Genome Sequence of Pseudomonas stutzeri 273 and Identification of the Exopolysaccharide EPS273 Biosynthesis Locus

Putative functions of EpsK in teichuronic acid synthesis and phosphate starvation in Bacillus licheniformis

Extracellular polymeric substances (EPSs) are extracellular macromolecules in bacteria, which function in cell growth and show potential for mechanism study and biosynthesis application. However, the biosynthesis mechanism of EPS is still not clear. We herein chose Bacillus licheniformis CGMCC 2876 as a target strain to investigate the EPS biosynthesis. epsK, a member of eps cluster, the predicted polysaccharide synthesis cluster, was overexpressed and showed that the overexpression of epsK led to a 26.54% decrease in the production of EPS and resulted in slenderer cell shape. Transcriptome analysis combined with protein-protein interactions analysis and protein modeling revealed that epsK was likely responsible for the synthesis of teichuronic acid, a substitute cell wall component of teichoic acid when the strain was suffering phosphate limitation. Further cell cultivation showed that either phosphate limitation or the overexpression of teichuronic acid synthesis genes, tuaB and tuaE could similarly lead to EPS reduction. The enhanced production of teichuronic acid induced by epsK overexpression triggered the endogenous phosphate starvation, resulting in the decreased EPS synthesis and biomass, and the enhanced bacterial chemotaxis. This study presents an insight into the mechanism of EPS synthesis and offers the potential in controllable synthesis of target products.

A Deep-Sea Bacterium Senses Blue Light via a BLUF-Dependent Pathway

Light is a ubiquitous energy source and environmental signal that broadly impacts the lifestyle of a large number of photosynthetic/nonphotosynthetic microorganisms living in the euphotic layer. However, the responses of deep-sea microbes to light are largely unknown, even though blue light is proposed to be distributed in the deep ocean. Here, we successfully cultured a novel bacterial species, named Spongiibacter nanhainus CSC3.9, from deep-sea cold seep samples by a blue light induction approach. The growth of strain CSC3.9 was obviously promoted by the illumination of blue light. We next determined BLUF (a typical blue light photoreceptor) was the most essential factor directing light sensing of strain CSC3.9 through a combined proteomic and genetic method. The function of light sensing mediated by BLUF was further confirmed by the in vitro-synthesized protein. Notably, homologs of BLUF widely existed across the marine microorganisms (containing Spongiibacter species) derived from different environments, including cold seeps. This strongly indicates that the distribution of light utilization by the nonphototrophic bacteria living in the ocean is broad and has been substantially underestimated.

IMPORTANCE Extensive studies have been conducted to explore the mechanisms of light sensing and utilization by microorganisms that live in the photic zone. Strikingly, accumulated evidence shows that light is distributed in the deep biosphere. However, the existence and process of light sensing and utilization by microbes inhabiting the deep ocean have been seldom reported. In the present study, a novel bacterial strain, Spongiibacter nanhainus CSC3.9, was enriched and purified from a deep-sea cold seep sample through a blue light induction method. Combined with genomic, proteomic, genetic, and biochemical approaches, the mechanism of this novel strain sensing blue light through a BLUF-dependent pathway was detailed. Our study provides a good model to study the mechanisms of light sensing mediated by deep-sea nonphototrophic bacteria.

Threonine dehydratase enhances bacterial cadmium resistance via driving cysteine desulfuration and biomineralization of cadmium sulfide nanocrystals

Biomineralization is often used by microorganisms to sequester heavy metal ions and provides a potential means for remediating increasing levels of heavy metal pollution. Bacteria have been shown to utilize cysteine for the biomineralization of metal sulfide. Indeed, in the present study, the supplement of L-cysteine was found to significantly improve both cadmium resistance and removal abilities of a deep-sea bacterium Pseudomonas stutzeri 273 through cadmium sulfide (CdS) nanoparticle biomineralization. With a proteomic approach, threonine dehydratase of P. stutzeri 273 (psTD) was proposed to be a key factor enhancing bacterial cadmium resistance through catalyzing L-cysteine desulfuration, H₂S generation and CdS nanoparticle biomineralization. Consistently, deletion of the gene encoding psTD in P. stutzeri 273 resulted in the decline of H₂S generation, decrease of cadmium resistance, and reduction of cadmium removal ability, confirming the unique function of psTD directing the formation of CdS nanoparticles. Correspondingly, the single-enzyme biomineralization of CdS nanoparticle driven by psTD was further developed, and psTD was shown to act as a capping reagent for the mineralization reaction, which controlling the size and structure of nanocrystals. Our results provide important clues for the construction of engineered bacteria for cadmium bioremediation and widen the synthesis methods of nanomaterials.

