The evolutionary life cycle of the polysaccharide biosynthetic gene cluster based on the Sphingomonadaceae

Optimization of welan gum extraction and purification using lysozyme and alkaline protease

Welan gum, a natural polysaccharide produced by Sphingomonas sp. ATCC 31555, has attracted considerable attention in the scientific community due to its desirable properties. However, challenges, such as high viscosity, residual bacterial cells, carotenoids, and protein complexation, hinder the widespread application of welan gum. In this study, we established a method for the extraction and purification of welan gum using a synergistic approach with lysozyme and alkaline protease. Lysozyme hydrolysis conditions were optimized by applying response surface methodology, and the best results for bacterial cell removal were achieved at 11 000 U/g, 44 °C, and pH 9 after 3 h of treatment. Subsequently, we evaluated protein hydrolysis through computer simulation and identified alkaline protease as the most suitable enzyme. Through experimental investigations, we found that the optimal conditions for alkaline protease hydrolysis were 7500 U/g, 50 °C, pH 10, and 600 rpm. These conditions resulted in a sugar recovery rate of 76.1%, carotenoid removal rate of 89.5%, bacterial removal rate of 95.2%, and protein removal rate of 87.3% after 3 h of hydrolysis. The purified welan gum exhibited high transparency and purity. Structural characterization and antioxidant activity evaluation revealed that enzymatically purified welan gum has potential application prospects. Our study provides valuable insights into the optimal method for the enzymatic extraction and purification of welan gum. Such a method is conducive to the development of the multiple potential applications of welan gum. KEY POINTS: • A novel process for the synergistic purification of welan gum using lysozyme and alkaline protease was established. • In silico virtual digestion was employed to select the purification enzyme. • Welan gum with high transparency and purity was obtained.

An exopolysaccharide pathway from a freshwater Sphingomonas isolate

Bacteria embellish their cell envelopes with a variety of specialized polysaccharides. Biosynthesis pathways for these glycans are complex, and final products vary greatly in their chemical structures, physical properties, and biological activities. This tremendous diversity comes from the ability to arrange complex pools of monosaccharide building blocks into polymers with many possible linkage configurations. Due to the complex chemistry of bacterial glycans, very few biosynthetic pathways have been defined in detail. As part of an initiative to characterize novel polysaccharide biosynthesis enzymes, we isolated a bacterium from Lake Michigan called Sphingomonas sp. LM7 that is proficient in exopolysaccharide (EPS) production. We identified genes that contribute to EPS biosynthesis in LM7 by screening a transposon mutant library for colonies displaying altered colony morphology. A gene cluster was identified that appears to encode a complete wzy/wzx-dependent polysaccharide assembly pathway. Deleting individual genes in this cluster caused a non-mucoid phenotype and a corresponding loss of EPS secretion, confirming the role of this gene cluster in polysaccharide production. We extracted EPS from LM7 cultures and determined that it contains a linear chain of 3- and 4-linked glucose, galactose, and glucuronic acid residues. Finally, we show that the EPS pathway in Sphingomonas sp. LM7 diverges from that of sphingan-family EPSs and adhesive polysaccharides such as the holdfast that are present in other Alphaproteobacteria. Our approach of characterizing complete biosynthetic pathways holds promise for engineering polysaccharides with valuable properties.

IMPORTANCE

Bacteria produce complex polysaccharides that serve a range of biological functions. These polymers often have properties that make them attractive for industrial applications, but they remain woefully underutilized. In this work, we studied a novel polysaccharide called promonan that is produced by Sphingomonas sp. LM7, a bacterium we isolated from Lake Michigan. We extracted promonan from LM7 cultures and identified which sugars are present in the polymer. We also identified the genes responsible for polysaccharide production. Comparing the promonan genes to those of other bacteria showed that promonan is distinct from previously characterized polysaccharides. We conclude by discussing how the promonan pathway could be used to produce new polysaccharides through genetic engineering.

