Enhanced phosphate uptake and polyphosphate accumulation in Burkholderia cepacia grown under low pH conditions

The Protein Scaffolding Functions of Polyphosphate

Inorganic polyphosphate (polyP), one of the first high-energy compound on earth, defies its extreme compositional and structural simplicity with an astoundingly wide array of biological activities across all domains of life. However, the underlying mechanism of such functional pleiotropy remains largely elusive. In this review, we will summarize recent studies demonstrating that this simple polyanion stabilizes protein folding intermediates and scaffolds select native proteins. These functions allow polyP to act as molecular chaperone that protects cells against protein aggregation, as pro-amyloidogenic factor that accelerates both physiological and disease-associated amyloid formation, and as a modulator of liquid-liquid phase separation processes. These activities help to explain polyP's known roles in bacterial stress responses and pathogenicity, provide the mechanistic foundation for its potential role in human neurodegenerative diseases, and open a new direction regarding its influence on gene expression through condensate formation. We will highlight critical unanswered questions and point out potential directions that will help to further understand the pleiotropic functions of this ancient and ubiquitous biopolymer.

Reevaluating the accuracy and specificity of EDTA-based polyphosphate quantification method

Feng et al. (2020) developed a simple, nondestructive, and cost-effective method to quantify polyphosphate (poly-P) in poly-P-accumulating organism (PAO)-enriched sludge samples through 30-h anaerobic exposure to 1 % (w/v) ethylenediaminetetraacetic acid (EDTA). This study optimized the N/P ratio (∼2) of the PAO culture medium in order to provide excess P for poly-P formation in PAO cells. Subsequently, the fluorescence microscopic observation of stained cells confirmed that Corynebacterium glutamicum was a PAO species capable of heterotrophic nitrification. Finally, this study reevaluated the accuracy and specificity of the EDTA-based quantification method, using two confirmed PAO biomass, three confirmed non-PAO biomass, and two sludge samples. The 1 % (w/v) EDTA treatment appears destructive to non-PAO cells, causes the release of other P forms, and is not effective for all PAO species. Under the conditions, the actual P release amount should be calculated by subtracting approximately 8 mg P g-1 total suspended solids from the determination. The amounts of P released from sludge samples was determined not only by the PAO fractions described by Feng et al. but also by PAO community structure and sludge P content.

Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner

Due to their frequent coexistence in many polymicrobial infections, including in patients with burn or chronic wounds or cystic fibrosis, recent studies have started to investigate the mechanistic details of the interaction between the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. P. aeruginosa rapidly outcompetes S. aureus under in vitro co-cultivation conditions, which is mediated by several of P. aeruginosa's virulence factors. Here, we report that polyphosphate (polyP), an efficient stress defense system and virulence factor in P. aeruginosa, plays a role for the pathogen's ability to inhibit and kill S. aureus in a contact-independent manner. We show that P. aeruginosa cells characterized by low polyP level are less detrimental to S. aureus growth and survival while the gram-positive pathogen is significantly more compromised by the presence of P. aeruginosa cells that produce high level of polyP. We show that the polyP-dependent phenotype could be a direct effect by the biopolymer, as polyP is present in the spent media and causes significant damage to the S. aureus cell envelope. However, more likely is that polyP's effects are indirect through the regulation of one of P. aeruginosa's virulence factors, pyocyanin. We show that pyocyanin production in P. aeruginosa occurs polyP-dependent and harms S. aureus through membrane damage and the generation of reactive oxygen species, resulting in increased expression of antioxidant enzymes. In summary, our study adds a new component to the list of biomolecules that the gram-negative pathogen P. aeruginosa generates to compete with S. aureus for resources.

Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations

Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.

Stress Response in Bifidobacteria

Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies.

Revisiting the growth rate hypothesis: Towards a holistic stoichiometric understanding of growth

The growth rate hypothesis (GRH) posits that variation in organismal stoichiometry (C:P and N:P ratios) is driven by growth-dependent allocation of P to ribosomal RNA. The GRH has found broad but not uniform support in studies across diverse biota and habitats. We synthesise information on how and why the tripartite growth-RNA-P relationship predicted by the GRH may be uncoupled and outline paths for both theoretical and empirical work needed to broaden the working domain of the GRH. We found strong support for growth to RNA (r²  = 0.59) and RNA-P to P (r²  = 0.63) relationships across taxa, but growth to P relationships were relatively weaker (r²  = 0.09). Together, the GRH was supported in ~50% of studies. Mechanisms behind GRH uncoupling were diverse but could generally be attributed to physiological (P accumulation in non-RNA pools, inactive ribosomes, translation elongation rates and protein turnover rates), ecological (limitation by resources other than P), and evolutionary (adaptation to different nutrient supply regimes) causes. These factors should be accounted for in empirical tests of the GRH and formalised mathematically to facilitate a predictive understanding of growth.

Genome-Wide Assessment of Stress-Associated Genes in Bifidobacteria

Over the last decade, the genomes of several Bifidobacterium strains have been sequenced, delivering valuable insights into their genetic makeup. However, bifidobacterial genomes have not yet been systematically mined for genes associated with stress response functions and their regulation. In this work, a list of 76 genes related to stress response in bifidobacteria was compiled from previous studies. The prevalence of the genes was evaluated among the genome sequences of 171 Bifidobacterium strains. Although genes of the protein quality control and DNA repair systems appeared to be highly conserved, genome-wide in silico screening for consensus sequences of putative regulators suggested that the regulation of these systems differs among phylogenetic groups. Homologs of multiple oxidative stress-associated genes are shared across species, albeit at low sequence similarity. Bee isolates were confirmed to harbor unique genetic features linked to oxygen tolerance. Moreover, most studied Bifidobacterium adolescentis and all Bifidobacterium angulatum strains lacked a set of reactive oxygen species-detoxifying enzymes, which might explain their high sensitivity to oxygen. Furthermore, the presence of some putative transcriptional regulators of stress responses was found to vary across species and strains, indicating that different regulation strategies of stress-associated gene transcription contribute to the diverse stress tolerance. The presented stress response gene profiles of Bifidobacterium strains provide a valuable knowledge base for guiding future studies by enabling hypothesis generation and the identification of key genes for further analyses.

IMPORTANCE Bifidobacteria are Gram-positive bacteria that naturally inhabit diverse ecological niches, including the gastrointestinal tract of humans and animals. Strains of the genus Bifidobacterium are widely used as probiotics, since they have been associated with health benefits. In the course of their production and administration, probiotic bifidobacteria are exposed to several stressors that can challenge their survival. The stress tolerance of probiotic bifidobacteria is, therefore, an important selection criterion for their commercial application, since strains must maintain their viability to exert their beneficial health effects. As the ability to cope with stressors varies among Bifidobacterium strains, comprehensive understanding of the underlying stress physiology is required for enabling knowledge-driven strain selection and optimization of industrial-scale production processes.

