Draft genome sequence data of Clostridium thermocellum PAL5 possessing high cellulose-degradation ability

Genomic analysis of Paenibacillus macerans strain I6, which can effectively saccharify oil palm empty fruit bunches under nutrient-free conditions

The improper disposal of palm oil industrial waste has led to serious environmental pollution. In this study, we isolated Paenibacillus macerans strain I6, which can degrade oil palm empty fruit bunches generated by the palm oil industry in nutrient-free water, from bovine manure biocompost and sequenced its genome on PacBio RSII and Illumina NovaSeq 6000 platforms. We obtained 7.11 Mbp of genomic sequences with 52.9% GC content from strain I6. Strain I6 was phylogenetically closely related to P. macerans strains DSM24746 and DSM24 and was positioned close to the head of the branch containing strains I6, DSM24746, and DSM24 in the phylogenetic tree. We used the RAST (rapid annotation using subsystem technology) server to annotate the strain I6 genome and discovered genes related to biological saccharification; 496 genes were related to carbohydrate metabolism and 306 genes were related to amino acids and derivatives. Among them were carbohydrate-active enzymes (CAZymes), including 212 glycoside hydrolases. Up to 23.6% of the oil palm empty fruit bunches was degraded by strain I6 under anaerobic and nutrient-free conditions. Evaluation of the enzymatic activity of extracellular fractions of strain I6 showed that amylase and xylanase activity was highest when xylan was the carbon source. The high enzyme activity and the diversity in the associated genes may contribute to the efficient degradation of oil palm empty fruit bunches by strain I6. Our results indicate the potential utility of P. macerans strain I6 for lignocellulosic biomass degradation.

Biological cellulose saccharification using a coculture of Clostridium thermocellum and Thermobrachium celere strain A9

Abstract

An anaerobic thermophilic bacterial strain, A9 (NITE P-03545), that secretes β-glucosidase was newly isolated from wastewater sediments by screening using esculin. The 16S rRNA gene sequence of strain A9 had 100% identity with that of Thermobrachium celere type strain JW/YL-NZ35. The complete genome sequence of strain A9 showed 98.4% average nucleotide identity with strain JW/YL-NZ35. However, strain A9 had different physiological properties from strain JW/YL-NZ35, which cannot secrete β-glucosidases or grow on cellobiose as the sole carbon source. The key β-glucosidase gene (TcBG1) of strain A9, which belongs to glycoside hydrolase family 1, was characterized. Recombinant β-glucosidase (rTcBG1) hydrolyzed cellooligosaccharides to glucose effectively. Furthermore, rTcBG1 showed high thermostability (at 60°C for 2 days) and high glucose tolerance (IC₅₀ = 0.75 M glucose), suggesting that rTcBG1 could be used for biological cellulose saccharification in cocultures with Clostridium thermocellum. High cellulose degradation was observed when strain A9 was cocultured with C. thermocellum in a medium containing 50 g/l crystalline cellulose, and glucose accumulation in the culture supernatant reached 35.2 g/l. In contrast, neither a monoculture of C. thermocellum nor coculture of C. thermocellum with strain JW/YL-NZ35 realized efficient cellulose degradation or high glucose accumulation. These results show that the β-glucosidase secreted by strain A9 degrades cellulose effectively in combination with C. thermocellum cellulosomes and has the potential to be used in a new biological cellulose saccharification process that does not require supplementation with β-glucosidases.

Key points

• Strain A9 can secrete a thermostable β-glucosidase that has high glucose tolerance

• A coculture of strain A9 and C. thermocellum showed high cellulose degradation

• Strain A9 achieves biological saccharification without addition of β-glucosidase

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11818-0.

Cellulolytic bacterium characterization and genome functional analysis: An attempt to lay the foundation for waste management

Lignocellulosic waste has offered a cost-effective and food security-wise substrate for the generation of biofuels and value-added products. Here, whole-genome sequencing and comparative genomic analyses were performed for Serratia sp. AXJ-M. The results showed that strain AXJ-M contained a high proportion of strain-specific genes related to carbohydrate metabolism. Furthermore, the genetic basis of strain AXJ-M for efficient degradation of cellulose was identified. Cellulase activity tests revealed strong cellulose degradation ability and cellulase activities in strain AXJ-M. mRNA expression indicated that GH1, GH3 and GH8 might determine the strain's cellulose degradation ability. The SWISS-MODEL and Ramachandran Plot were used to predict and evaluate the 3D structure, respectively. High performance liquid chromatography (HPLC) and gas chromatography-mass spectrometer (GC-MS) were used to analyze the cellulose degradation products. Further research is needed to elucidate the cellulose degradation mechanism and to develop industrial applications for lignocellulosic biomass degradation and waste management.

Symbiotic chitin degradation by a novel anaerobic thermophilic bacterium Hydrogenispora sp. UUS1-1 and the bacterium Tepidanaerobacter sp. GT38

Chitin is the second most abundant organic compound in nature. Although mesophilic bacteria degrade insoluble chitin, there is a paucity of data describing degradation of insoluble chitin by anaerobic thermophilic bacteria. In this report, we screened cow manure compost for new chitin degradation systems, and identified a chitinolytic bacterial community (CBC) that showed high chitin degradation activity under thermophilic conditions, i.e., 1% (w/v) chitin powder degraded completely within 7 days at 60 °C. Metagenomic analysis revealed that the CBC was dominated by two bacterial genera from Hydrogenispora, an uncultured taxonomic group, and Tepidanaerobacter. Hydrogenispora were abundant in the early-to-mid stages of culturing with chitin, whereas the population of Tepidanaerobacter increased during the later stages of culturing. Strains UUS1-1 and GT38, which were isolated as pure cultures using the roll-tube method with colloidal chitin, N-acetyl-d-glucosamine, and glucose as carbon sources, were found to be closely related to H. ethanolica and T. acetatoxydans, respectively. Strain UUS1-1 readily degraded chitin and is the first anaerobic thermophilic chitinolytic bacterium reported, whereas strain GT38 showed no chitinolytic activity. Based on phylogenetic analysis, UUS1-1 and GT38 should be classified as novel genera and species. Zymogram analysis revealed that UUS1-1 produces at least two chitinases with molecular weights of 150 and 40 kDa. A coculture of UUS1-1 and GT38 degraded crystalline chitin faster with lower accumulation of lactate compared with UUS1-1 alone, indicating that the strains maintained a symbiotic association through assimilation of organic acids in chitin degradation and that strain GT38 consumed end-products to reduce end-product inhibition and enhance the degradation of crystalline chitin.