Study on isolating novel biphenyl-degrading bacteria from typical soils in eastern China

To better excavate and utilize microbial dark matter, we developed a novel strategy that integrates single-cell-level isolation with microfluidics and culture with resuscitation-promoting factor (Rpf) to isolate biphenyl-degrading bacteria from four typical soils in eastern China. Multitudinous bacteria were successfully isolated and cultured; some of the identified clades have not been previously linked to biphenyl biodegradation. Soil microcosmic experiments validated that some bacteria are responsible for biphenyl degradation in soil microcosms. In addition, genomic sequencing and Illumina MiSeq sequencing of 16S rRNA genes proved that exogenous Rpf mainly promotes the recovery and growth of bacteria containing endogenous Rpf-encoding genes.