Phosphorus Concentration in Water Affects the Biofilm Community and the Produced Amount of Extracellular Polymeric Substances in Reverse Osmosis Membrane Systems

Biofouling is a problem that hinders sustainable membrane-based desalination and the stratification of bacterial populations over the biofilm's height is suggested to compromise the efficiency of cleaning strategies. Some studies reported a base biofilm layer attached to the membrane that is harder to remove. Previous research suggested limiting the concentration of phosphorus in the feed water as a biofouling control strategy. However, the existence of bacterial communities growing under phosphorus-limiting conditions and communities remaining after cleaning is unknown. This study analyzes the bacterial communities developed in biofilms grown in membrane fouling simulators (MFSs) supplied with water with three dosed phosphorus conditions at a constant biodegradable carbon concentration. After biofilm development, biofilm was removed using forward flushing (an easy-to-implement and environmentally friendly method) by increasing the crossflow velocity for one hour. We demonstrate that small changes in phosphorus concentration in the feed water led to (i) different microbial compositions and (ii) different bacterial-cells-to-EPS ratios, while (iii) similar bacterial biofilm populations remained after forward flushing, suggesting a homogenous bacterial community composition along the biofilm height. This study represents an exciting advance towards greener desalination by applying non-expensive physical cleaning methods while manipulating feed water nutrient conditions to prolong membrane system performance and enhance membrane cleanability.

Simultaneous removal of nitrogen and phosphorus by a novel aerobic denitrifying phosphorus-accumulating bacterium, Pseudomonas stutzeri ADP-19

A novel denitrifying phosphorus-accumulating bacterium was isolated from contaminated sediment and identified as Pseudomonas stutzeri ADP-19. Bio-safety assays demonstrated that the strain was γ-hemolytic, antibiotic-sensitive, and had no decarboxylase activity. It removed 96.5% of NH₄⁺-N and 73.3% of PO₄^3--P (at initial concentrations of 100 mg/L and 20 mg/L) under aerobic conditions, and the corresponding maximum removal rates were 3.44 and 0.41 mg/L/h, respectively. Nitrogen removal was achieved through a fully nitrification-denitrification pathway [NH₄⁺-N → NH₂OH → NO₂^--N → NO₃^--N → NO₂^--N → (N_xO) → N₂], while phosphorus removal mainly depended on the phosphate assimilation and the excessive poly-P accumulation. Strain ADP-19 also showed a strong salt tolerance within a wide salinity range of 0-5%. The enhanced biological treatment of anaerobic-digested wastewater in a sequencing batch reactor (SBR) indicated that the strain improved the microbial diversity of the activated sludge and significantly enhanced the nitrogen and phosphorus removal efficiency.

Nutrient-imbalanced conditions shift the interplay between zooplankton and gut microbiota

Background

Nutrient stoichiometry of phytoplankton frequently changes with aquatic ambient nutrient concentrations, which is mainly influenced by anthropogenic water treatment and the ecosystem dynamics. Consequently, the stoichiometry of phytoplankton can markedly alter the metabolism and growth of zooplankton. However, the effects of nutrient-imbalanced prey on the interplay between zooplankton and their gut microbiota remain unknown. Using metatranscriptome, a 16 s rRNA amplicon-based neutral community model (NCM) and experimental validation, we investigated the interactions between Daphnia magna and its gut microbiota in a nutrient-imbalanced algal diet.

Results

Our results showed that in nutrient-depleted water, the nutrient-enriched zooplankton gut stimulated the accumulation of microbial polyphosphate in fecal pellets under phosphorus limitation and the microbial assimilation of ammonia under nitrogen limitation. Compared with the nutrient replete group, both N and P limitation markedly promoted the gene expression of the gut microbiome for organic matter degradation but repressed that for anaerobic metabolisms. In the nutrient limited diet, the gut microbial community exhibited a higher fit to NCM (R² = 0.624 and 0.781, for N- and P-limitation, respectively) when compared with the Control group (R² = 0.542), suggesting increased ambient-gut exchange process favored by compensatory feeding. Further, an additional axenic grazing experiment revealed that the growth of D. magna can still benefit from gut microbiota under a nutrient-imbalanced diet.

Conclusions

Together, these results demonstrated that under a nutrient-imbalanced diet, the microbes not only benefit themselves by absorbing excess nutrients inside the zooplankton gut but also help zooplankton to survive during nutrient limitation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07333-z.

Is there a link between inorganic polyphosphate (polyP), mitochondria, and neurodegeneration?

Mitochondrial dysfunction - including increased apoptosis, calcium and protein dyshomeostasis within the organelle, and dysfunctional bioenergetics and oxidative status - is a common, early feature in all the major neurodegenerative diseases, including Alzheimer's Disease (AD) and Parkinson's Disease (PD). However, the exact molecular mechanisms that drive the organelle to dysfunction and ultimately to failure in these conditions are still not well described. Different authors have shown that inorganic polyphosphate (polyP), an ancient and well-conserved molecule, plays a key role in the regulation of mitochondrial physiology under basal conditions. PolyP, which is present in all studied organisms, is composed of chains of orthophosphates linked together by highly energetic phosphoanhydride bonds, similar to those found in ATP. This polymer shows a ubiquitous distribution, even if a high co-localization with mitochondria has been reported. It has been proposed that polyP might be an alternative to ATP for cellular energy storage in different organisms, as well as the implication of polyP in the regulation of many of the mitochondrial processes affected in AD and PD, including protein and calcium homeostasis. Here, we conduct a comprehensive review and discussion of the bibliography available regarding the role of polyP in the mitochondrial dysfunction present in AD and PD. Taking into account the data presented in this review, we postulate that polyP could be a valid, innovative and, plausible pharmacological target against mitochondrial dysfunction in AD and PD. However, further research should be conducted to better understand the exact role of polyP in neurodegeneration, as well as the metabolism of the polymer, and the effect of different lengths of polyP on cellular and mitochondrial physiology.

