Comprehensive Genome Analysis of Cellulose and Xylan-Active CAZymes from the Genus Paenibacillus: Special Emphasis on the Novel Xylanolytic Paenibacillus sp. LS1.

Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units. Complete degradation of xylan requires an arsenal of xylanolytic enzymes that can remove the substitutions and mediate internal hydrolysis of the xylan backbone. Here, we describe the xylan degradation potential and underlying enzyme machinery of the strain, Paenibacillus sp. LS1. The strain LS1 was able to utilize both beechwood and corncob xylan as the sole source of carbon, with the former being the preferred substrate. Genome analysis revealed an extensive xylan-active CAZyme repertoire capable of mediating efficient degradation of the complex polymer. In addition to this, a putative xylooligosaccharide ABC transporter and homologues of the enzymes involved in the xylose isomerase pathway were identified. Further, we have validated the expression of selected xylan-active CAZymes, transporters, and metabolic enzymes during growth of the LS1 on xylan substrates using qRT-PCR. The genome comparison and genomic index (average nucleotide identity [ANI] and digital DNA-DNA hybridization) values revealed that strain LS1 is a novel species of the genus Paenibacillus. Lastly, comparative genome analysis of 238 genomes revealed the prevalence of xylan-active CAZymes over cellulose across the Paenibacillus genus. Taken together, our results indicate that Paenibacillus sp. LS1 is an efficient degrader of xylan polymers, with potential implications in the production of biofuels and other beneficial by-products from lignocellulosic biomass. IMPORTANCE Xylan is the most abundant hemicellulose in the lignocellulosic (plant) biomass that requires cooperative deconstruction by an arsenal of different xylanolytic enzymes to produce xylose and xylooligosaccharides. Microbial (particularly, bacterial) candidates that encode such enzymes are an asset to the biorefineries to mediate efficient and eco-friendly deconstruction of xylan to generate products of value. Although xylan degradation by a few Paenibacillus spp. is reported, a complete genus-wide understanding of the said trait is unavailable till date. Through comparative genome analysis, we showed the prevalence of xylan-active CAZymes across Paenibacillus spp., therefore making them an attractive option towards efficient xylan degradation. Additionally, we deciphered the xylan degradation potential of the strain Paenibacillus sp. LS1 through genome analysis, expression profiling, and biochemical studies. The ability of Paenibacillus sp. LS1 to degrade different xylan types obtained from different plant species, emphasizes its potential implication in lignocellulosic biorefineries.

Hopanoid inventory of Rhodoplanes spp.

Hopanoids are pentacyclic triterpenoid lipids and are important for bacterial membrane stability and functioning. These pentacyclic triterpenoids of hopane series are biomarkers for eubacteria and can be used as chemotaxonomic markers. Anoxygenic phototrophic bacteria are good producers of hopanoids, and their inventory to date is restricted to a few members. Rhodoplanes spp. are phototrophic prokaryotes which grow and thrive in subsurface and sediment environments. A study on the diversity of hopanoids of several species of Rhodoplanes revealed a rich diversity of hopanoids with carbon length of C30/C31 and C35. Hop-22(29)-ene (II), diplopterol (V), tetrahymanol (VII), 2-methyldiplopterol (VI), 2-methyltetrahymanol (VIII), bacteriohopanetetrol (IX), bacteriohopaneaminotriol (X) and bacteriohopanepolyols [BHP-492 (XIII), BHP-550 (XIV), BHP-508 (XII)] are the major hopanoids of the genus Rhodoplanes. Tetrahymanol (VII) content is high (38-60 %) among all the members, except for Rhodoplanes elegans. Hopanoid fingerprints allowed differentiation of species of the genus Rhodoplanes. Statistical analyses also indicate hopanoids as good chemotaxonomic markers to distinguish species of the genus Rhodoplanes.

Cohaesibacter haloalkalitolerans sp. nov., isolated from a soda lake, and emended description of the genus Cohaesibacter.

Two novel Gram-stain-negative, motile, catalase-negative and oxidase-positive strains of bacteria (JC131(T) and JC112) were isolated from Lonar, a soda lake in India. Based on 16S rRNA gene sequence similarity studies, strains JC131(T) and JC112 belong to the family Cohaesibacteraceae of the class Alphaproteobacteria and were most closely related to Cohaesibacter marisflavi DQHS21(T) (98.0 %) and Cohaesibacter gelatinilyticus CL-GR15(T) (96.0 %). Polar lipids of strains JC131(T) and JC112 include phosphatidylglycerol, phosphatidylethnolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified lipids (L1 and L2). Both strains have diplopterol, diploptene, an unidentified hopane (UH) and bacteriohopane derivatives (BHD1 and 2) as major hopanoids and an unidentified pigment (P1). The predominant isoprenoid quinone of both strains was ubiquinone-10 (Q10). Whole-cell fatty acid analysis of both strains revealed that C18 : 1ω7c was the predominant cellular fatty acid and significant proportions of C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), 11-methyl C18 : 1ω7c, C18 : 1ω9c, C18 : 0 and C20 : 1ω7c were also detected. The DNA G+C content of strains JC131(T) and JC112 was 54.6 and 53.8 mol%, respectively. The genome reassociation (based on DNA-DNA hybridization) of strains JC131(T) and JC112 with Cohaesibacter marisflavi NCCB 100300(T) ( = DQHS21(T)) was about 58 %, while between JC131(T) and JC112 it was about 87 %. On the basis of physiological, biochemical and chemotaxonomical properties, strains JC131(T) and JC112 are differentiated from the other two members of the genus Cohaesibacter. Strains JC131(T) and JC112 represent a novel species of the genus Cohaesibacter, for which the name Cohaesibacter haloalkalitolerans sp. nov. is proposed. The type strain is JC131(T) ( = KCTC 32038(T) = NBRC 109022(T)). An emended description of the genus Cohaesibacter is presented.