A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.

a b s t r a c tA 16S rRNA gene multiplex 454 pyrosequencing approach was used to characterize the structure of the bacterial community in subsurface flow constructed wetlands planted with Typha angustifolia and unplanted wetland mesocosms receiving ibuprofen-enriched wastewater at a concentration of 250 g L −1 . The removal efficiency of ibuprofen (IBP) in the planted beds (78.5%) was significantly higher than that in the unplanted beds (57.9%) (P ≤ 0.05). The presence of ibuprofen significantly (P ≤ 0.05) reduced the diversity of the bacterial community. In total, 20 phyla comprising 265 genera were identified. The most predominant phyla were Firmicutes (27.6%), Actinobacteria (26.0%) and Proteobacteria (24.9%), making up 57-95% of the 16S rDNA sequences. Other dominating phyla in wetland soils were Chloroflexi (7.3%), Bacteroidetes (2.7%), Synergistetes (2.1%), and Acidobacteria (2.0%). A distinct profile of bacterial community in the wetland mesocosms was observed after IBP enrichment. IBP-enrichment enhanced the relative abundance of Actinobacteria, Bacilli and ␥-Proteobacteria at class level. The efficient ibuprofen removal observed in this study suggested that the IBP-enriched wetland systems may have selected a restricted group of bacteria that was able to survive best in the disturbed condition and participate in the IBP biodegradation. Our findings also indicated that the presence of macrophytes may have a vital impact on the microbial community and planted wetlands may be more robust and buffered against significant shifts in microbial composition in response to IBP-disturbance.

A 454 high-throughput pyrosequencing approach was used to characterize the structures of microbial communities in wetland mesocosms receiving caffeine-enriched wastewater at a concentration of 250 μg L −1. The removal efficiencies of caffeine in the planted beds (93.0 %) were significantly (p < 0.05) higher than those in the unplanted beds (81.4 %). Bacterial diversity was decreased by 25 and 22.4 %, respectively, in both planted and unplanted mesocosms after 210-day operation. The results of taxonomic analyses suggested that chronic exposure of wetland ecosystems to caffeine could lead to moderate shifts in microbial community composition. In total, 2156 operational taxonomic units (OTUs) were generated and 20 phyla comprising 260 genera were identified. The major phylogenetic groups at phylum level included Firmicutes (39 %), Actinobacteria (25.1 %), Proteobacteria (17.1 %), Synergistetes (5.6 %), and Chloroflexi (5.5 %).Bacilli and Synergistia increased in abundance in the planted mesocosms, while for the unplanted mesocosms, Actinobacterial, Clostridia and Betaproteobacteria exhibited increased proportion under the exposure of caffeine. At genus level, Propionibacterium, Staphylococcus, Bacillus, and Streptococcus were found to be increased in abundance after caffeine treatment. As for the response of fungal community to caffeine enrichment, genus like Cladosporium, Emericellopsis, Aspergillus, and Phoma were found to be resistant to caffeine disturbance. When compared to the microbial community between planted and unplanted mesocosms, a distinct community profile for both bacteria and fungi community was observed. The presence of plants had a remarkable effect on the structure of microbial community, helping buffer against the stress associated with caffeine exposure.

The treatment performance of ibuprofen (IBP)-enriched wastewater by horizontal subsurface flow constructed wetlands planted with cattail (Typha angustifolia) and unplanted control mesocosms was investigated. Removal efficiencies of IBP were significantly (p < .05) enhanced in the planted mesocosms (78.5%) compared to those in the unplanted beds (57.9%). An 18S rRNA gene high-throughput pyrosequencing approach was used to investigate the effects of IBP on the structure of the fungal community in these wetland systems. The overall diversity of the fungal community was reduced under the IBP exposure. Taxonomic analysis revealed that 62.2% of the fungal sequences were affiliated with Basidiomycota, followed by Ascomycota (37.4%) at the phylum level. Uncultured fungus (48.2%), Chaetomium sp. (14.2%), Aspergillus sp. (12.4%), Trichoderma sp. (5.7%), Cladosporium sp. (5.4%), and Emericellopsis sp. (5.2%) were identified as dominant genera. At the genus level, a distinct profile of the fungal community in the IBP-enriched mesocosms was observed as compared to the control beds, and as well specific fungal genera were enhanced in the planted beds, regardless of IBP enrichment. However, despite these differences, the composition of the fungal community (as measured by Bray-Curtis similarity) was mostly unaffected by the significant IBP enrichment. On the other hand, a consistent similarity pattern of fungal community structure in the planted mesocosms suggests that the presence of higher macrophytes in the wetland systems may well help shape the fungal community structure.