The production of ultrahigh molecular weight xanthan gum from a Sphingomonas chassis capable of co-utilising glucose and xylose from corn straw

Corn straw is an abundant and renewable alternative for microbial biopolymer production. In this paper, an engineered Sphingomonas sanxanigenens NXG-P916 capable of co-utilising glucose and xylose from corn straw total hydrolysate to produce xanthan gum was constructed. This strain was obtained by introducing the xanthan gum synthetic operon gum as a module into the genome of the constructed chassis strain NXdPE that could mass produce activated precursors of polysaccharide, and in which the transcriptional levels of gum genes were optimised by screening for a more appropriate promoter, P916 . As a result, strain NXG-P916 produced 9.48 ± 0.34 g of xanthan gum per kg of fermentation broth (g/kg) when glucose was used as a carbon source, which was 2.1 times improved over the original engineering strain NXdPE::gum. Furthermore, in batch fermentation, 12.72 ± 0.75 g/kg xanthan gum was produced from the corn straw total hydrolysate containing both glucose and xylose, and the producing xanthan gum showed an ultrahigh molecular weight (UHMW) of 6.04 × 107  Da, which was increased by 15.8 times. Therefore, the great potential of producing UHMW xanthan gum by Sphingomonas sanxanigenens was proved, and the chassis NXdPE has the prospect of becoming an attractive platform organism producing polysaccharides derived from biomass hydrolysates.

Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health

The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.

A novel exopolysaccharide pathway from a freshwater Sphingomonas isolate

Bacteria embellish their cell envelopes with a variety of specialized polysaccharides. Biosynthesis pathways for these glycans are complex, and final products vary greatly in their chemical structures, physical properties and biological activities. This tremendous diversity comes from the ability to arrange complex pools of monosaccharide building blocks into polymers with many possible linkage configurations. Due to the complex chemistry of bacterial glycans, very few biosynthetic pathways have been defined in detail. To better understand the breadth of polysaccharide production in nature we isolated a bacterium from Lake Michigan called Sphingomonas sp. LM7 that is proficient in exopolysaccharide (EPS) production. We identified genes that contribute to EPS biosynthesis in LM7 by screening a transposon mutant library for colonies displaying altered colony morphology. A gene cluster was identified that appears to encode a complete wzy/wzx-dependent polysaccharide assembly pathway. Deleting individual genes in this cluster caused a non-mucoid phenotype and a corresponding loss of EPS secretion, confirming that LM7 assembles a novel wzy/wzx-dependent polysaccharide. We extracted EPS from LM7 cultures and showed that it contains a linear chain of 3- and 4- linked glucose, galactose, and glucuronic acid residues. Finally, we found that the EPS pathway we identified diverges from those of adhesive polysaccharides such as the holdfast that are conserved in higher Alphaproteobacteria. Our approach of characterizing complete biosynthetic pathways holds promise for engineering of polysaccharides with valuable properties.

Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid

A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753 T).

Characterization of a polysaccharide hydrogel with high elasticity produced by a mutant strain Sphingomonas sanxanigenens NX03

Microbial polysaccharides as renewable bioproducts have attracted lots of attention in various industries. Hesan (Highly elastic Sanxan), an exopolysaccharide produced by a plasma mutagenic strain Sphingomonas sanxanigenens NX03, was characterized. It possessed the same monosaccharide composition as the original polysaccharide Sanxan produced from wild-type strain NX02, but significantly reduced acetyl and glyceryl contents. Textural analysis showed the springiness and cohesiveness of Hesan gel was much higher than Sanxan gel, and rheological behaviors indicated it possessed a lower loss factor, and its conformational transition temperatures at different concentrations were obviously lower than Sanxan gel and high-acyl gellan gel, which suggested that Hesan gel was highly elastic and temperature-sensitive. Additionally, Hesan gel could be efficiently produced through micro-aerobic static culture in shallow (10.46 ± 0.30 g/L) and deep liquids (3.21 ± 0.32 g/L), which was significantly different from the fermentation of other water-soluble polysaccharides. In short, this study characterizes a new mutant strain and its polysaccharide products.