MerF is a novel regulator of deep-sea Pseudomonas stutzeri flagellum biogenesis and motility

MerF, a proposed bacterial mercury transporter, was surprisingly found to play key roles in the flagellum biogenesis and motility but not mercuric resistance of the deep-sea bacterium Pseudomonas stutzeri 273 in our previous study. However, the mechanism behind this interesting discovery has not been elucidated. Here, we firstly applied the combined transcriptomic and proteomic analysis to the P. stutzeri 273 wild type and merF deletion mutant. The results showed that expressions of extracellular flagellar components and FliS, a key factor controlling the biogenesis of extracellular flagellar filament, were significantly downregulated in the merF deletion mutant. In combination of genetic and biochemical methods, MerF was further demonstrated to regulate the expression of fliS via directly binding to its promoter, which is consistent with the discovery that MerF is essential for bacterial flagellum biogenesis and motility. Importantly, the expression of merF and fliS could be simultaneously upregulated by different heavy metals and MerF homologues exist in both bacterial and archaeal domains. To the best of our knowledge, this is the first report linking the heavy metal transporter and the flagellum biogenesis and motility in microorganisms, which provides a good model to investigate the unexplored adaptation strategies of deep-sea microbes against harsh conditions.

Transcriptional profiling of Pseudomonas aeruginosa PAO1 in response to anti-biofilm and anti-infection agent exopolysaccharide EPS273

AIMS

Relatively, few anti-biofilm polysaccharides against Pseudomonas aeruginosa were done to investigate the underlying molecular mechanism. Exopolysaccharide EPS273 can clearly reduce biofilm formation and infection of P. aeruginosa. This study aims to investigate its anti-biofilm and anti-infection mechanism on transcriptional level.

METHODS AND RESULTS

Herein, we used an RNA-Seq transcriptomic approach to investigate the underlying anti-biofilm and anti-infection mechanism of EPS273. The expression levels of a large number of genes were changed after P. aeruginosa PAO1 was treated with EPS273. Especially, the genes related to biofilm formation, such as gene involved in production of extracellular matrix and virulence factor, genes involved in flagella and cell motility and genes involved in iron acquisition. Notably, the expression levels of genes involved in regulatory and signal transduction were markedly downregulated, such as two-component system PhoP-PhoQ and quorum sensing (QS) system LasI/LasR and RhlI/RhlR. Furthermore, when genes phoP and phoQ were disrupted, respectively, the reduction of biofilm formation and cell motility in mutant △phoP or △phoQ was also detected.

CONCLUSION

EPS273 may exert its anti-biofilm and anti-infection function by downregulating gene expression of two-component system PhoP-PhoQ and QS systems LasI/LasR and RhlI/RhlR of P. aeruginosa, which further regulated expression of genes involved in biofilm formation.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our data will expand understanding of anti-biofilm mechanisms of polysaccharides on transcriptomic level.

A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea

Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA in converting thiosulfate to tetrathionate (⁻O₃S–S–S–SO₃⁻), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions. Notably, homologs of TsdA, SoxB, and SdoA/SdoB widely exist across the bacteria including in Erythrobacter species derived from different environments. This strongly indicates that this novel thiosulfate oxidation pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in nature.

Characterization of Microbial Communities Associated with Ceramic Raw Materials as Potential Contributors for the Improvement of Ceramic Rheological Properties