Effects of aging and transformation of anatase and rutile TiO2 nanoparticles on biological phosphorus removal in sequencing batch reactors and related toxic mechanisms

The effect of nanomaterials aging, namely the transformation of comprehensive characteristics after experiencing real or complex environmental behaviors, on their ecotoxicology is still lacking. Moreover, the mechanisms by which NPs influence biological phosphorus (P) removal during sewage treatment require further elucidation. Therefore, we used both pristine and aged anatase (TiO₂-A) and rutile (TiO₂-R) NPs to investigate the mechanisms by which NPs affect P removal in a SBR. At 0.1 mg/L, the four types of NPs (pristine and aged) had no significant effect on sludge purification after acute (72-h) exposure under simulated sunlight. However, at 50 mg/L-regardless of the crystalline phase of the NPs-SOP and COD removal efficiency dropped steeply to approximately 42.2-82.4 % (p < 0.05) and 69.8-83.3 % (p < 0.05), respectively, especially in the pristine TiO₂-NPs groups because of decrease of richness and diversity of genus level of PAOs and enzyme activity of both PPK and PPX, and the sluggish transformation of PHA and glycogen. Aging reduced the ability of NPs toxicity. The toxicity mechanisms of TiO₂-NPs included lipid peroxidation and contact damage, or leakage from bacterial cytoplasmic membrane, which are closely related to photooxidation capacity and aqueous solution stability-i.e., nanoscale effects-and the impacts of aging or inclusion.

Bacterial Defense Systems against the Neutrophilic Oxidant Hypochlorous Acid

Neutrophils kill invading microbes and therefore represent the first line of defense of the innate immune response. Activated neutrophils assemble NADPH oxidase to convert substantial amounts of molecular oxygen into superoxide, which, after dismutation into peroxide, serves as the substrate for the generation of the potent antimicrobial hypochlorous acid (HOCl) in the phagosomal space. In this minireview, we explore the most recent insights into physiological consequences of HOCl stress. Not surprisingly, Gram-negative bacteria have evolved diverse posttranslational defense mechanisms to protect their proteins, the main targets of HOCl, from HOCl-mediated damage. We discuss the idea that oxidation of conserved cysteine residues and partial unfolding of its structure convert the heat shock protein Hsp33 into a highly active chaperone holdase that binds unfolded proteins and prevents their aggregation. We examine two novel members of the Escherichia coli chaperone holdase family, RidA and CnoX, whose thiol-independent activation mechanism differs from that of Hsp33 and requires N-chlorination of positively charged amino acids during HOCl exposure. Furthermore, we summarize the latest findings with respect to another bacterial defense strategy employed in response to HOCl stress, which involves the accumulation of the universally conserved biopolymer inorganic polyphosphate. We then discuss sophisticated adaptive strategies that bacteria have developed to enhance their survival during HOCl stress. Understanding bacterial defense and survival strategies against one of the most powerful neutrophilic oxidants may provide novel insights into treatment options that potentially compromise the ability of pathogens to resist HOCl stress and therefore may increase the efficacy of the innate immune response.

Effects of Selected Functional Bacteria on Maize Growth and Nutrient Use Efficiency

Plant growth-promoting rhizobacteria (PGPR), which include isolates from genera Paraburkholderia, Burkholderia and Serratia, have received attention due to their numerous plant growth-promoting mechanisms such as their ability to solubilize insoluble phosphates and nitrogen-fixation. However, there is a dearth of information on the potential plant growth-promoting effects of these three groups of bacteria on non-legumes such as maize. This study determined the influences of the aforementioned strains on soil properties, maize growth, nutrient uptake and nutrient use efficiency. A pot trial using maize as a test crop was done using a randomized complete block design with 7 treatments each replicated 7 times. The treatments used in this study were: Control (no fertilizer), chemical fertilizer (CF), organic-chemical fertilizers combination without inoculum (OCF) and with inocula consisting of single strains [cellulolytic bacteria (TC), organic fertilizer and chemical fertilizer with N-fixing bacteria (TN), organic fertilizer and chemical fertilizer with P-solubilizing bacteria (TP)) and three-strain inocula (TCNP), respectively. The variables measured included plant growth and nutrient content, soil nutrient content and functional rhizospheric bacterial populations. Paraburkholderia nodosa NB1 and Burkholderia cepacia PB3 showed comparable effects on maize biomass and also improved N and P use efficiencies when compared to full chemical fertilization. Nitrogen-fixing rhizobacteria had a positive effect on above-ground biomass of maize. Paraburkholderia nodosa NB1 improved soil total C and organic matter contents, besides being the only bacterial treatment that improved K use efficiency compared to OCF. The results suggest that P. nodosa NB1 and B. cepacia PB3 have potential usage in bio-fertilizers. In contrast, treatments with Serratia nematodiphila C46d and consortium strains showed poorer maize nutrient uptake and use efficiency than the other single strain treatments. Bacterial treatments generally showed comparable or higher overall N and P use efficiencies than full chemical fertilization. These findings suggest that at least half the amounts of N and P fertilizers could be reduced through the use of combined fertilization together with beneficial bacteria.

The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a > 5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical phosphate starvation control.

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms-the plant microbiota-are exposed to direct influence by the soil's phosphorus (P) content itself as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient and compared the composition of their shoot and root microbiota to wild-type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota than soil P concentrations in both roots and shoots. To dissect plant-microbe interactions under variable P conditions, we conducted a microbiota reconstitution experiment. Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift was accompanied by changes in microbiota composition: the genus Burkholderia was specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrated that in the absence of Burkholderia from the SynCom, plant shoots accumulated higher ortophosphate (Pi) levels than shoots colonized with the full SynCom but only under Pi starvation conditions. Therefore, Pi-stressed plants are susceptible to colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant's Pi starvation.

Inorganic polyphosphate, a multifunctional polyanionic protein scaffold

Polyphosphate (polyP) consists of a linear arrangement of inorganic phosphates and defies its structural simplicity with an astounding number of different activities in the cell. Already well known for its ability to partake in phosphate, calcium, and energy metabolism, polyP recently gained a new functional dimension with the discovery that it serves as a stabilizing scaffold for protein-folding intermediates. In this review, we summarize and discuss the recent studies that have identified polyP not only as a potent protein-like chaperone that protects cells against stress-induced protein aggregation, but also as a robust modifier of amyloidogenic processes that shields neuronal cells from amyloid toxicity. We consider some of the most pressing questions in the field, the obstacles faced, and the potential avenues to take to provide a complete picture about the working mechanism and physiological relevance of this intriguing biopolymer.

Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system

The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment-hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate-reducing bacteria and sulfur-oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast-associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.

