Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology

Abstract

Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.

Characterization of simultaneous uptake of xylose and glucose in Caldicellulosiruptor kronotskyensis for optimal hydrogen production

“…This sugar preference pinpoints to an adaptation to a specific niche within the thermophilic lignocellulosic degradation community. Other such specialization within lignocellulosic degradation communities has been indicated before [ 23 ].…”

Characterization of Simultaneous Uptake of Xylose and Glucose in Caldicellulosiruptor Kronotskyensis for Optimal Hydrogen Production

“…This sugar preference pinpoints to an adaptation to a specific niche within the thermophilic lignocellulosic degradation community. Other such specialization within lignocellulosic degradation communities has been indicated before [26].…”

Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus <i>Caldicellulosiruptor</i>

“…CP002219.1), and C. saccharolyticus DSM 8903 (accession no. CP000679.1) ( Van De Werken et al , 2008 ; Kataeva et al , 2009 ; Blumer-Schuette et al , 2011 ; Wai et al , 2015 ; Blumer-Schuette, 2020 ). NifN was not found in the genomes based on the annotation using eggNOG-mapper v2 ( Huerta-Cepas et al , 2017 ; 2019 ).…”

“… Nishihara et al (2018c) also performed a nifH gene amplicon analysis of chemosynthetic microbial communities at temperatures between 72 and 77°C, and the findings obtained showed that the relative abundance of the nifH gene from Caldicellulosiruptor were 7.42, 48.97, 73.12, and 94.58% in the four samples analyzed. The genus Caldicellulosiruptor comprises thermophilic fermentative bacteria that exhibit cellulolytic activities ( Zverlov et al , 1998 ; Blumer-Schuette et al , 2012 ; Brunecky et al , 2013 ) and is widely distributed in globally diverse thermal environments ( Lee et al , 2018 ; Blumer-Schuette, 2020 ). Genes related to nitrogen fixation are found in the genomes of some species in this genus (CP002330.1, CP002326.1, CP002219.1, CP003001.1, CP000679.1, LACO01000001.1, LACM01000001.1, and LACN01000001.1); however, their nitrogenase activities and dinitrogen-dependent growth have not yet been demonstrated.…”