Polyphosphate kinase of Lysinibacillus sphaericus and its effects on accumulation of polyphosphate and bacterial growth

Klebsiella pneumoniae under xylose pressure: the growth adaptation, antimicrobial susceptibility, global proteomics analysis and role of XylA and XylB proteins

Klebsiella pneumoniae can be cultured in medium with xylose as the sole carbon source. However, the effect of xylose exposure on its growth adaptation, virulence, antimicrobial susceptibility, and proteomic response remain unclear. Here, we show that low concentrations of xylose (≤ 2%) promote the planktonic growth of three K. pneumoniae isolates (K2044, EKP19, and EKP108) in a concentration-dependent manner, while 8% xylose consistently inhibits their planktonic growth. Notably, the xylose-induced isolate K2044-8Xyl-60G, when exposed to various xylose concentrations, exhibited the longest logarithmic growth phase and the highest optical density (OD) after logarithmic growth, compared to K2044. In contrast, the xylose-induced isolates EKP19 and EKP108 did not successfully reshape growth adaptation under persistent xylose pressure compared to K2044. Additionally, while the growth adaptation of K2044-8Xyl-60G under xylose pressure was confirmed, no amino acid mutations were detected in the functional proteins of this xylose-induced isolate, suggesting that persistent xylose pressure does not cause nonsense mutations in the bacterial genome. Xylose exposure reduced the gentamicin minimum inhibitory concentration (MIC) in all three K. pneumoniae isolates (K2044, EKP108, and EKP19) and their xylose-induced derivatives. In a Galleria mellonella infection model, significantly decreased virulence was observed in the xylose-induced isolates of K2044 and EKP19. Proteomic analysis of K2044-8Xyl-60G treated with 8% xylose revealed upregulation of proteins involved in glycolysis, the pentose phosphate pathway, and transmembrane transport. We also constructed K2044-ΔxylA (with deletion of the xylA gene) and K2044-ΔxylB (with deletion of the xylB gene). Our data showed that K2044-ΔxylA exhibited enhanced planktonic growth compared to K2044 when exposed to xylose concentrations of ≥ 4%, while K2044-ΔxylB displayed significantly reduced growth capacity regardless of xylose exposure. The virulence of K2044-ΔxylA was also significantly reduced, as demonstrated by the increased survival rates in G. mellonella infection models. Additionally, xylose exposure strongly enhanced membrane depolarization in both K2044-ΔxylA and K2044-ΔxylB compared to the wild-type K2044. Proteomic analysis indicated that the deletion of xylA primarily affected functional proteins related to ribosomes, xylose transmembrane transporters and capsular polysaccharides, while the deletion of xylB impacted the expression of xylose metabolism-related proteins. In conclusion, xylose exposure can reshape the growth adaptation, virulence, and antimicrobial susceptibility of K. pneumoniae in an isolate-specific manner, with xylA playing a more critical role than xylB under high xylose concentrations.

Harnessing microbial power: Enhancing phosphorus recovery through initial carbon and phosphorus ratio modulation in sewage sludge compost

Phosphorus is an essential nutrient for organisms, but excessive amounts can cause environmental pollution. Phosphorus-rich sludge can solve the problem of the loss of phosphorus resources after resource treatment.This study aimed to explore the mechanism between phosphorus functional genes and phosphorus availability by regulating the initial carbon and phosphorus ratio in sludge compost, with the goal of improving sludge phosphorus recovery efficiency. The results showed that a higher initial carbon and phosphorus ratiocan promote the conversion of phosphorusfrom sludge to Olsen phosphorus and increase the contents of Water soluble phosphorusand Citric acid phosphorusin compost products. With the increase of the initial carbon and phosphorus ratio,phoDgene andpqqCgene abundance (P < 0.05) were significantly up-regulated, thus increasing the secretion of phosphodiesterase and organic acid, improving the phosphorus availability in compost products.The potential host of phosphorus solubilizing geneswas gradually transitionedfrom Proteobacteria to Firmicutes. Theppkgene and phosphorus accumulating bacteria abundance were significantly higher (CP20, CP25) at the later stage of composting (P < 0.05), indicating that the phosphorusaccumulating potential of the bacterial community was more prominent in the low initial carbon and phosphorus ratiocompost. This study elucidated the potential mechanism of action between functional genes and phosphorus availability, and demonstrated the feasibility of improving sludge phosphorus recovery efficiency by regulating the initial carbon and phosphorus ratio.

Aspirin Reduces Colorectal Tumor Development in Mice and Gut Microbes Reduce its Bioavailability and Chemopreventive Effects

BACKGROUND & AIMS

Alterations in the intestinal microbiota affect development of colorectal cancer and drug metabolism. We studied whether the intestinal microbiota affect the ability of aspirin to reduce colon tumor development in mice.