Highly Effective Polyphosphate Synthesis, Phosphate Removal, and Concentration Using Engineered Environmental Bacteria Based on a Simple Solo Medium-Copy Plasmid Strategy

Microbial polyphosphate (polyP) production is vital to the removal of phosphate from wastewater. However, to date, engineered polyP synthesis using genetically accessible environmental bacteria remains a challenge. This study develops a simple solo medium-copy plasmid-based polyphosphate kinase (PPK1) overexpression strategy for achieving maximum intracellular polyphosphate accumulation by environmental bacteria. The polyP content of the subsequently engineered Citrobacter freundii (CPP) could reach as high as 12.7% of its dry weight. The biomass yield of CPP was also guaranteed because of negligible metabolic burden effects resulting from the medium plasmid copy number. Consequently, substantial removal of phosphate (P_i) from the ambient environment was achieved simultaneously. Because of the need for exogenous P_i for in vivo ATP regeneration, CPP could thoroughly remove P_i from synthetic municipal wastewater when it was applied for the "one-step" removal of P_i with a bench-scale sequence batch membrane reactor. Almost all the phosphorus except for that assimilated by CPP for cellular growth could be recovered in the form of more concentrated P_i. Overall, engineering environmental bacteria to overexpress PPK1 via a solo medium-copy plasmid strategy may represent a valuable general option for not only biotechnological research based on sufficient intracellular polyP production but also removal of P_i from wastewater and P_i enrichment.

Influence of CeO2 NPs on biological phosphorus removal and bacterial community shifts in a sequencing batch biofilm reactor with the differential effects of molecular oxygen

The effects of CeO₂ nanoparticles (CeO₂ NPs) on a sequencing batch biofilm reactor (SBBR) with established biological phosphorus (P) removal were investigated from the processes of anaerobic P release and aerobic P uptake. At low concentration (0.1mg/L), no significant impact was observed on total phosphorus (TP) removal after operating for 8h. However, at a concentration of 20mg/L, TP removal efficiency decreased from 83.68% to 55.88% and 16.76% when the CeO₂ NPs were added at the beginning of the anaerobic and aerobic periods, respectively. Further studies illustrated that the inhibition of the specific P release rate was caused by the reversible states of Ce³⁺ and Ce⁴⁺, which inhibited the activity of exopolyphosphatase (PPX) and transformation of poly-β-hydoxyalkanoates (PHA) and glycogen, as well as the uptake of volatile fatty acids (VFAs). The decrease in the specific P uptake rate was mainly attributed to the significantly suppressed energy generation and decreased abundance of Burkholderia caused by excess reactive oxygen species. The removal of chemical oxygen demand (COD) was not influenced by CeO₂ NPs under aerobic conditions, due to the increased abundance of Acetobacter and Acidocella after exposure. The inhibitory effects of CeO₂ NPs with molecular oxygen were reduced after anaerobic exposure due to the enhanced particle size and the presence of Ce³⁺.

Microbial phylogenetic and functional responses within acidified wastewater communities exhibiting enhanced phosphate uptake

Acid stimulated accumulation of insoluble phosphorus within microbial cells is highly beneficial to wastewater treatment but remains largely unexplored. Using single cell analyses and next generation sequencing, the response of active polyphosphate accumulating microbial communities under conditions of enhanced phosphorus uptake under both acidic and aerobic conditions was characterised. Phosphorus accumulation activities were highest under acidic conditions (pH 5.5>8.5), where a significant positive effect on bioaccumulation was observed at pH 5.5 when compared to pH 8.5. In contrast to the Betaproteobacteria and Actinobacteria dominated enhanced biological phosphorus removal process, the functionally active polyP accumulators at pH 5.5 belonged to the Gammaproteobacteria, with key accumulators identified as members of the families Aeromonadaceae and Enterobacteriaceae. This study demonstrated a significant enrichment of key polyphosphate kinase and exopolyphosphatase genes within the community metagenome after acidification, concomitant with an increase in P accumulation kinetics.

Formation of polyphosphate by polyphosphate kinases and its relationship to poly(3-hydroxybutyrate) accumulation in Ralstonia eutropha strain H16

A protein (PhaX) that interacted with poly(3-hydroxybutyrate) (PHB) depolymerase PhaZa1 and with PHB granule-associated phasin protein PhaP2 was identified by two-hybrid analysis. Deletion of phaX resulted in an increase in the level of polyphosphate (polyP) granule formation and in impairment of PHB utilization in nutrient broth-gluconate cultures. A procedure for enrichment of polyP granules from cell extracts was developed. Twenty-seven proteins that were absent in other cell fractions were identified in the polyP granule fraction by proteome analysis. One protein (A2437) harbored motifs characteristic of type 1 polyphosphate kinases (PPK1s), and two proteins (A1212, A1271) had PPK2 motifs. In vivo colocalization with polyP granules was confirmed by expression of C- and N-terminal fusions of enhanced yellow fluorescent protein (eYFP) with the three polyphosphate kinases (PPKs). Screening of the genome DNA sequence for additional proteins with PPK motifs revealed one protein with PPK1 motifs and three proteins with PPK2 motifs. Construction and subsequent expression of C- and N-terminal fusions of the four new PPK candidates with eYFP showed that only A1979 (PPK2 motif) colocalized with polyP granules. The other three proteins formed fluorescent foci near the cell pole (apart from polyP) (A0997, B1019) or were soluble (A0226). Expression of the Ralstonia eutropha ppk (ppkReu) genes in an Escherichia coli Δppk background and construction of a set of single and multiple chromosomal deletions revealed that both A2437 (PPK1a) and A1212 (PPK2c) contributed to polyP granule formation. Mutants with deletion of both genes were unable to produce polyP granules. The formation and utilization of PHB and polyP granules were investigated in different chromosomal backgrounds.

Responses of microbial communities to single-walled carbon nanotubes in phenol wastewater treatment systems

The expanding use of single-walled carbon nanotubes (SWCNTs) raises environmental concerns. Wastewater treatment systems are potential recipients of SWCNTs containing influent, yet the impacts of SWCNTs on these systems are poorly documented. In this study, the microbial responses to SWCNTs in simulated phenol wastewater treatment systems were investigated. The phenol removal rates were improved in all SWCNTs-treated sequencing batch reactors during the first 20 days, but when facing higher phenol concentration (1000 mg/L) after 60 days, reactors with the highest concentration (3.5 g/L) of SWCNTs exhibited a notably decreased phenol removal capacity. Cell viability tests, scanning electron microscopy analysis and DNA leakage data suggested that SWCNTs protected microbes from inactivation, possibly by producing more bound extracellular polymeric substances (EPS), which could create a protective barrier for the microbes. Illumina sequencing of 16S rRNA gene amplicons revealed that the bacterial diversity did not change significantly except for a minor reduction after the immediate addition of SWCNTs. Bacterial community structure significantly shifted after SWCNTs addition and did not recover afterward. Zoogloea increased significantly upon SWCNTs shocking. At the final stage, Rudaea and Mobilicoccus increased, while Burkholderia, Singulisphaera, Labrys and Mucilaginibacter decreased notably. The shifts of these dominant genera may be associated with altered sludge settling, aromatic degradation and EPS production. This study suggested that SWCNTs exerted protective rather than cytotoxic effects on sludge microbes of phenol wastewater treatment systems and they affected the bacterial community structure and diversity at test concentrations. These findings provide new insights into our understanding of the potential effects of SWCNTs on wastewater treatment processes.

