Shared strategies for β-lactam catabolism in the soil microbiome

Abstract

The soil microbiome can produce, resist, or degrade antibiotics and even catabolize them. While resistance genes are widely distributed in the soil, there is a dearth of knowledge concerning antibiotic catabolism. Here we describe a pathway for penicillin catabolism in four isolates. Genomic and transcriptomic sequencing revealed β-lactamase, amidase, and phenylacetic acid catabolon up-regulation. Knocking out part of the phenylacetic acid catabolon or an apparent penicillin utilization operon (put) resulted in loss of penicillin catabolism in one isolate. A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product. To test the generality of this strategy, an E. coli strain was engineered to co-express a β-lactamase and a penicillin amidase or the put operon, enabling it to grow using penicillin or benzylpenicilloic acid, respectively. Elucidation of additional pathways may allow for bioremediation of antibiotic-contaminated soils and discovery of antibiotic-remodeling enzymes with industrial utility.

Dual RNase and β-lactamase activity of a single enzyme encoded in most Archaea

“…However, the MBL protein sequences of this bacterial genus compared to those of archaea reveal low similarities (less than 36%) and this therefore suggests an ancient HGT from an archaic phylum to this bacterial group, which furthermore exhibited β-lactam hydrolysis activity, previously considered to be fairly atypical for a bacterium ( Table S3 ). Indeed, because archaea are naturally resistant to ß-lactams, the role of these β-lactamases in these microorganisms remains to be clarified, but the digestion of β-lactams by β-lactamases in Archae to use it as a carbon source, as in bacteria, should be investigated (13).…”

“…Finally, the existence of β-lactamases in the world of archaea is showing that β-lactamases are not only a defense system against β-lactams. The use of antibiotics as a nutriment sources for archaea as key to degrade β-lactam molecules and use them as carbon sources as described in bacteria, is a plausible hypothesis (13, 18–20).…”

Urban and agricultural soils in Southern California are a reservoir of carbapenem‐resistant bacteria

“…Recent findings in other parts of the world, especially in Europe, have found CRB in agricultural and nonagricultural soil samples (Borowiak et al, 2017; Djenadi et al, 2018; Fischer et al, 2013; Gudeta et al, 2016; Hrenovic et al, 2019) and suggest that soil may be an underrecognized reservoir of CRB. In the United States, 3 CRB isolates were identified among a collection of penicillin‐resistant isolates obtained from soil samples from the Midwestern United States (Crofts et al, 2018). However, studies that specifically address the distribution and characteristics of CRB in United States soils are still lacking.…”

Living materials with programmable functionalities grown from engineered microbial co-cultures

“…Importantly, these materials retain activity following drying and re-hydration storage under ambient conditions. Our approach could be applied to the production of immobilised enzyme materials used in various industrial processes, such as lipases in the interesterification of food fats and oils 37 , laccases in bioremediation of industrial waste products [38][39][40][41][42] or β-lactamases in decontamination of antibiotic-contaminated soil and wastewater 43,44 . and with dried then re-hydrated pellicle samples from co-cultures with S. cerevisiae BY4741 (WT), yCG04 (BLA) and yCG05 (BLA-CBD).…”