METHODS

We performed studies with APC^min/+ mice and mice given azoxymethane and dextran sulfate sodium to induce colorectal carcinogenesis. Some mice were given antibiotics to deplete intestinal microbes, with or without aspirin, throughout the entire experiment. Germ-free mice were studied in validation experiments. Colon tissues were collected and analyzed by histopathology, quantitative reverse-transcription polymerase chain reaction, and immunoblots. Blood samples and gut luminal contents were analyzed by liquid chromatography/mass spectrometry and an arylesterase activity assay. Fecal samples were analyzed by 16S ribosomal RNA gene and shotgun metagenome sequencing.

RESULTS

Administration of aspirin to mice reduced colorectal tumor number and load in APC^min/+ mice and mice given azoxymethane and dextran sulfate sodium that had been given antibiotics (depleted gut microbiota), but not in mice with intact microbiota. Germ-free mice given aspirin developed fewer colorectal tumors than conventionalized germ-free mice given aspirin. Plasma levels of aspirin were higher in mice given antibiotics than in mice with intact gut microbiota. Analyses of luminal contents revealed that aerobic gut microbes, including Lysinibacillus sphaericus, degrade aspirin. Germ-free mice fed L sphaericus had lower plasma levels of aspirin than germ-free mice that were not fed this bacterium. There was an inverse correlation between aspirin dose and colorectal tumor development in conventional mice, but this correlation was lost with increased abundance of L sphaericus. Fecal samples from mice fed aspirin were enriched in Bifidobacterium and Lactobacillus genera, which are considered beneficial, and had reductions in Alistipes finegoldii and Bacteroides fragili, which are considered pathogenic.

CONCLUSIONS

Aspirin reduces development of colorectal tumors in APC^min/+ mice and mice given azoxymethane and dextran sulfate sodium, depending on the presence of intestinal microbes. L sphaericus in the gut degrades aspirin and reduced its chemopreventive effects in mice. Fecal samples from mice fed aspirin were enriched in beneficial bacteria, with reductions in pathogenic bacteria.

Phosphorus and ammonium removal characteristics from aqueous solutions by a newly isolated plant growth-promoting bacterium

An indigenous plant growth-promoting bacterium isolated from Peganum Harmala rhizosphere in the arid ecosystem was found to solubilize and accumulate phosphates. This isolate was identified as Pseudomonas sp. (PHR6) by partial 16S rRNA gene sequence analysis. Controlled batch experiments on nutrients removal by this isolate in mineral medium showed relatively high efficiencies after 24 h of aerobic incubation with average values of 117.59 and 335.38 mg gVSS^-1 for phosphorus (P-PO₄) and nitrogen (N-NH₄), respectively. Furthermore, the strain performed heterotrophic nitrification ranging from 48.81% to 84.24% of the total removed nitrogen. On the other hand, the experimental results showed that a short idle period (24 h) significantly enhanced P accumulation (up to 95%) and N assimilation (up to 50%) of the total removed amounts. However, long idle period (20 days) revealed firstly aerobic phosphorous release phase succeeded by another removal one within 24 h of incubation. Overall, the idle treatment enhances P removal efficiency from the mineral liquid medium without significant effects on N-NH₄ removal performance. The isolated strain showed also significant nutrient removal ability from synthetic wastewater providing an accumulated fraction of 98% from the total removed phosphorus amount. This study highlights the potential contribution of the selected rhizobacterium PHR6 to both environmental nutrient recycling and pollution control especially regarding phosphorus.

Treatment of Low Biodegradability Leachates in a Serial System of Aged Refuse-Filled Bioreactors

This paper presents a technology based on the use of aged refuse that has proven to be highly effective in the treatment of low biodegradability leachates. The tests were developed using two filled bioreactors arranged in series and operated at steady state. The aged refuse used as filling material was extracted from a city located in the southeast of Mexico and characterized by particle size, humidity, volatile solids, and volumetric weight. On the other hand, bacterial characterization made it possible to identify the presence of species related to the degradation and mineralization of organic compounds, as well as to processes of nitrification or reduction of phosphates and Cr (VI). The bioreactor system was operated under four hydraulic loads (10, 20, 35, and 50 L/m3·d). Maximum removal efficiencies of 85, 86.1, 87.9, 98.6, 97.8, and 97.4% were achieved in COD, BOD5, Color, TP, TN, and N-NH3, respectively, complying with Mexican regulations (NOM-001-SEMARNAT-1996). The system also proved to be stable against shock loads, such as organic load fluctuations in the influent or pH variations. The results of this study show that, in countries such as Mexico, aged refuse extracted from landfills represents a promising option as a sustainable alternative for leachate treatment.