Role of phosphate fertilizers in heavy metal uptake and detoxification of toxic metals

As a nonrenewable resource, phosphorus (P) is the second most important macronutrient for plant growth and nutrition. Demand of phosphorus application in the agricultural production is increasing fast throughout the globe. The bioavailability of phosphorus is distinctively low due to its slow diffusion and high fixation in soils which make phosphorus a key limiting factor for crop production. Applications of phosphorus-based fertilizers improve the soil fertility and agriculture yield but at the same time concerns over a number of factors that lead to environmental damage need to be addressed properly. Phosphate rock mining leads to reallocation and exposure of several heavy metals and radionuclides in crop fields and water bodies throughout the world. Proper management of phosphorus along with its fertilizers is required that may help the maximum utilization by plants and minimum run-off and wastage. Phosphorus solubilizing bacteria along with the root rhizosphere of plant integrated with root morphological and physiological adaptive strategies need to be explored further for utilization of this extremely valuable nonrenewable resource judiciously. The main objective of this review is to assess the role of phosphorus in fertilizers, their uptake along with other elements and signaling during P starvation.

Accumulation and enhanced cycling of polyphosphate by Sargasso Sea plankton in response to low phosphorus

Phytoplankton alter their biochemical composition according to nutrient availability, such that their bulk elemental composition varies across oceanic provinces. However, the links between plankton biochemical composition and variation in biogeochemical cycling of nutrients remain largely unknown. In a survey of phytoplankton phosphorus stress in the western North Atlantic, we found that phytoplankton in the phosphorus-depleted subtropical Sargasso Sea were enriched in the biochemical polyphosphate (polyP) compared with nutrient-rich temperate waters, contradicting the canonical oceanographic view of polyP as a luxury phosphorus storage molecule. The enrichment in polyP coincided with enhanced alkaline phosphatase activity and substitution of sulfolipids for phospholipids, which are both indicators of phosphorus stress. Further, polyP appeared to be liberated preferentially over bulk phosphorus from sinking particles in the Sargasso Sea, thereby retaining phosphorus in shallow waters. Thus, polyP cycling may form a feedback loop that attenuates the export of phosphorus when it becomes scarce, contributes bioavailable P for primary production, and supports the export of carbon and nitrogen via sinking particles.

The impact of microbial ecology and chemical profile on the enhanced biological phosphorus removal (EBPR) process: a case study of Northern Wastewater Treatment Works, Johannesburg

The impact of polyphosphate-accumulating organism (PAO) and glycogen-accumulating organism (GAO) populations as well as of the chemical profile on the performance of Unit-3 (open elutriation tanks) and Unit-5 (covered elutriation tank) of the City of Johannesburg Northern Wastewater Treatment Works was determined. Physicochemical parameters of wastewater samples were measured using standard methods. Bacterial diversity was determined using 16S rRNA gene amplicon pyrosequencing of the variable region V1-3. Results showed soluble COD concentrations from settled sewage for Unit-3 at 192.8 mg COD/L and for Unit-5 at 214.6 mg COD/L, which increased to 301.8 mg COD/L and 411.6 mg COD/L in the overflow from elutriation tanks and decreased to 170.9 mg COD/L and 256.3 mg COD/L at the division boxes, respectively. Both long-chain volatile fatty acids (heptanoic acid, isobutyric acid, 3-methylbutanoic acid, pentanoic acid, 4-methylpentanoic acid, methylheptanoic acid) and short-chain volatile fatty acids (acetic acid, propionic acid, isobutyric acid) were present within concentration ranges of 17.19 mg/L to 54.98 mg/L and 13.64 mg/L to 87.6 mg/L for Unit 3 and 38.61 mg/L to58.85 mg/L and 21.63 mg/L to 92.39 mg/L for Unit 5, respectively. In the secondary settling tanks, the phosphate-removal efficiency in Unit-5 appeared to be slightly higher (0.08 mg P/L) compared to that of Unit-3 (0.11 mg P/L). The average DO concentrations (2.1 mg/L and 2.2 mg/L) as well as the pH values (pH 7 to pH 7.5) were found to be slightly higher in Unit-5 in the aerobic zones. The high presence of PAOs in the bioreactors (Unit-5: Dechloromonas (14.96%), Acinetobacter (6.3%), Zoogloea (4.72%) in the anaerobic zone and Dechloromonas (22.37 %) in the aerobic zone; Unit-3: Dechloromonas (37.25%) in the anaerobic zone and Dechloromonas (23.97%) in the aerobic zone) confirmed the phosphate-removal efficiencies of both units. Negligible GAOs were found in the aerobic zones (Defluviicoccus spp.: 0.33% for Unit-5 and 0.68% for Unit-3) and in the anaerobic zones (Defluviicoccus: 9.8% for Unit-3). The high microbial diversity and a negligible percentage of GAOs in Unit-5 could contribute to its high phosphate-removal efficiency, although results did not indicate statistically significant differences between the unit with a covered elutriation tank (Unit-5) and that with open elutriation tanks (Unit-3).

Accumulation of polyphosphate in Lactobacillus spp. and its involvement in stress resistance

Polyphosphate (poly-P) is a polymer of phosphate residues synthesized and in some cases accumulated by microorganisms, where it plays crucial physiological roles such as the participation in the response to nutritional stringencies and environmental stresses. Poly-P metabolism has received little attention in Lactobacillus, a genus of lactic acid bacteria of relevance for food production and health of humans and animals. We show that among 34 strains of Lactobacillus, 18 of them accumulated intracellular poly-P granules, as revealed by specific staining and electron microscopy. Poly-P accumulation was generally dependent on the presence of elevated phosphate concentrations in the culture medium, and it correlated with the presence of polyphosphate kinase (ppk) genes in the genomes. The ppk gene from Lactobacillus displayed a genetic arrangement in which it was flanked by two genes encoding exopolyphosphatases of the Ppx-GppA family. The ppk functionality was corroborated by its disruption (LCABL_27820 gene) in Lactobacillus casei BL23 strain. The constructed ppk mutant showed a lack of intracellular poly-P granules and a drastic reduction in poly-P synthesis. Resistance to several stresses was tested in the ppk-disrupted strain, showing that it presented a diminished growth under high-salt or low-pH conditions and an increased sensitivity to oxidative stress. These results show that poly-P accumulation is a characteristic of some strains of lactobacilli and may thus play important roles in the physiology of these microorganisms.

