Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation

Abstract

The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.

Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes

“…Another gene of interest from this space was S80_1a7091_mxb_fly_p.002 ~ BEPAJJ_15120, carried by a MAG classified as Ochrobactrum_B sp014138095 . This MAG was abundant in the minimal lignocellulolytic consortium constructed by Rodríguez and colleagues for lignin and plastics transformation 55 . Ochrobactrum has previously been reported to degrade UV-treated low-density polyethylene; however, this study identified the corresponding organism(s) only at the 16S level 86 .…”

Ultra-Accurate Classification and Discovery of Functional Protein-Coding Genes from Microbiomes Using FunGeneTyper: An Expandable Deep Learning-Based Framework

“…In conclusion, FunGeneTyper provides an innovative and unified framework with deep learning models (i.e., FunTrans and FunRep), expandable classifier toolkits (e.g., ARGTyper and VFGTyper) and customizable structured databases for the ultra-accurate classification and discovery of functional genes (e.g., ARGs and VFGs) that have scientific and biotechnological significance. This framework will contribute to the robust monitoring of function genes and discovery of novel enzymatic resources from diverse microbiomes and uncultured microbes therein, which is critical to understand and harness the microbiome sciences underlying environment (biogeochemistry, bio-restoration, and bioremediation) 14 bioeconomy (bioenergy and bioresources) 13 , and human systems (food and health) 20, 46 .…”

“…Therefore, it is crucial to develop intelligent and accurate classification paradigm and bioinformatic tools to overcome limitations of existing SA-based classification approaches. Importantly, this endeavor will accelerate discovery of new genes in future metagenomic-based environmental and human microbiome studies 13, 14 .…”

“…Importantly, this endeavor will accelerate discovery of new genes in future metagenomic-based environmental and human microbiome studies 13,14 .…”

Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency

“…Lignocellulose, the most abundant biopolymer on earth, is composed of two carbohydrate polymers, cellulose (9–80%) and hemicellulose (10–50%), and lignin (5–35%), a heteropolymer of aromatic units. , Cellulose and hemicellulose, both of which are polymers of sugars, can be easily metabolized by soil microbes, but lignin is considered highly recalcitrant to biodegradation . However, several bacteria and fungi produce extracellular oxidative enzymes that can depolymerize lignin, thereby providing lignin derivatives for further metabolism by a subset of microbes with pathways for aromatic carbon catabolism. − Pseudomonas species, which represent important members of the Gammaproteobacteria widely present in soil microbial communities, , are able to metabolize sugars as well as lignin-related aromatic derivatives such as p -coumarate, ferulate, vanillate, and 4-hydroxybenzoate. − Therefore, given the ubiquity and metabolic versatility of Pseudomonas species, they present ideal candidate species for probing the bacterial metabolism underlying the ssCUE of lignocellulose-related compounds.…”