Evidence from Thermal Aging Indicating That the Synergistic Effect of Glyoxal and Sodium Sulfite Improved the Thermal Stability of Conformational Modified Xanthan Gum

Xanthan gum is prone to thermal oxidative degradation, which limits its applications. However, conformational changes in xanthan gum and appropriate stabilizers may improve its thermal stability. Therefore, in this study, we aimed to establish a strategy to maintain the viscosity of xanthan gum during long-term storage at high temperatures. We modified the original strain used for xanthan gum production by genetic engineering and added stabilizers during the production process. The structure and thermal stability of the resulting xanthan gum samples were then determined. Pyruvyl deficiency, combined with the addition of sodium sulfite and glyoxal during the production process, was found to significantly improve the maintenance of viscosity. The apparent viscosity of the new xanthan gum solution remained above 100 mPa·s after being stored at 90 °C for 48 days. Fourier-transform infrared spectra and scanning electron microscopy images showed that pyruvate-free xanthan gum with added stabilizers had more extensive cross-linking than natural xanthan gum. In conclusion, these findings may contribute to the use of xanthan gum in applications that require high temperatures for a long period of time.

Total nitrogen influence bacterial community structure of active layer permafrost across summer and winter seasons in Ny-Ålesund, Svalbard

The permafrost in the polar regions is vital for maintaining the status quo of the earth's climate by limiting greenhouse gas emissions. The present study aims to investigate the seasonal variations and the influence of physicochemical parameters on the bacterial diversity and community structure of active layer permafrost (AL) around Ny-Ålesund, Svalbard. The AL soil samples were collected from four different geographical locations around Ny-Ålesund during the winter and summer seasons. The 16S rDNA amplicon sequencing was carried out to investigate the diversity and distribution profiles of bacterial communities among the collected AL samples. Physico-chemical parameters including soil pH, moisture content, total carbon (TC), total nitrogen (TN), and trace metals concentrations were measured. Bacterial phyla, Proteobacteria (15.4%-26%) and Chloroflexi (9.6%-22.5%) were predominantly distributed across both seasons. In the winter samples, Verrucomicrobiota (14.12%-23.39%) phylum, consisting of genera Chthoniobacter and Opitutus were highly abundant (Lefse, p < 0.05), whereas in summer bacterial genera belonging to Gemmatimonadota (3.3%-13.74%) and Acidobacteriota (18.02%-28.52%) phyla were highly abundant. The bacterial richness and diversity index were not significantly different between the winter and summer seasons. Principal coordinate analysis (PCoA) has revealed a distinct grouping between two seasons (PERMANOVA, p < 0.05). Bacterial community structure was significantly varied between winter and summer seasons, whereas the physico-chemical variable, TN, influenced the community structure. About 37.8% of the total operational taxonomic units (OTUs) were shared between seasons, whereas 25.4% and 36.8% of OTUs were unique to the summer and winter seasons. The present study revealed that the conditions prevailing during winter and summer has shaped bacterial community structure in AL samples albeit the stable diversity and most of the variation was explained by TN, indicating its critical role in oligotrophic permafrost.

Genomic and molecular evidence reveals novel pathways associated with cell surface polysaccharides in bacteria

Amino acid (acyl carrier protein) ligases (AALs) are a relatively new family of bacterial amino acid adenylating enzymes with unknown function(s). Here, genomic enzymology tools that employ sequence similarity networks and genome context analyses were used to hypothesize the metabolic function(s) of AALs. In over 50% of species, aal and its cognate acyl carrier protein (acp) genes, along with three more genes, formed a highly conserved AAL cassette. AAL cassettes were strongly associated with surface polysaccharide gene clusters in Proteobacteria and Actinobacteria, yet were prevalent among soil and rhizosphere-associated α- and β-Proteobacteria, including symbiotic α- and β-rhizobia and some Mycolata. Based on these associations, AAL cassettes were proposed to encode a noncanonical Acp-dependent polysaccharide modification route. Genomic-inferred predictions were substantiated by published experimental evidence, revealing a role for AAL cassettes in biosynthesis of biofilm-forming exopolysaccharide in pathogenic Burkholderia and expression of aal and acp genes in nitrogen-fixing Rhizobium bacteroids. Aal and acp genes were associated with dltBD-like homologs that modify cell wall teichoic acids with d-alanine, including in Paenibacillus and certain other bacteria. Characterization of pathways that involve AAL and Acp may lead to developing new plant and human disease-controlling agents as well as strains with improved nitrogen fixation capacity.

