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

A systematic study of regulating inorganic polyphosphates production in Saccharomyces cerevisiae

Inorganic polyphosphate (polyP), a linear polymer of orthophosphate residues, plays critical roles in diverse biological processes spanning blood coagulation, immunomodulation, and post-translational protein modifications in eukaryotes. Notably, long-chain polyP (>100 phosphate units) exhibits distinct biological functionalities compared to shorter-chain counterparts. While Saccharomyces cerevisiae serves as a promising microbial platform for polyP biosynthesis, the genetic regulatory mechanisms underlying polyP metabolism remain poorly elucidated. Here, we systematically investigated the genetic determinants governing intracellular polyP levels and chain length dynamics in yeast. Through screening a library of 55 single-gene knockout strains, we identified six mutants (Δddp1, Δvip1, Δppn1, Δppn2, Δecm33, and Δccr4) exhibiting elevated polyP accumulation, whereas deletions of vtc1, kcs1, vma22, vma5, pho85, vtc4, vma2, vma3, ecm14, and vph2 resulted in near-complete polyP depletion. Subsequent combinatorial deletions in the Δppn1 background revealed that the Δppn1Δvip1 double mutant achieved synergistic enhancement in both polyP concentration (53.01 mg-P/g-DCW) and chain length, attributable to increased ATP availability and reduced polyphosphatase activity. Leveraging CRISPR/Cas9-mediated overexpression in Δppn1Δvip1, we engineered strain PP2 (vtc4 overexpression), which demonstrated a 2-fold increase in polyP yield (62.6 mg-P/g-DCW) relative to wild-type BY4741, with predominant synthesis of long-chain species. Mechanistically, qRT-PCR analysis confirmed that PP2 exhibited 46-fold up-regulation of vtc4 coupled with down-regulation of polyphosphatases encoding genes, ppn2, ddp1, and ppx1. This study performed a systematic study of regulating inorganic polyphosphates production in yeast and provides a synthetic biology strategy to engineer high-yield polyP-producing strains, advancing both fundamental understanding and biotechnological applications.

From kitchen to crop: The efficacy and safety of the microbial consortium treated dishwasher wastewater for the Zero Mile system

A microbial consortium, based on the functional integration of photosynthetic and heterotrophic microorganisms, is the core of the Zero Mile System. This system is designed for reusing and upcycling household greywaters, a still untapped water resource. The previous challenges of dishwasher wastewater bioremediation demonstrated the capability of an ad hoc consortium (including a photosynthetic cyanobacterium and three heterotrophic bacterial isolates from dishwasher wastewater) to reclaim the wastewater at small/medium scale. In this study the wastewater treatment demonstrated to be effective in nutrient recycling and upcycling at a larger scale, i.e. 4 L (in three replicates to treat the total amount of wastewater discharged by the dishwasher), by removing high percentage of N and P from the wastewater (70% nitrogen, 50% phosphorous, respectively). Again, the reclaimed wastewater successfully fertilized lettuce plants both indoor (in the Zero Mile System demonstrator) and outdoor (in open field). Plants showed a significant higher biomass productivity in fresh weight compared to control plants and comparable or better values of the pigments and quality indices (e.g., soluble solids, total phenols, total flavonoids). Furthermore, the safety of the reclaimed wastewater is demonstrated by the analysis of the metabolic/ecologically relevant functions of the microbial communities in both untreated and treated wastewater. Colonizers were mainly organic matter degraders and bacteria involved in nitrogen cycling. The human related genera are quite few and no pathogens or potential microbiological contaminants of water bodies (as E. coli), were found. Hence, the utilization of treated dishwasher wastewater does not imply biological risks to agricultural products, soil, or groundwater.

Recovery of Phosphorus in Wastewater in the Form of Polyphosphates: A Review

As non-renewable resource, the recovery and utilization of phosphorus from wastewater is an enduring topic. Stimulated by the advances in research on polyphosphates (polyP) as well as the development of Enhanced Biological Phosphorus Removal (EBPR) technology to achieve the efficient accumulation of polyP via polyphosphate accumulating organisms (PAOs), a novel phosphorus removal strategy is considered with promising potential for application in real wastewater treatment processes. This review mainly focuses on the mechanism of phosphorus aggregation in the form of polyP during the phosphate removal process. Further discussion about the reuse of polyP with different chain lengths is provided herein so as to suggest possible application pathways for this biosynthetic product.

Candidatus Kaistella beijingensis sp. nov., Isolated from a Municipal Wastewater Treatment Plant, Is Involved in Sludge Foaming

Biological foaming (or biofoaming) is a frequently occurring problem in wastewater treatment plants (WWTPs) and is attributed to the overwhelming growth of filamentous bulking and foaming bacteria (BFB). Biological foaming has been intensively investigated, with BFB like Microthrix and Skermania having been identified from WWTPs and implicated in foaming. Nevertheless, studies are still needed to improve our understanding of the microbial diversity of WWTP biofoams and how microbial activities contribute to foaming. In this study, sludge foaming at the Qinghe WWTP of China was monitored, and sludge foams were investigated using culture-dependent and culture-independent microbiological methods. The foam microbiomes exhibited high abundances of Skermania, Mycobacterium, Flavobacteriales, and Kaistella. A previously unknown bacterium, Candidatus Kaistella beijingensis, was cultivated from foams, its genome was sequenced, and it was phenotypically characterized. Ca. K. beijingensis exhibits hydrophobic cell surfaces, produces extracellular polymeric substances (EPS), and metabolizes lipids. Ca. K. beijingensis abundances were proportional to EPS levels in foams. Several proteins encoded by the Ca. K. beijingensis genome were identified from EPS that was extracted from sludge foams. Ca. K. beijingensis populations accounted for 4 to 6% of the total bacterial populations in sludge foam samples within the Qinghe WWTP, although their abundances were higher in spring than in other seasons. Cooccurrence analysis indicated that Ca. K. beijingensis was not a core node among the WWTP community network, but its abundances were negatively correlated with those of the well-studied BFB Skermania piniformis among cross-season Qinghe WWTP communities. IMPORTANCE Biological foaming, also known as scumming, is a sludge separation problem that has become the subject of major concern for long-term stable activated sludge operation in decades. Biological foaming was considered induced by foaming bacteria. However, the occurrence and deterioration of foaming in many WWTPs are still not completely understood. Cultivation and characterization of the enriched bacteria in foaming are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the understanding of their relationships with foaming and performance of WWTPs.

