Bacterial community diversity associated with four marine sponges from the South China Sea based on 16S rDNA-DGGE fingerprinting

Culture-independent 16S rDNA-DGGE fingerprinting and phylogenetic analysis were used to reveal the community structure and diversity of the predominant bacteria associated with the four sponges Stelletta tenui, Halichrondria, Dysidea avara, and Craniella australiensis from the South China Sea for the first time. Sponge total community DNA extracted with a direct grinding disruption based method was used successfully after series dilution for 16S rDNA PCR amplification, which simplifies the current procedure and results in good DGGE banding profiles. 16S rDNA-V3 fragments from 42 individual DGGE bands were sequenced and the detailed corresponding bacteria were found in sponges for the fist time based on BLAST results. The sponge-associated bacteria are sponge host-specific because each of the tested four sponges from the same geographical location has different predominant bacterial diversity. Proteobacteria, e.g. α, β and γ subdivisions, make up the majority of the predominant bacteria in sponges and are perhaps in close symbiotic relationship with sponges. Though similar bacteria with close phylogenetic relationships were found among different sponges, the sponge-associated predominant bacterial community structures differ. Sponge C. australiensis has the greatest bacterial diversity, with the four bacteria phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, followed by the sponge D. avara with the two phyla Proteobacteria and Bacteroidetes, and the sponges S. tenui and Halichrondria with the phylum Proteobacteria. DGGE fingerprint-based analysis should ideally be integrated with band cloning and sequencing, phylogenetic analysis and molecular techniques to obtain precise results in terms of the microbial community and diversity.     

Microbial Biomass, N Mineralization and Nitrification, Enzyme Activities, and Microbial Community Diversity in Tea Orchard Soils

Understanding the chronological changes in soil microbial and biochemical properties of tea orchard ecosystems after wasteland has been reclaimed is important from ecological, environmental, and management perspectives. In this study, we determined microbial biomass, net N mineralization, and nitrification, enzyme (invertase, urease, proteinase, and acid phosphatase) activities, microbial community diversity assessed by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA polymerase chain reaction (PCR) products, and related ecological factors in three tea orchard systems (8-, 50-, and 90-year-old tea orchards), adjacent wasteland and 90-year-old forest. Soil microbial biomass C (C_mic) and activity, i.e., soil basal respiration (R_mic), microbial biomass C as a percent of soil organic C (C_mic/C_org), N mineralization, invertase, urease, proteinase, and acid phosphatase, significantly increased after wasteland was reclaimed; however, with the succeeding development of tea orchard ecosystems, a decreasing trend from the 50- to 90-year-old tea orchard became apparent. Soil net nitrification showed an increasing trend from the 8- to 50-year-old tea orchard and then a decreasing trend from the 50- to 90-year-old tea orchard, and was significantly higher in the tea orchards compared to the wasteland and forest. Urea application significantly stimulated soil net nitrification, indicating nitrogen fertilizer application may be an important factor leading to high-nitrification rates in tea orchard soils. The Shannon’s diversity index (H) and richness (S) based on DGGE profiles of 16S rRNA genes were obviously lower in all three tea orchards than those in the wasteland; nevertheless, they were significantly higher in all three tea orchards than those in the forest. As for the three tea orchard soils, comparatively higher community diversity was found in the 50-year-old tea orchard.