Inorganic polyphosphates in extremophiles and their possible functions

Many extremophilic microorganisms are polyextremophiles, being confronted with more than one stress condition. For instance, some thermoacidophilic microorganisms are in addition capable to resist very high metal concentrations. Most likely, they have developed special adaptations to thrive in their living environments. Inorganic polyphosphate (polyP) is a molecule considered to be primitive in its origin and ubiquitous in nature. It has many roles besides being a reservoir for inorganic phosphate and energy. Of special interest are those functions related to survival under stressing conditions in all kinds of cells. PolyP may therefore have a fundamental part in extremophilic microorganism's endurance. Evidence for a role of polyP in the continued existence under acidic conditions, high concentrations of toxic heavy metals and elevated salt concentrations are reviewed in the present work. Actual evidence suggests that polyP may provide mechanistic alternatives in tuning microbial fitness for the adaptation under stressful environmental situations and may be of crucial relevance amongst extremophiles. The enzymes involved in polyP metabolism show structure conservation amongst bacteria and archaea. However, the lack of a canonical polyP synthase in Crenarchaea, which greatly accumulate polyP, strongly suggests that in this phylum a different enzyme may be in charge of its synthesis.

Correlation of community dynamics and process parameters as a tool for the prediction of the stability of wastewater treatment

Wastewater treatment often suffers from instabilities and the failure of specific functions such as biological phosphorus removal by polyphosphate accumulating organisms. Since most of the microorganisms involved in water clarification are unknown it is challenging to operate the process accounting for the permanent varying abiotic parameters and the complex composition and unrevealed metabolic capacity of a wastewater microbial community. Fulfilling the demands for water quality irrespective of substrate inflow conditions may emit severe problems if the limited management resources of municipal wastewater treatment plants are regarded. We used flow cytometric analyses of cellular DNA and polyphosphate to create patterns mirroring dynamics in community structure. These patterns were resolved in up to 15 subclusters, the presence and abundances of which correlated with abiotic data. The study used biostatistics to determine the kind and strength of the correlation. Samples investigated were obtained from a primary clarifier and two activated sludge basins. The stability of microbial community structure was found to be high in the basins and low in the primary clarifier. Despite major abiotic changes certain subcommunities were dominantly present (up to 80% stability), whereas others emerged only sporadically (down to 3% stability, both according to equivalence testing). Additionally, subcommunities of diagnostic value were detected showing positive correlation with substrate influxes. For instance blackwater (r(s) = 0.5) and brewery inflow (both r(s) = 0.6) were mirrored by increases in cell abundances in subclusters 1 and 6 as well as 4 and 8, respectively. Phosphate accumulation was obviously positively correlated with nitrate (r(s) = 0.4) and the presence of denitrifying organisms (Rhodacyclaceae). Various other correlations between community structure and abiotic parameters were apparent. The bacterial composition of certain subcommunities was determined by cell sorting and phylogenetic tools like T-RFLP. In essence, we developed a monitoring tool which is quick, cheap and causal in its interpretation. It will make laborious PCR based technique less obligatory as it allows reliable process monitoring and control in wastewater treatment plants.

Amino acids involved in polyphosphate synthesis and its mobilization are distinct in polyphosphate kinase-1 from Mycobacterium tuberculosis

BACKGROUND

In bacteria polyphosphates (poly-P) are involved in cellular metabolism and development especially during stress. The enzyme, principally involved in polyphosphate biosynthesis and its mobilization leading to generation of NTPs, is known as polyphosphate kinase (PPK).

PRINCIPAL FINDINGS

Among two genes of polyphosphate kinases present in Mycobacterium tuberculosis, we cloned and expressed PPK1 in Escherichia coli as histidine-tagged protein. This ∼86 kDa protein is capable of autophosphorylation and synthesis of poly-P as well as NTP. Among 22 conserved histidine residues, we found only His-491 is autophosphorylated and crucial for any enzymatic activity. Substitution of His-510 caused mPPK1 protein deficient but not defective in autophosphorylation, thereby contrary to earlier reports negating any role of this residue in the process. However, mutation of His-510 with either Ala or Gln affected ATP or poly-P synthesis depending on the substitution; while such effects were severe with H510A but mild with H510Q. Furthermore, mPPK1 also renders auxiliary nucleotide diphosphate kinase function by synthesizing virtually all NTPs/dNTPs from their cognate NDPs/dNDPs by utilizing poly-P as the phosphate donor albeit with varied efficiency. To assess the influence of other catalytic domain residues of mPPK1 towards its functionality, we designed mutations based on E. coli PPK1 crystal structure since it owes 68% amino acid sequence similarity with mPPK1. Interestingly, our results revealed that mutations in mPPK1 affecting poly-P synthesis always affected its ATP synthesizing ability; however, the reverse may not be true.

CONCLUSIONS/SIGNIFICANCE

We conclude that amino acid residues involved in poly-P and ATP synthesizing activities of mPPK1 are distinct. Considering conserved nature of PPK1, it seems our observations have broader implications and not solely restricted to M. tuberculosis only.

Interaction between phosphorus and biodegradable organic carbon on drinking water biofilm subject to chlorination

AIMS

To examine whether phosphorus and biodegradable organic carbon interact to impact biofilm density and physiological function of biofilm-forming bacteria under conditions relevant to chlorinated drinking water distribution systems.

MATERIALS AND RESULTS

The 2 x 2 factorial experiments with low and high levels of phosphorus and biodegradable organic carbon were performed on 4 -week-old drinking water biofilms in four separate pipe systems in the presence of chlorine. Experimental results revealed that biofilm heterotrophic plate count levels increased with the increase in biodegradable organic carbon concentration, showed no response to increases in levels of phosphorus and was not affected by interaction between phosphorus and biodegradable organic carbon. However, a significant positive interaction between phosphorus and biodegradable organic carbon was found to exist on biofilm mass and physiological function and/or metabolic potentials of biofilm communities; the effects of biodegradable organic carbon on biofilm mass and physiological function of biofilm-forming bacteria were accelerated in going from low to high level of phosphorus.

CONCLUSIONS

Biodegradable organic carbon was found to be the primary nutrient in regulating biofilm formation in drinking water regardless of the presence of chlorine. It can be therefore concluded that the removal of an easily biodegradable organic carbon is necessary to minimize the biofilm growth potential induced by the intrusion of phosphorus.

SIGNIFICANCE AND IMPACT OF THE STUDY

Phosphorus introduced to drinking water may interact with biodegradable organic carbon, thus leading to measurable impact on the biofilm formation.

