Culture‐dependent and culture‐independent characterization of potentially functional biphenyl‐degrading bacterial community in response to extracellular organic matter from Micrococcus luteus

Abstract

Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes.

Resuscitation of viable but non‐culturable bacteria to enhance the cellulose‐degrading capability of bacterial community in composting

“…Overall, at the phylum level, the 10 isolates can be divided into three groups 1, 2 and 3 which belonged to Proteobacteria , Firmicutes and Actinobacteria respectively. Strains in group 1 belonged to Gram‐negative bacteria, which were well supported by the studies that Rpf also resuscitated and stimulated the growth of some Gram‐negative bacteria (Su et al ., ,b, ,b,c,d). In particular, ZS2R8 was closely related to uncultured bacterium clone FW2_72B () which was detected at low‐level waste site with cellulosic contaminants (Field et al ., ).…”

“…Additionally, our previous studies found that extracellular organic matter (EOM) from M . luteus containing the Rpf could stimulate and resuscitate uncultured bacteria belonging to phylum Actinobacteria (Su et al ., ,b,c,d). Therefore, the results of these cultivation studies are in line with the resuscitating and stimulating functions of Rpf on cellulose‐degrading bacteria in the compost sample.…”

“…Remarkably, there are few available reports about the effect of Rpf on cellulase activity. In previous studies, the resuscitation and stimulation functions of proteins in the EOM of M. luteus have been verified (Su et al ., ,b, ,b,c,d). This study suggested that Rpf as an efficient additive could significantly promote the growth of cellulolytic bacteria, which will provide a new insight into the potential cellulose‐degrading bacteria within the uncultured microorganisms.…”

“…Definitely, our understanding of the degradation of cellulosic material is still limited, because most of the microbial diversity cannot be cultivated using conventional bacteriological media and remains inaccessible (Epstein, ). As well known, numerous bacteria including pollutant‐degrading bacteria can enter into a viable but non‐culturable (VBNC) state when exposed to adverse environmental conditions (Colwell et al ., ; Oliver, ; Su et al ., ,b; Su et al ., ,b,c,d). For example, it was previously reported that a novel biphenyl‐degrading bacterium Rhodococcus biphenylivorans could enter the VBNC state under oligotrophic and low‐temperature conditions (Su et al ., ,b,c,d).…”

“…As well known, numerous bacteria including pollutant‐degrading bacteria can enter into a viable but non‐culturable (VBNC) state when exposed to adverse environmental conditions (Colwell et al ., ; Oliver, ; Su et al ., ,b; Su et al ., ,b,c,d). For example, it was previously reported that a novel biphenyl‐degrading bacterium Rhodococcus biphenylivorans could enter the VBNC state under oligotrophic and low‐temperature conditions (Su et al ., ,b,c,d). Most investigators believe the VBNC state is a survival strategy which contributes to long‐term maintenance of cells viability (Keep et al ., ; Oliver, ).…”