Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses
Authors: Lee Laura L. , Blumer-Schuette Sara E. , Izquierdo Javier A. , Zurawski Jeffrey V. , Loder Andrew J. , Conway Jonathan M. , Elkins James G. , Podar Mircea , Clum Alicia , Jones Piet C. , Piatek Marek J. , Weighill Deborah A. , Jacobson Daniel A. , Adams Michael W. W. , Kelly Robert M. 
Published: March 2018

ABSTRACT

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic
Caldicellulosiruptor
. The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species,
Caldicellulosiruptor
sp. strain Rt8.B8 (renamed here
Caldicellulosiruptor morganii
),
Thermoanaerobacter cellulolyticus
strain NA10 (renamed here
Caldicellulosiruptor naganoensis
), and
Caldicellulosiruptor
sp. strain Wai35.B1 (renamed here
Caldicellulosiruptor danielii
), degraded Avicel and lignocellulose (switchgrass).
C. morganii
was more efficient than
Caldicellulosiruptor bescii
in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of
Caldicellulosiruptor obsidiansis
, but there was also evidence for other thermophilic fermentative anaerobes (
Caldanaerobacter
,
Fervidobacterium
,
Caloramator
, and
Clostridium
). One enrichment, containing 89.8%
Caldicellulosiruptor
and 9.7%
Caloramator
, had a capacity for switchgrass solubilization comparable to that of
C. bescii
. These results refine the known biodiversity of
Caldicellulosiruptor
and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.

IMPORTANCE
The genus
Caldicellulosiruptor
contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.