Technical ceramics are being widely employed in the electric power, medical and engineering industries because of their thermal and mechanical properties, as well as their high resistance qualities. The manufacture of technical ceramic components involves complex processes, including milling and stirring of raw materials in aqueous solutions, spray drying and dry pressing. In general, the spray-dried powders exhibit an important degree of variability in their performance when subjected to dry-pressing, which affects the efficiency of the manufacturing process. Commercial additives, such as deflocculants, biocides, antifoam agents, binders, lubricants and plasticizers are thus applied to ceramic slips. Several bacterial and fungal species naturally occurring in ceramic raw materials, such as Sphingomonas, Aspergillus and Aureobasidium, are known to produce exopolysaccharides. These extracellular polymeric substances (EPS) may confer unique and potentially interesting properties on ceramic slips, including viscosity control, gelation, and flocculation. In this study, the microbial communities present in clay raw materials were identified by both culture methods and DNA-based analyses to select potential EPS producers based on the scientific literature for further assays based on the use of EPS for enhancing the performance of technical ceramics. Potential exopolysaccharide producers were identified in all samples, such as Sphingomonas sp., Pseudomonas xanthomarina, P. stutzeri, P. koreensis, Acinetobacter lwoffi, Bacillus altitudinis and Micrococcus luteus, among bacteria. Five fungi (Penicillium citrinum, Aspergillus niger, Fusarium oxysporum, Acremonium persicinum and Rhodotorula mucilaginosa) were also identified as potential EPS producers.

Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation

Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri. A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri. Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.

Comparative Genomics of Pseudomonas sp. Strain SI-3 Associated With Macroalga Ulva prolifera, the Causative Species for Green Tide in the Yellow Sea

Algae-bacteria associations occurred widely in marine habitats, however, contributions of bacteria to macroalgal blooming were almost unknown. In this study, a potential endophytic strain SI-3 was isolated from Ulva prolifera, the causative species for the world's largest green tide in the Yellow Sea, following a strict bleaching treatment to eliminate epiphytes. The genomic sequence of SI-3 was determined in size of 4.8 Mb and SI-3 was found to be mostly closed to Pseudomonas stutzeri. To evaluate the characteristics of SI-3 as a potential endophyte, the genomes of SI-3 and other 20 P. stutzeri strains were compared. We found that SI-3 had more strain-specific genes than most of the 20 P. stutzeri strains. Clusters of Orthologous Groups (COGs) analysis revealed that SI-3 had a higher proportion of genes assigned to transcriptional regulation and signal transduction compared with the 20 P. stutzeri strains, including four rhizosphere bacteria, indicating a complicated interaction network between SI-3 and its host. P. stutzeri is renowned for its metabolic versatility in aromatic compounds degradation. However, significant gene loss was observed in several aromatic compounds degradation pathways in SI-3, which may be an evolutional adaptation that developed upon association with its host. KEGG analysis revealed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification, two competing dissimilatory nitrate reduction pathways, co-occurred in the genome of SI-3, like most of the other 20 P. stutzeri strains. We speculated that DNRA of SI-3 may contribute a competitive advantage in nitrogen acquisition of U. prolifera by conserving nitrogen in NH4+ form, as in the case of microalgae bloom. Collectively, these data suggest that Pseudomonas sp. strain SI-3 was a suitable candidate for investigation of the algae-bacteria interaction with U. prolifera and the ecological impacts on algal blooming.

Genetic and Physiological Adaptations of Marine Bacterium Pseudomonas stutzeri 273 to Mercury Stress

Mercury-mediated toxicity remains one of the greatest barriers against microbial survival, even though bacterial resistance to mercury compounds can occur. However, the genetic and physiological adaptations of bacteria to mercury stress still remains unclear. Here, we show that the marine bacterium Pseudomonas stutzeri 273 is resistant to 50 μM Hg²⁺ and removes up to 94% Hg²⁺ from culture. Using gene homologous recombination and complementation, we show that genes encoding Hg²⁺-transport proteins MerT, MerP, the mercuric reductase MerA and the regulatory protein MerD are essential for bacterial mercuric resistance when challenged with Hg²⁺. Further, mercury stress inhibits flagellar development, motility, chemotaxis and biofilm formation of P. stutzeri 273, which are verified by transcriptomic and physiological analyses. Surprisingly, we discover that MerF, a previously reported Hg²⁺-transporter, determines flagellar development, motility and biofilm formation in P. stutzeri 273 by genetic and physiological analyses. Our results strongly indicate that MerF plays an integral role in P. stutzeri 273 to develop physiological responses to mercury stress. Notably, MerF homologs are also prevalent in different human pathogens. Using this unique target may provide novel strategies to control these pathogenic bacteria, given the role of MerF in flagella and biofilm formation. In summary, our data provide an original report on MerF in bacterial physiological development and suggest that the mer in marine bacteria has evolved through progressive, sequential recruitment of novel functions over time.