CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.

Draft Genome Sequence of Cupriavidus sp. Strain IK-TO18, Isolated from Antimony-Contaminated Sediment

Cupriavidus sp. strain IK-TO18 was isolated from antimony-contaminated sediment. The draft genome sequence of the isolate contains 6,605 predicted protein-coding sequences, including genes associated with heavy metal resistance and the aerobic degradation of aromatic hydrocarbons. This sequence will provide valuable information regarding the functional versatility of the genus Cupriavidus .

An Aerobic Degradation Model for Landfilled Municipal Solid Waste

Municipalities output large amounts of solid waste into landfills, but degradation slows during the middle and late stages of treatment. Therefore, accelerating the treatment of degradable substances to achieve rapid stabilization, excavation, screening, and reuse would increase landfill utility and reduce economic costs. This article provides an aerobic degradation model for landfilled municipal solid waste that includes two types of biochemical reactions. Using degradable solid-phase organic matter and ammonia nitrogen as limiting substrates, an equation describing degradation over time was obtained. Both aerobic organic matter hydrolysis and the synchronous nitrification and denitrification reaction followed a kinetic, first-order equation. The influences of temperature, water content, oxygen concentration, and carbon to nitrogen ratio on the kinetic reactions were considered. Similarly, the exothermic reaction characteristics were considered. The model was applied to two previously conducted experiments. The results showed that the model can accurately reflect the degradation laws of various substances under aerobic degradation conditions. SDC and ammonia nitrogen were rapidly degraded and reached very low levels in a short time under aerobic conditions. This indicated that aeration has a significant effect on the degradation of aged waste, which can be used in the accelerated stabilization of aged landfills in the future.