Complete Genome Sequence of Sphingobium xenophagum PH3-15, Isolated from La Roche-Posay Thermal Water Sources

We report here the complete genome sequence of Sphingobium xenophagum strain PH3-15, which was isolated from La Roche-Posay thermal water sources. The assembled 4.6-Mbp genome consisted of two chromosomes and three plasmids. These data will provide valuable information and important insights into the physiology and metabolism of this Sphingobium organism.

Efficient simultaneous utilization of glucose and xylose from corn straw by Sphingomonas sanxanigenens NX02 to produce microbial exopolysaccharide

Lignocellulosic biomass is a cheap and abundant carbon source in the microbial manufacturing industry. The native co-utilization of glucose and xylose from corn straw total hydrolysate (CSTH) by Sphingomonas sanxanigenens NX02 to produce exopolysaccharide Sanxan was investigated. Batch fermentation demonstrated that, compared to single sugar fermentation, co-substrate of glucose and xylose accelerated cell growth and Sanxan production in the initial 24 h with the same consumption rate. Additionally, NX02 converted CSTH into Sanxan with a yield of 13.10 ± 0.35 g/Kg, which is slightly higher than that of glucose fermentation. Coexistence of three xylose metabolic pathways (Xylose isomerase, Weimberg, and Dahms pathway), incomplete phosphoenolpyruvate-dependent phosphotransferase system, and reinforced fructose metabolism were recognized as the co-utilization mechanism through comparative transcriptome analysis. Therefore, strain NX02 has a prospect of becoming an attractive platform organism to produce polysaccharides and other bio-based products derived from agricultural waste hydrolysate rich in both glucose and xylose.

Genetic and physiological analysis of biofilm formation on different plastic surfaces by Sphingomonas sp. strain S2M10 reveals an essential function of sphingan biosynthesis

Alphaproteobacteria belonging to the group of the sphingomonads are frequently found in biofilms colonizing pure-water systems, where they cause technical and hygienic problems. In this study, physiological properties of sphingomonads for biofilm formation on plastic surfaces were analysed. Sphingomonas sp. strain S2M10 was isolated from a used water-filtration membrane and submitted to transposon mutagenesis for isolating mutants with altered biofilm formation. Mutants showing strongly decreased biofilm formation carried transposon insertions in genes for the biosynthesis of the polysaccharide sphingan and for flagellar motility. Flagella-mediated attachment was apparently important for biofilm formation on plastic materials of intermediate hydrophobicity, while a mutant with defect in spnB, encoding the first enzyme in sphingan biosynthesis, showed no biofilm formation on all tested materials. Sphingan-dependent biofilm formation was induced in the presence of specific carbon sources while it was not induced in complex medium with yeast extract and tryptone. The regulation of sphingan-based biofilm formation was investigated by interfering with the CckA/ChpT/CtrA phosphorelay, a central signal-transduction pathway in most Alphaproteobacteria. Construction and ectopic expression of a kinase-deficient histidine kinase CckA caused cell elongation and massive sphingan-dependent cell aggregation. In addition, it caused increased activity of the promotor of spnB. In conclusion, these results indicate that sphingan-based biofilm formation by sphingomonads might be triggered by specific carbon sources under prototrophic conditions resembling a milieu that often prevails in pure-water systems.

Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes

Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.

Extracellular polysaccharide biosynthesis in Cordyceps

Cordyceps is a parasitic edible fungus with a variety of metabolically active ingredients. The main active ingredient, extracellular polysaccharide (EPS), shows favourable application prospects in prevention and treatment of certain diseases. EPS extracted from different parts of various Cordyceps species can be used in health foods or medicinal preparations because of the structural diversity and multiple bioactivities. In terms of the complexity of composition and structure, researchers have speculated on the anabolic pathways of EPSs and the genes involved in the synthesis process. Studies to increase the yield of polysaccharides are limited because the synthesis pathways and anabolic regulation mechanisms of Cordyceps exopolysaccharide remain unknown. This review summarises the current researches in the yield of Cordyceps polysaccharides. A mechanism for the biosynthesis of Cordyceps polysaccharides was proposed by referring to the polysaccharide synthesis in other species. Furthermore, we also discuss the future perspective and ongoing challenges of EPS in uses of health foods and pharmaceutics.

The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C₄₀ carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.