, 2010). Optimal PCR conditions utilized 30 cycles of 94 °C (30 s), 52 °C (30 s), and 72 °C (30 s), with an initial denaturation at 95 °C (5 min) and a final extension at 72 °C (5 min), and the same concentrations of reagents as used for 16S rRNA gene PCR. Clone libraries based on the 16S rRNA gene and the GHF48 gene were constructed by pooling amplicon DNA, purifying from PCR and cloning into a pMD18-T

vector (TaKaRa Biotechnology Co. Ltd., Dalian, China). Two vector-specific primers were used for the amplification selleck chemicals of the DNA inserts: M13-47 (5′-CGCCAGGGTTTTCCCAGTCACGAC-3′) and RV-M (5′-GAGCGGATAACAATTTCACACAGG-3′). PCR amplification was using 30 cycles of 94 °C (30 s), 54 °C (45 s), and 72 °C (2 min), with an initial denaturation at 95 °C (5 min) and a final extension at 72 °C (10 min). Clones were screened by agarose gel electrophoresis to check the inserts were the correct size. The PCR products were purified using the TaKaRa agarose gel DNA purification kit (TaKaRa Biotech Co.) and were sequenced by Shanghai Biosune (Shanghai, China) with an Applied

Biosystems automatic sequencer (ABI3730). A total of 50 clones from each clone find more library were screened. dnastar lasergene software was used for manual editing of the amplified 16S rRNA and GHF48 gene sequences. Operational taxonomic units (OTUs) definition at 97% sequence similarity was determined using the dotur software package (Schloss & Handelsman, 2005). The rarefaction curve was generated by past software package with a confidence threshold of 95% (Hammer et al., 2001). The

identification of phylogenetic neighbors and the calculation of pairwise 16S rRNA and GHF48 gene sequence similarities were achieved by blasting in EzTaxon-E database and NCBI (Kim et al., 2012). Sequences were classified into different bacterial taxa by RDP naive Bayesian rRNA classifier Version 2.4 Sitaxentan with a confidence threshold of 80% (Cole et al., 2009). Phylogenetic analysis was performed with the software package mega version 4.0 (Tamura et al., 2007) after multiple alignment of data by clustalx (Chenna et al., 2003). The phylogenetic trees were constructed using neighbor-joining (NJ) methods. Bootstrap values were calculated based on 1000 replicates. The nucleotide sequences of both the 16S rRNA genes and GHF48 genes from the clone libraries have been deposited in the GenBank database under accession numbers JQ741978–JQ741999. The isolated microbial community could degrade FP and Avicel under anaerobic conditions at 60 °C within 3 days, as shown in Fig. 1a. Initially, the FP became soft, then sticky, and eventually it dissolved completely. The phenomenon of the FP decomposition differed from that of C. thermocellum LQR1, in which the FP initially became thin and then dissolved. The fermentation products of the cellulolytic culture were detected by HPLC for 6 days.