Microbiology Resource of the Month: The Serratia quinivorans 124R Genome Sequence

May 31, 2019

Announcement: Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source.

Resource: A lignin-degrading Serratia quinivorans genome.

Lignin is a complex aromatic polymer found in the cell wall of many plants. Global production of items like paper and bioethanol produce lignin as a byproduct, offering manufacturers the opportunity to convert this complex carbon molecule into other useful commodities. However, lignin is extremely resistant to chemical degradation, and thus scientists have turned to the microorganisms that naturally break down lignin to discover how microbial enzymes can help with this process.
Many lignin-degrading microorganisms remain yet to be discovered. Gina Chaput and Kristen DeAngelis, along with a team of scientists, recently identified and sequenced the name of a new lignin-degrading bacterium, Serratia quinivorans 124R. Here, they explain the importance of their scientific discovery.

What is lignin degradation and why is it important to study?

Chaput: Lignin is a complex aromatic biopolymer that is component of the plant cell wall. This complexity makes it very difficult to break down, or degrade, in the soil once the plant dies since it requires special enzymes that can break the aromatic rings.
Most known mechanisms of lignin degradation require oxygen. We know how enzymes, such as laccases and peroxidases, work, as well as unique mechanisms such as chelator mediated Fenton chemistry (CMF), used by both fungi and bacteria. However, in this study, we wanted to know how bacteria could be degrading lignin when oxygen is not present.
Mechanisms of lignin degradation that do not require oxygen can be applied in biotechnology for biofuel or secondary chemical production from plant biowaste. The idea is that being able to degrade lignin to specific compounds under anoxic conditions could be more cost effective to use compared to methods that require constant aeration.  

How did you identify this Serratia quinivorans isolate and why do you think it may contribute to lignin degradation? 

DeAngelis: We originally took organic horizon soil samples and used this as inoculum for anoxic media that contained lignin as the sole carbon source. These cultures were transferred every 4 to 9 weeks for 465 days into fresh media.
Striated layers of soil, known as soil horizons, vary in physical and chemical environments. Different layers sustain unique varieties of microbial life. A schematic is shown on the left and a representative photo on the right.

To obtain isolates from this enriched microbial community, we diluted the cells down to 1 to 5 cells per ml onto a 0.001% five-carbon mixture and incubated for another 6 weeks anoxically at room temperature. These cultures, that now ideally would have 1-5 healthy growing isolates, were then streaked onto plates for isolation.
Once we had monoxenic cultures from these isolations, we then screened for anoxic lignin depolymerization capabilities using the lignin-mimicking dyes malachite green and Congo red. A clearing zone should form if the cells have the phenotype. It was in this screen that we identified Serratia quinivorans 124R, which has lignolytic potential for both dyes. 

A zone of clearance (arrows) on malachite green (top) and Congo red (bottom) surrounds Serratia quinivorans 124R, which has lignolytic potential for both dyes. Photo courtesy G. Chaput.

What metabolic potential did the genome sequence suggest? 

Chaput: Within the genome of Serratia quinivorans 124R, putative aromatic metabolic pathways included a total of 76 enzymes encompassing 41 functions under KEGG map 01220, including complete metabolism of benzoate and 4-hydroxyphenylacetate under oxic conditions. Additionally, 2 homologues to the Nu-class glutathione-S-transferases (GSTs) were identified. As for genes for anaerobic degradation of lignin, enzymes for gallate, phenylacetate, and 4-coumarate metabolism were found. 

How will you use the Serratia quinivorans genome sequence in your research? 

DeAngelis: Serratia quinivorans 124R is part of a larger project initiative in understanding how these isolates from the enriched community worked together to degrade lignin and use it as a carbon source. We hope to further characterize mechanisms being used as well as identify enzymes that could have potential in being used for a bio-energy or -material application.

How will this resource help other scientists with their research?

Chaput: There is a growing need to reduce reliance on non-renewable fuels, especially fossil fuels which contribute to the climate crisis. We hope that by identifying organisms such as Serratia quinivorans 124R, we can provide more avenues in how we can utilize plant lignocellulose as an energy source.   

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Author: Julie Wolf

Julie Wolf
Dr. Julie Wolf is a Science Communications Specialist for ASM and host of the Meet the Microbiologist podcast. She also runs workshops at ASM conferences to help scientists improve their own communication skills. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.