Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea

Abstract

Background Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes. Results Three bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified as Bacillus paralicheniformis and showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis. Conclusions Our study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates as Bacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates’ genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-β-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes.

Comprehensive genomic analysis of Bacillus subtilis and Bacillus paralicheniformis associated with the pearl millet panicle reveals their antimicrobial potential against important plant pathogens

“…The second prominent isolate, Bacillus paralicheniformis PBl 36 produced creamy white rough lichen-like wrinkled colonies with an irregular margin and found motile, gram-positive bacteria with cellulase and starch hydrolysis activity. The morpho-biochemical characters were identical to those of previous characterization studies [ 51 – 53 ]. In 16S rRNA-based phylogenetic analysis, Bacillus subtilis PBs 12 (OL674150) showed close clustering with the plant-beneficial bacterial strains Bacillus subtilis KA9 (MT491101.1) and Bacillus subtilis IB22 (MT590663.1), and Bacillus licheniformis PBl 36 (OL674149) showed close clustering with the isolate Bacillus licheniformis PZ54 (MT184872.1), a beneficial seed endophyte of wheat expected in vertical transmission from Peninsular India ( https://www.ncbi.nlm.nih.gov/nuccore/MT184872.1/ ).…”

Biostimulation of Petroleum-Contaminated Soil Using Organic and Inorganic Amendments

“…The diameter of halo zones (also called the zone of clearance) generated from the lignocellulose degradation screening indicates that some of the isolates were capable of degrading lignocellulose in the water hyacinth ( Table 3 ), with isolate B1 exhibiting the greatest cellulase-producing ability. The formation of the halo zone is an indication of the ability of bacteria to produce certain enzymes [ 53 ], and the occurrence of such halo zones on the CMC agar plate is the identifying property of cellulase producers [ 54 , 55 ]. Similarly, the hydrocarbon-metabolizing potentials of the isolates, evident from the OD 600 values ( Figure 1 ) revealed that isolate B1 is a potent petroleum degrader, indicative of its potential wider application for both composting and hydrocarbon biodegradation.…”

“…After 15 min, the plates were rinsed with 1M of NaCl, and the zones of clearance were determined [ 69 ]. The formation of a halo zone (a differentiated zone surrounding a central zone) is an indication of the ability of bacteria to produce certain enzymes [ 53 ]. The occurrence of halo zones on CMC agar plate is the identifying property of cellulase producers [ 54 , 55 ].…”

Effect of Different Host Plants on the Diversity of Gut Bacterial Communities of Spodoptera frugiperda (J. E. Smith, 1797)

“…Bacillus and Enterbacter were detected in our study with high relative abundance in the S. frugiperda fed on honeysuckle leaves. Bacillus is one of the main symbiotic bacteria that produces digestive enzymes in insects, which can produce cellulase, protease, and lipase [ 56 , 57 ]. Enterbacter plays an important role in glucose metabolism, which can also degrade cellulose [ 21 , 58 ].…”