Identification of Campylobacter jejuni genes contributing to acid adaptation by transcriptional profiling and genome-wide mutagenesis

In order to cause disease, the food- and waterborne pathogen Campylobacter jejuni must face the extreme acidity of the host stomach as well as cope with pH fluctuations in the intestine. In the present study, C. jejuni NCTC 11168 was grown under mildly acidic conditions mimicking those encountered in the intestine. The resulting transcriptional profiles revealed how this bacterium fine-tunes gene expression in response to acid stress. This adaptation involves the differential expression of respiratory pathways, the induction of genes for phosphate transport, and the repression of energy generation and intermediary metabolism genes. We also generated and screened a transposon-based mutant library to identify genes required for wild-type levels of growth under mildly acidic conditions. This screen highlighted the important role played by cell surface components (flagella, the outer membrane, capsular polysaccharides, and lipooligosaccharides) in the acid stress response of C. jejuni. Our data also revealed that a limited correlation exists between genes required for growth under acidic conditions and genes differentially expressed in response to acid. To gain a comprehensive picture of the acid stress response of C. jejuni, we merged transcriptional profiles obtained from acid-adapted cells and cells subjected to acid shock. Genes encoding the transcriptional regulator PerR and putative oxidoreductase subunits Cj0414 and Cj0415 were among the few up-regulated under both acid stress conditions. As a Cj0415 mutant was acid sensitive, it is likely that these genes are crucial to the acid stress response of C. jejuni and consequently are important for host colonization.

Identification of Campylobacter jejuni genes involved in the response to acidic pH and stomach transit

Campylobacter jejuni causes food- and waterborne gastroenteritis, and as such it must survive passage through the stomach in order to reach the gastrointestinal tract. While little is known about how C. jejuni survives transit through the stomach, its low infectious dose suggests it is well equipped to sense and respond to acid shock. In this study, the transcriptional profile of C. jejuni NCTC 11168 was obtained after the organism was exposed to in vitro and in vivo (piglet stomach) acid shock. The observed down-regulation of genes encoding ribosomal proteins likely reflects the need to reshuffle energy toward the expression of components required for survival. Acid shock also caused C. jejuni to up-regulate genes involved in stress responses. These included heat shock genes as well as genes involved in the response to oxidative and nitrosative stress. A role for the chaperone clpB in acid resistance was confirmed in vitro. Some genes showed expression patterns that were markedly different in vivo and in vitro, which likely reflects the complexity of the in vivo environment. For instance, transit through the stomach was characterized by up-regulation of genes that encode products that are involved in the use of nitrite as a terminal electron acceptor and down-regulation of genes that are involved in capsular polysaccharide expression. In conclusion, this study has enabled us to understand how C. jejuni modulates gene expression in response to acid shock in vitro and to correlate this with gene expression profiles of C. jejuni as it transits through the host stomach.

Solubilization of insoluble inorganic phosphate by Burkholderia cepacia DA23 isolated from cultivated soil

A mineral phosphate solubilizing bacterium, Burkholderia cepacia DA23 has been isolated from cultivated soils. Phosphate-solubilizing activities of the strain against three types of insoluble phosphate were quantitatively determined. When 3% of glucose concentration was used for carbon source, the strain had a marked mineral phosphate-solubilizing activity. Mineral phosphate solubilization was directly related to the pH drop by the strain. Analysis of the culture medium by high pressure liquid chromatography identified gluconic acid as the main organic acid released by Burkholderia cepacia DA23. Gluconic acid production was apparently the result of the glucose dehydrogenase activity and glucose dehydrogenase was affected by phosphate regulation.

Phosphate removal under denitrifying conditions byBrachymonassp. strain P12 andParacoccus denitrificansPP15

In this study, we used the denitrifying phosphorus-removing bacterium Brachymonas sp. strain P12 to investigate the enhanced biologic phosphorus-removal (EBPR) mechanism involved with polyhydroxybutyrate (PHB), glycogen, and phosphorus uptake in the presence of acetate under anoxic or aerobic conditions. The results showed that excess acetate concentration and aerobic cultivation can enhance PHB formation efficiency and that PHB formation might be stimulated by glycogenolysis of the cellular glycogen. The efficiency of the uptake of anoxic phosphorus was greater when PHB production was lower. The EBPR mechanism of Brachymonas sp. strain P12 for PHB, phosphorus, and glycogen was similar to the conventional anaerobic–aerobic (or anaerobic–anoxic) EBPR models, but these models were developed under anoxic or aerobic conditions only, without an anaerobic stage. The anoxic or aerobic log phase of growth is divided into two main phases: the early log phase, in which acetate and glycogen are consumed to supply enough energy and reducing power for PHB formation and cell growth (phosphorus assimilation), and the late log phase, which ends the simultaneous degradation of PHB and remaining acetate for polyphosphate accumulation. Glycogenolysis plays a significant role in the alternate responses between PHB formation and phosphorus uptake under anoxic or aerobic conditions. After the application of the denitrifying phosphorus-removing bacterium Brachymonas sp. strain P12, aerobic cultivation increases the level of PHB production, and anoxic cultivation further increases phosphorus uptake.

Polyphosphate accumulation by Pseudomonas putida CA-3 and other medium-chain-length polyhydroxyalkanoate-accumulating bacteria under aerobic growth conditions

Pseudomonas putida CA-3 accumulates polyphosphate (polyP) and medium-chain-length polyhydroxyalkanoate (mclPHA) concurrently under nitrogen limitation. Five other mclPHA-accumulating Pseudomonas strains are capable of simultaneous polyP and mclPHA biosynthesis. It appears that polyP is not the rate-limiting step for mclPHA accumulation in these Pseudomonas strains.

Effect of reduced pH on inorganic polyphosphate accumulation by Burkholderia cepacia complex isolates

AIMS

Burkholderia cepacia complex (Bcc) isolates causing pulmonary infection in cystic fibrosis (CF) patients grow within an acidic environment in the lung. As exposure to acid pH has been shown to increase intracellular inorganic polyphosphate (polyP) formation in some bacteria, we investigated the inter-relationship between acidic pH and polyP accumulation in Bcc isolates.

METHODS AND RESULTS

The formation of polyP by one Burkholderia cenocepacia clinical isolate was initially examined at a range of pH values by measuring total intracellular polyP accumulation and phosphate uptake. The pattern of polyP accumulation corresponded with the pattern of phosphate uptake with the maximum for both occurring at pH 5.5. Phosphate uptake and formation of polyP by this isolate was further determined over 48 h at pH 5.5, 6.5 and 7.5; formation of polyP was maximal at pH 5.5 at all time points studied. Sixteen of 17 additional clinical and environmental Bcc isolates examined also exhibited maximum phosphate uptake at pH 5.5.

CONCLUSIONS

Both clinical and environmental Bcc isolates, of five genomovars, show enhanced formation of polyP in an acidic environment. Given both the speculated role of polyP in pathogenesis, cell signalling and biofilm formation and the acidic nature of the CF lung, this may be of considerable clinical importance.

SIGNIFICANCE AND IMPACT OF THE STUDY

Growth of Bcc in an acidic environment, such as that found in the lungs of CF patients may be influenced in part by polyP accumulation.

