[Genetic diversity of psbA of cyanophage from paddy floodwater in northeast China].

Objective: To provide scientific data for studying the ecology of cyanophage, we studied the genetic diversity of psbA of cyanophage from paddy floodwater in northeast China and its phylogenetic positions. Methods: Membrane separation and concentration of cyanophage, PCR-cloning-sequencing were applied to study the diversity of psbA of cyanophage from paddy floodwater in northeast China. Results: In total 17 psbA sequences of cyanophage were obtained. Novel cyanophages were found by phylogenetic analysis. Compared to those of Japanese paddy floodwater, marine and lakes, psbA gene assemblage of paddy floodwater in northeast China was significantly different. Conclusion: This is the first report to study genetic diversity of cyanophage from paddy floodwater in northeast China with a molecular marker of psbA by PCR-cloning-sequencing. The novel psbA assembly of cyanophage was found in paddy floodwater in northeast China.

[Isolation and phylogenetic analysis of related genes of cultivable cyanophages in Daqing Wetland].

Objective: To provide scientific data for studying the ecology of cyanophages isolated from Daqing wetland by analyzing their genetic diversity and phylogenetic positions. Methods: Liquid enrichment culture and double-layer plate methods were used to isolate cultivable cyanophages by using host cyanobacteria Anabaena PCC7120, and the DNA of cultivable cyanophages was extracted. The biomarker genes of g20 encoding capsid assembly protein and pol encoding DNA polymerase in podoviruses were PCR amplified. The PCR products were cloned and sequenced. The sequences were constructed with references sequences into the phylogenetic trees to clarify the phylogenetic positions of cultivable cyanophage. Results: One g20 sequence and four pol sequences were obtained. Phylogenetic analysis showed that the g20 sequence belongs to the cultivable cyanophage group (Cluster δ). Three pol sequences were closely related to cyanophage groups PG-Pol-I and PG-Pol-II that were observed in an alkaline paddy floodwater in Da'an, Jilin province, China; another pol sequence formed a unique clade. Conclusion: The g20 gene from cultivable cyanophages infecting Anabaena PCC7120 belongs to the Cluster δ, and the pol genes are closely related to those of paddy floodwater in Da'an, China.

Phylogenetic distribution of the capsid assembly protein gene (g20) of cyanophages in paddy floodwaters in Northeast China.

Numerous studies have revealed the high diversity of cyanophages in marine and freshwater environments, but little is currently known about the diversity of cyanophages in paddy fields, particularly in Northeast (NE) China. To elucidate the genetic diversity of cyanophages in paddy floodwaters in NE China, viral capsid assembly protein gene (g20) sequences from five floodwater samples were amplified with the primers CPS1 and CPS8. Denaturing gradient gel electrophoresis (DGGE) was applied to distinguish different g20 clones. In total, 54 clones differing in g20 nucleotide sequences were obtained in this study. Phylogenetic analysis showed that the distribution of g20 sequences in this study was different from that in Japanese paddy fields, and all the sequences were grouped into Clusters α, ß, γ and ε. Within Clusters α and ß, three new small clusters (PFW-VII∼-IX) were identified. UniFrac analysis of g20 clone assemblages demonstrated that the community compositions of cyanophage varied among marine, lake and paddy field environments. In paddy floodwater, community compositions of cyanophage were also different between NE China and Japan.

[Genetic diversity of capsid assembly protein genes (g20) of cyanophage in different natural environment--a review].

With the development of molecular biological techniques and progress of sequencing virus genome, scientists pay great attentions to the genetic diversity of viruses, which are ubiquitous and abundant in natural environments. So far, no universal genetic marker, analogous to 16S rDNA and 18S rDNA used for microbial communities exists throughout all viruses. However, some family-specific genes encoding conserved amino acids have been proposed for the evaluation of phage diversity and a series of breakthrough achievements were obtained. In this paper, we targeted the capsid assembly protein genes (g20) of cyanophages and reviewed the recent progress on their genetic diversity in natural environments of marines, lakes and paddy fields and discussed the relationship between distribution of g20 gene of cyanophages and its environments. Those studies showed that the distribution of g20 gene varied with environments and many unique clusters were found in different natural environment. In final, several research issues and the future research tendencies for the study of environmental g20 gene were also addressed in this paper.

Characterization of a microbial consortium capable of degrading lignocellulose.

A microbial consortium, designated WCS-6, was established by successive subcultivation in the presence of rice straw under static conditions. The degradation efficiencies of WSC-6 for 0.5 g filter paper, cotton and rice straw after 3 days of cultivation were 99.0±0.7%, 76.9±1.5% and 81.3±0.8%, respectively as determined by gravimetrical methods. Nine bacterial isolates were obtained from WCS-6 plated under aerobic conditions, and sequencing of their 16S rDNA indicated that these bacteria were related to Bacillus thermoamylovorans BTa, Paenibacillus barengoltzii SAFN-016, Proteobacterium S072, Pseudoxanthomonas taiwanensis CB-226, Rhizobiaceae str. M100, Bacillus sp. E53-10, Beta proteobacterium HMD444, Petrobacter succinimandens 4BON, and Tepidiphilus margaritifer N2-214. DGGE (denaturing gradient gel electrophoresis) and sequencing of 16S rDNA sequences amplified from total consortium DNA revealed the presence of sequences related to those of Ureibacillus thermosphaericus, uncultured bacterium clone GC3, uncultured Clostridium sp. clone A1-3, Clostridium thermobutyricum, and Clostridium thermosuccinogenes in addition to the sequences identified from the cultured bacteria. The microbial community identified herein is a potential candidate consortium for the degradation of waste lignocellulosic biomass.

[Biodiversity of mesophilic microbial community BYND-8 capability of lignocellulose degradation and its effect on biogas production].

The biodiversity of a mesophilic microbial community BYND-8 capable of degrading lignocellulose at 30 degrees C was detected using denaturing gradient gel electrophoresis (DGGE) and the isolation of pure cultures, and the effect of the liquid of rice straw degradation by BYND-8 on biogas production was measured. Six bacterial strains were isolated using peptone cellulose solution medium, and the highest similarities of their 16S rDNA gene sequences to Serratia sp. PSGB 13, S. marcescens strain UFLA-25LS, S. marcescens strain DAP33, Alcaligenes sp. YcX-20, Stenotrophomonas maltophilia strain C6, Bacillus cereus isolate BRL02-71 were 99%, 100%, 96%, 100%, 100% and 99%, respectively. In addition, one band was detected besides six bands of cultured isolates on the DGGE gel, and it showed 100% sequence similarity to uncultured bacterium clone ATB-KS-1446. The cumulative biogas and methane productions of biogas fermentation system added with the liquid of rice straw degraded by BYND-8 were 13 167 mL and 7 248 mL, 44.5% and 95.3% higher than those of the control, respectively, in the early 15 days of fermentation. The results showed that the biodiversity of microbial community BYND-8 was very high, and the time of producing biogas was put forward and biogas production was increased with application of microbial community for rice straw pretreatment during the biogas fermentation.