Novel Mechanism for Surface Layer Shedding and Regenerating in Bacteria Exposed to Metal-Contaminated Conditions

Surface layers (S-layers) are components of the cell walls throughout the Bacteria and the Archaea that provide protection for microorganisms against diverse environmental stresses, including metal stress. We have previously characterized the process by which S-layers serve as a nucleation site for metal mineralization in an archaeon for which the S-layer represents the only cell wall component. Here, we test the hypothesis originally proposed in cyanobacteria that a “shedding” mechanism exists for replacing S-layers that have become mineral-encrusted, using Lysinibacillus sp. TchIII 20n38, metallotolerant gram-positive bacterium, as a model organism. We characterize for the first time a mechanism for resistance to metals through S-layer shedding and regeneration. S-layers nucleate the formation of Fe-mineral on the cell surface, depending on physiological state of the cells and metal exposure times, leading to the encrustation of the S-layer and changes in the cell morphology as observed by scanning electron microscopy. Using Nanoscale Secondary Ion Mass Spectrometry, we show that mineral-encrusted S-layers are shed by the bacterial cells after a period of latency (2 days under the conditions tested) in a heterogeneous fashion likely reflecting natural variations in metal stress resistance. The emerging cells regenerate new S-layers as part of their cell wall structure. Given the wide diversity of S-layer bearing prokaryotes, S-layer shedding may represent an important mechanism for microbial survival in metal-contaminated environments.

Improved xylose tolerance and 2,3-butanediol production of Klebsiella pneumoniae by directed evolution of rpoD and the mechanisms revealed by transcriptomics

BACKGROUND

The biological production of 2,3-butanediol from xylose-rich raw materials from Klebsiella pneumoniae is a low-cost process. RpoD, an encoding gene of the sigma factor, is the key element in global transcription machinery engineering and has been successfully used to improve the fermentation with Escherichia coli. However, whether it can regulate the tolerance in K. pneumoniae remains unclear.

RESULTS

In this study, the kpC mutant strain was constructed by altering the expression quantity and genotype of the rpoD gene, and this exhibited high xylose tolerance and 2,3-butanediol production. The xylose tolerance of kpC strain was increased from 75 to 125 g/L, and the yield of 2,3-butanediol increased by 228.5% compared with the parent strain kpG, reaching 38.6 g/L at 62 h. The RNA sequencing results showed an upregulated expression level of 500 genes and downregulated expression level of 174 genes in the kpC mutant strain. The pathway analysis further showed that the differentially expressed genes were mainly related to signal transduction, membrane transport, carbohydrate metabolism, and energy metabolism. The nine most-promising genes were selected based on transcriptome sequencing, and were evaluated for their effects on xylose tolerance. The overexpression of the tktA encoding transketolase, pntA encoding NAD(P) transhydrogenase subunit alpha, and nuoF encoding NADH dehydrogenase subunit F conferred increased xylose consumption and increased 2,3-butanediol production to K. pneumoniae.

CONCLUSIONS

These results suggest that the xylose tolerance and 2,3-butanediol production of K. pneumoniae can be greatly improved by the directed evolution of rpoD. By applying transcriptomic analysis, the upregulation of tktA, pntA, and nuoF that were coded are essential for the xylose consumption and 2,3-butanediol production. This study will provide reference for further research on improving the fermentation abilities by means of other organisms.

Regulator DegU is required for multicellular behavior in Lysinibacillus sphaericus

DegS and DegU make up a two component system belonging to a class of signal transduction systems that play important roles in a broad range of bacterial responses to the environment. However, little study has been done to explore the physiological functions of DegS-DegU in mosquitocidal Lysinibacillus sphaericus. In this study, it was found that deletion of degU or degS-degU inhibited the swarming motility, biofilm formation, sporulation and binary toxin production through regulating the related genes, and phosphorylation was necessary for the functions of DegU. Based on the findings, a regulation network mediated by DegU was delineated. Both DegU-pi and Spo0A-pi positively regulates genes which are linked with the transition from stage Ⅱ to the end of the sporulation process and also influences the production of binary toxins via regulation on sigE. Both DegU-pi and Spo0A-pi negatively regulate abrB/sinR and influence the biofilm formation. DegU-pi can positively regulate the motility via the regulation on sigD. Whether the regulations are directly or indirectly need to be explored. Moreover, Spo0A-pi may indirectly regulate the swarming motility through negatively regulating DegU. It was concluded that DegU is a global transcriptional regulator on cell swarming motility, biofilm formation, sporulation and virulence in L. sphaericus.