Pilot-scale evaluation of the application of low pH-inducible polyphosphate accumulation to the biological removal of phosphate from wastewaters

To investigate the possible biotechnological application of the phenomenon of low pH-inducible phosphate uptake and polyphosphate accumulation, previously reported using pure microbial cultures and under laboratory conditions, a 2000 L activated sludge pilot plant was constructed at a municipal sewage treatment works. When operated as a single-stage reactor this removed more than 60% of influent phosphate from primary settled sewage at a pH of 6.0, as opposed to approximately 30% at the typical operational pH for the works of 7.0-7.3-yet without any deleterious effect on other treatment parameters. At these pH values the phosphorus content of the sludge was, respectively, 4.2% and 2.0%. At pH 6.0 some 33.9% of sludge microbial cells were observed to contain polyphosphate inclusions; the corresponding value at pH 7.0 was 18.7%. Such a process may serve as a prototype for the development of alternative biological and chemical options for phosphate removal from wastewaters.

Polyphosphate kinase: a new colonization factor of Helicobacter pylori

In order to elucidate the role of polyphosphate kinase (PPK) during the course of an infection by Helicobacter pylori, PPK deficient mutants were constructed using two genetic backgrounds: Hp141v and X47-2AL. The efficiencies of the parental strains and the derivative mutants at colonizing the gastric mucosa of mice were compared. When animals received the Hp141v and the X47-2AL parental strains, 100% of the mice remained colonized for the duration of the 45 days experiment. In contrast, none of the mice that were given the PPK deficient X47-2AL derivative strain had a detectable bacterial load in their gastric mucosa, while the deficient Hp141v derivative strain was detected in 100%, 20% and 40% of the mice at days 3, 15 and 45 post-inoculation (p.i.), respectively. The absence of PPK expression did not impair the in vitro growth of the ppk mutants. However, the reduced ability of the ppk defective mutants to colonize mice was associated with a significant decrease in both motility and in an accumulation of polyP in the bacterial cells. These results are consistent with an essential role of PPK during the initial steps of colonisation of the mouse gastric mucosa and confirm that PPK may act on the virulence of H. pylori partly through an energy dependent mechanism.

In vitro detection and characterisation of a polyphosphate synthesising activity in the yeast Candida humicola G-1

An in vitro detectable polyphosphate-synthesising activity was characterised using two independent assay systems in extracts of the yeast Candida humicola G-1. Its properties were similar to those of a range of bacterial polyphosphate kinase enzymes. PCR amplification of C. humicola genomic DNA using universal primers for bacterial polyphosphate kinase genes yielded a product whose translated sequence showed up to 34% amino acid similarity to the bacterial enzyme.

Recent advances in removing phosphorus from wastewater and its future use as fertilizer (1997-2003)

Large quantities of phosphate present in wastewater is one of the main causes of eutrophication that negatively affects many natural water bodies, both fresh water and marine. It is desirable that water treatment facilities remove phosphorus from the wastewater before they are returned to the environment. Total removal or at least a significant reduction of phosphorus is obligatory, if not always fulfilled, in most countries. This comprehensive review summarizes the current status in phosphorus-removal technologies from the most common approaches, like metal precipitation, constructed wetland systems, adsorption by various microorganisms either in a free state or immobilized in polysaccharide gels, to enhanced biological phosphorus removal using activated sludge systems, and several innovative engineering solutions. As chemical precipitation renders the precipitates difficult, if not impossible, to recycle in an economical industrial manner, biological removal opens opportunities for recovering most of the phosphorus and beneficial applications of the product. This review includes the options of struvite (ammonium-magnesium-phosphate) and hydroxyapatite formation and other feasible options using, the now largely regarded contaminant, phosphorus in wastewater, as a raw material for the fertilizer industry. Besides updating our knowledge, this review critically evaluates the advantage and difficulties behind each treatment and indicates some of the most relevant open questions for future research.

Growth of polychlorinated-biphenyl-degrading bacteria in the presence of biphenyl and chlorobiphenyls generates oxidative stress and massive accumulation of inorganic polyphosphate

Inorganic polyphosphate (polyP) plays a significant role in increasing bacterial cell resistance to unfavorable environmental conditions and in regulating different biochemical processes. Using transmission electron microscopy of the polychlorinated biphenyl (PCB)-degrading bacterium Pseudomonas sp. strain B4 grown in defined medium with biphenyl as the sole carbon source, we observed large and abundant electron-dense granules at all stages of growth and following a shift from glucose to biphenyl or chlorobiphenyls. Using energy dispersive X-ray analysis and electron energy loss spectroscopy with an integrated energy-filtered transmission electron microscope, we demonstrated that these granules were mainly composed of phosphate. Using sensitive enzymatic methods to quantify cellular polyP, we confirmed that this polymer accumulates in PCB-degrading bacteria when they grow in the presence of biphenyl and chlorobiphenyls. Concomitant increases in the levels of the general stress protein GroEl and reactive oxygen species were also observed in chlorobiphenyl-grown cells, indicating that these bacteria adjust their physiology with a stress response when they are confronted with compounds that serve as carbon and energy sources and at the same time are chemical stressors.

Modification in the ppk gene of Helicobacter pylori during single and multiple experimental murine infections

The bacterial pathogen Helicobacter pylori is highly adapted to the human stomach, and a high level of polymorphism is observed among clinical isolates. This polymorphism may be the consequence of adaptive changes during colonization, making a strain better able to survive, to evade the immune system, and to provoke a chronic infection. To investigate the mechanisms involved in the acquisition of diversity in H. pylori, mouse models of single infections, coinfections, and superinfections were developed. These experimental infections were conducted with strain SS1, well known to be mouse adapted, and with two strains freshly isolated from infected patients: Hp141 and Hp145. Genetic modifications occurring in these strains were studied over time by comparing randomly selected colonies of the emerging strains to those of the infecting strains by using randomly amplified polymorphic DNA fingerprinting with six different primers and by using PCR to amplify the vacA and cagA genes. We showed that, regardless of the number of infecting strains, only one emerged from the animals and that the establishment of a first strain thwarted the implantation of a second strain. During both a single infection and a coinfection with SS1, Hp141 was replaced by a genetic variant (Hp141v) that overcame SS1 in coinfection experiments. Hp141v exhibited a deletion of a 102-bp repeated sequence within the ppk gene, which encodes polyphosphate kinase (PPK), an enzyme involved in the physiological adaptation of the microbial cell to nutritional and environmental stresses. The deletion led to higher enzymatic activity of PPK, and the variant exhibited a better capacity to colonize mice. Considering that the modified gene is known to be involved in adaptation to a new environment, our results are consistent with an adaptive change in strain Hp141 and suggest that PPK is an important virulence factor in H. pylori.