Shuguang Xie

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.

Aerobic biodegradation of bisphenol A in river sediment and associated bacterial community change

Bisphenol A (BPA) is one of the commonly detected endocrine-disrupting chemicals in the environment. Biodegradation plays a major role in elimination of BPA pollution in the environment. However, information on the structure of BPA-degrading microbial community is still lacking. In this study, microcosms with different treatments were constructed to investigate the microbial community structure in river sediment and its shift during BPA biodegradation. BPA could be quickly depleted in the BPA-spiked sediment. BPA amendment had a significant impact on sediment bacterial community, influenced by dosage levels. Gammaproteobacteria and Alphaproteobacteria were the predominant bacterial groups in BPA-degrading sediment microcosm. A consortium of microorganisms from different bacterial genera might be involved in BPA biodegradation in river sediment. This study provides some new insights towards BPA biodegradation and microbial ecology in BPA-degrading environment.

Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils

Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson’s correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems.

Microbial community changes in contaminated soils in response to phenanthrene amendment

Leachate and reclaimed wastewater have become the important sources of polycyclic aromatic hydrocarbons in soils. However, the information on bioremediation of leachate and reclaimed wastewater-contaminated soils is still lacking. Identification of changes in microbial structure or of enriched genera related to biodegradation could aid identification of particular organisms or consortia capable of degrading polycyclic aromatic hydrocarbons in these contaminated soils. In this study, terminal restriction fragment length polymorphism, coupled with 16S Ribosomal ribonucleic acid clone library analysis, was applied to investigate the composition of bacterial community in leachate-contaminated soil or grassland soil irrigated reclaimed wastewater and the response to phenanthrene amendment. Results showed that phenanthrene amendment had significant but different impacts on microbial community structure, dependent on soil source. Several greatly enriched terminal restriction fragments with phenanthrene biodegradation were identified. Moreover, genus rhizobacteria, possibly linked to phenanthrene biodegradation, was firstly reported in this study. This work might provide some new insights into bioremediation of polycyclic aromatic hydrocarbons-contaminated soils.

Atrazine biodegradation by Arthrobacter strain DAT1: effect of glucose supplementation and change of the soil microbial community

The objective of this study was to investigate the impact of glucose supplementation on the soil microbiota inoculated with the atrazine-degrading Arthrobacter strain DAT1. Soil microcosms with different treatments were constructed for biodegradation tests. The impact of glucose supplementation on atrazine degradation capacity of the strain DAT1 and the strain’s survival and growth were assessed. The densities of the 16S rRNA gene and the atrazine-metabolic trzN gene were determined using quantitative PCR. The growth of the strain DAT1 and the bacterial community structure were characterized using terminal restriction fragment length polymorphism. Glucose supplementation could affect atrazine degradation by the strain DAT1 and the strain’s trzN gene density and growth. The density of the16S rRNA gene decreased during the incubation period. Glucose supplementation could alter the bacterial community structure during the bioaugmentation process. Glucose supplementation could promote the growth of the autochthonous soil degraders that harbored novel functional genes transforming atrazine. Further study will be necessary in order to elucidate the impact of exogenous carbon on autochthonous and inoculated degraders. This study could add some new insights on atrazine bioremediation.

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role.

Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson’s correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

Stable isotope probing identifies anthracene degraders under methanogenic conditions

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in groundwater. The remediation of PAH-contaminated groundwater often involves anaerobic biodegradation. The knowledge about the microorganisms responsible for PAH degradation in anaerobic subsurface environment is still lacking. DNA-based stable isotope probing (SIP) was applied to discover the microorganisms responsible for anaerobic anthracene degradation within microcosms inoculated with aquifer sediment from landfill leachate-contaminated site. Three phylotypes were identified as the degraders, all falling within the phylum Proteobacteria. Two anthracene degraders were classified within the genera Methylibium and Legionella, while another one was an unclassified Rhizobiales species. They all were first linked to PAH degradation. These findings also provide an illustration of the utility of SIP to discover the roles of uncultured microorganisms in PAH-degrading processes.

CHARACTERIZATION OF MICROBIAL COMMUNITIES IN A GRANULAR ACTIVATED CARBON-SAND DUAL MEDIA FILTER FOR DRINKING WATER TREATMENT

Modification of conventional rapid sand filter into granular activated carbon–sand dual media filter has become increasingly attractive to drinking water producers in many Chinese urban regions. In this study, a pilot-scale dual media filter was constructed to monitor its performance. The operational results indicated that the dual media filter performed well both on nitrification and on reduction of chemical oxygen demand. Microbial community structures at different sampling sites were also compared using 16S ribosomal ribonucleic acid gene clone library analysis to identify the spatial heterogeneity the filter. Clone library analysis illustrated the difference of microbial community structure and an increase of microbial diversity along the filter depth. Moreover, potential pathogens from genera Chromobacterium and Sphingomonas were detected in the filter samples, which deserved further serious consideration in downstream treatment such as disinfection. These findings also provided an illustration of the utility of molecular techniques to discover microbial community change and potential pathogens in the drinking water biofilters.

Biodegradation of antibiotic ciprofloxacin: pathways, influential factors, and bacterial community structure

Antibiotic ciprofloxacin is ubiquitous in the environment. However, little is known about ciprofloxacin dissipation by microbial community. The present study investigated the biodegradation potential of ciprofloxacin by mixed culture and the influential factors and depicted the structure of ciprofloxacin-degrading microbial community. Both the original microbiota from drinking water biofilter and the microbiota previously acclimated to high levels of ciprofloxacin could utilize ciprofloxacin as sole carbon and nitrogen sources, while the acclimated microbiota had a much stronger removal capacity. Temperature rise and the presence of carbon or nitrogen sources favored ciprofloxacin biodegradation. Many novel biotransformation products were identified, and four different metabolic pathways for ciprofloxacin were proposed. Bacterial community structure illustrated a profound shift with ciprofloxacin biodegradation. The ciprofloxacin-degrading bacterial community was mainly composed of classes Gammaproteobacteria, Bacteroidia, and Betaproteobacteria. Microorganisms from genera Pseudoxanthomonas, Stenotrophomonas, Phenylobacterium, and Leucobacter might have links with the dissipation of ciprofloxacin. This work can provide some new insights towards ciprofloxacin biodegradation.