity and alkalinity, as well as lack of nutrients. However, long term weathering processes could improve residue properties to support the plant establishment. Here we investigate the development of bacterial communities and the geochemical drivers in bauxite residue, using Illumina high-throughput sequencing technology. Long term weathering reduced the pH in bauxite residue and increased its nutrients content. The bacterial community also significantly developed during long term weathering processes. Taxonomic analysis revealed that natural weathering processes encouraged the populations of Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes, whereas reducing the populations of Firmicutes and Actinobacteria. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was the dominant factors affecting microbial structure. The results have demonstrated that natural weathering processes improved the soil development on the abandoned bauxite residue disposal areas, which also increased our understanding of the correlation between microbial variation and residue properties during natural weathering processes in Bauxite residue disposal areas.     

Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

This study investigates the dynamics of pyrene degradation rates, microbial communities, and functional gene copy numbers during the incubation of pyrene-spiked soils. Spiking pyrene to the soil was found to have negligible effects on the bacterial community present. Our results demonstrated that there was a significant difference in nidA gene copy numbers between sampling dates in QZ soil. Mycobacterium 16S rDNA clone libraries showed that more than 90% mycobacteria detected were closely related to fast-growing PAH-degrading Mycobacterium in pyrene-spiked soil, while other sequences related to slow-growing Mycobacterium were only detected in the control soil. It is suggested that nidA gene copy number and fast-growing PAH-degrading Mycobacterium could be used as indicators to predict pyrene contamination and its degradation activity in soils.     

Effect of birch (Betula spp.) and associated rhizoidal bacteria on the degradation of soil polyaromatic hydrocarbons, PAH-induced changes in birch proteome and bacterial community

Two birch clones originating from metal-contaminated sites were exposed for 3 months to soils (sand-peat ratio 1:1 or 4:1) spiked with a mixture of polyaromatic hydrocarbons (PAHs; anthracene, fluoranthene, phenanthrene, pyrene). PAH degradation differed between the two birch clones and also by the soil type. The statistically most significant elimination (p ≤ 0.01), i.e. 88% of total PAHs, was observed in the more sandy soil planted with birch, the clearest positive effect being found with Betula pubescens clone on phenanthrene. PAHs and soil composition had rather small effects on birch protein complement. Three proteins with clonal differences were identified: ferritin-like protein, auxin-induced protein and peroxidase. Differences in planted and non-planted soils were detected in bacterial communities by 16S rRNA T-RFLP, and the overall bacterial community structures were diverse. Even though both represent complex systems, trees and rhizoidal microbes in combination can provide interesting possibilities for bioremediation of PAH-polluted soils.     

Long-term agricultural contamination shaped diversity response of sediment microbiome

The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems, altering the structure and function of river ecosystems. Differences in microbial community structure provide useful information about the impact of agricultural pollution on the biological integrity of ecosystems, but generally convey little information regarding ecosystem functions. In this study, using Illumina MiSeq sequencing technology based on the 16S rRNA gene, river sediment samples associated with four different types of agricultural pollution were comprehensively analyzed. The results show that the total organic carbon (TOC) content was highest at the YZS site (animal husbandry sewage) among the assayed sites, but the species richness and uniformity were lowest at this site, which may have been caused by the high nutrient source of the sewage. Furthermore, in the three YZS samples affected by the long-term discharge of aquaculture tail-water, the unique genus Dechloromonas and the genus Candidatus-Competitor were observed, which are strongly correlated with phosphorus conversion. The formation of network modules may correspond to the coexistence of functional bacteria accustomed to multiple niche combinations under different agricultural pollution conditions in river sediments. According to the PICRUSt functional prediction, the bacterial community in the agricultural polluted river sediment primarily harbored 46 subfunctions, exhibiting richness of functions. Overall, our results provide a more comprehensive understanding of the structure and ecological processes associated with the aggregation of bacterial communities, which is beneficial for the management of river environments.     

Nutrient depletion is the main limiting factor in the crude oil bioaugmentation process

The biodegradation was considered as the prime mechanism of crude oil degradation. To validate the efficacy and survival of the crude oil-degrading strain in a bioremediation process, the enhanced green fluorescent protein gene (egfp) was introduced into Acinetobacter sp. HC8–3S. In this study, an oil-contaminated sediment microcosm was conducted to investigate the temporal dynamics of the physicochemical characterization and microbial community in response to bacterium amendment. The introduced strains were able to survive, flourish and degrade crude oil quickly in the early stage of the bioremediation. However, the high abundance cannot be maintained due to the ammonium (NH₄⁺-N) and phosphorus (PO₄^3?-P) contents decreased rapidly after 15 days of remediation. The sediment microbial community changed considerably and reached relatively stable after nutrient depletion. Therefore, the addition of crude oil and degrading cells did not show a long-time impact on the original microbial communities, and sufficient nitrogen and phosphorus nutrients ensures the survive and activity of degrader. Our studies expand the understanding of the crude oil degradative processes, which will help to develop more rational bioremediation strategies.     

Characterization of bacterial communities during persistent fog and haze events in the Qingdao coastal region

• Light haze had little effect on bacterial communities. • Fog and heavy haze had significant effects on these communities. • Air pollution exerted a greater influence than particle size on bacterial community. Here, we report the characteristics of bacterial communities in aerosols with different particle sizes during two persistent fog and haze events in December of 2015 and 2016 in Qingdao, China. In the early stage of pollution, the accumulation of PM_2.5 led to the accumulation of microorganisms, thus increasing the bacterial richness and diversity of fine particle sizes. With the persistence and aggravation of pollution, the toxic effect was strengthened, and the bacterial richness and diversity of each particle size decreased. When the particle concentration was highest, the richness and diversity were low for each particle size. Light haze had little influence on bacterial communities. The occurrence of highly polluted humid weather and heavy haze resulted in significant changes in bacterial community diversity, composition and structure, and air pollution exerted a greater influence than particle size on bacterial community structure. During persistent fog and haze events, with the increase of pollutants, bacteria associated with each particle size may be extensively involved in aerosol chemistry, but the degree of participation varies, which requires further study.