Effect of phosphorus concentration and light/dark condition on phosphorus uptake and distribution with microalgae

In this study, the effects of P concentration and light/dark condition on the distribution of P in microalgae were tracked with Scenedesmus sp.393. Results showed that different culture conditions affected the accumulation capacity and transformation of P in intracellular polymeric substances (IPS), extracellular polymeric substances (EPS), and soluble microbial products (SMP). At low P concentration (0.70 mg P/L), inorganic phosphorus (IP) absorbed in EPS (19.40%) and organic phosphorus (OP) accumulated in IPS (70.98%) were mainly P forms in microalgae. High P concentration (>21.42 mg P/L) promoted the luxury uptake and accumulation of IP by IPS, and the conversion of IP to OP. However, the adsorption of IP by EPS was inhibited when exposed to high external P concentration. Continuous illumination promoted the microalgae growth, and dark condition stimulated the P accumulation in microalgae biomass. The results of this study could provide valuable information for P recovery with microalgae.

Biomedical Applications of Bacteria-Derived Polymers

Plastics have found widespread use in the fields of cosmetic, engineering, and medical sciences due to their wide-ranging mechanical and physical properties, as well as suitability in biomedical applications. However, in the light of the environmental cost of further upscaling current methods of synthesizing many plastics, work has recently focused on the manufacture of these polymers using biological methods (often bacterial fermentation), which brings with them the advantages of both low temperature synthesis and a reduced reliance on potentially toxic and non-eco-friendly compounds. This can be seen as a boon in the biomaterials industry, where there is a need for highly bespoke, biocompatible, processable polymers with unique biological properties, for the regeneration and replacement of a large number of tissue types, following disease. However, barriers still remain to the mass-production of some of these polymers, necessitating new research. This review attempts a critical analysis of the contemporary literature concerning the use of a number of bacteria-derived polymers in the context of biomedical applications, including the biosynthetic pathways and organisms involved, as well as the challenges surrounding their mass production. This review will also consider the unique properties of these bacteria-derived polymers, contributing to bioactivity, including antibacterial properties, oxygen permittivity, and properties pertaining to cell adhesion, proliferation, and differentiation. Finally, the review will select notable examples in literature to indicate future directions, should the aforementioned barriers be addressed, as well as improvements to current bacterial fermentation methods that could help to address these barriers.

Biotechnology of Rhodococcus for the production of valuable compounds

Bacteria belonging to Rhodococcus genus represent ideal candidates for microbial biotechnology applications because of their metabolic versatility, ability to degrade a wide range of organic compounds, and resistance to various stress conditions, such as metal toxicity, desiccation, and high concentration of organic solvents. Rhodococcus spp. strains have also peculiar biosynthetic activities that contribute to their strong persistence in harsh and contaminated environments and provide them a competitive advantage over other microorganisms. This review is focused on the metabolic features of Rhodococcus genus and their potential use in biotechnology strategies for the production of compounds with environmental, industrial, and medical relevance such as biosurfactants, bioflocculants, carotenoids, triacylglycerols, polyhydroxyalkanoate, siderophores, antimicrobials, and metal-based nanostructures. These biosynthetic capacities can also be exploited to obtain high value-added products from low-cost substrates (industrial wastes and contaminants), offering the possibility to efficiently recover valuable resources and providing possible waste disposal solutions. Rhodococcus spp. strains have also recently been pointed out as a source of novel bioactive molecules highlighting the need to extend the knowledge on biosynthetic capacities of members of this genus and their potential utilization in the framework of bioeconomy. KEY POINTS: • Rhodococcus possesses promising biosynthetic and bioconversion capacities. • Rhodococcus bioconversion capacities can provide waste disposal solutions. • Rhodococcus bioproducts have environmental, industrial, and medical relevance. Graphical abstract.

Bacterial biopolymers: from pathogenesis to advanced materials

Bacteria are prime cell factories that can efficiently convert carbon and nitrogen sources into a large diversity of intracellular and extracellular biopolymers, such as polysaccharides, polyamides, polyesters, polyphosphates, extracellular DNA and proteinaceous components. Bacterial polymers have important roles in pathogenicity, and their varied chemical and material properties make them suitable for medical and industrial applications. The same biopolymers when produced by pathogenic bacteria function as major virulence factors, whereas when they are produced by non-pathogenic bacteria, they become food ingredients or biomaterials. Interdisciplinary research has shed light on the molecular mechanisms of bacterial polymer synthesis, identified new targets for antibacterial drugs and informed synthetic biology approaches to design and manufacture innovative materials. This Review summarizes the role of bacterial polymers in pathogenesis, their synthesis and their material properties as well as approaches to design cell factories for production of tailor-made bio-based materials suitable for high-value applications.

Bioaccumulations and potential human health risks assessment of heavy metals in ppk-expressing transgenic rice

In order to reduce the phosphorus (P) resource consume, the polyphosphatekinase (ppk)-expressing transgenic rice (ETR) with high utilization efficiency of P fertilizer had been constructed. However, synthesis polyphosphates (polyP) mediated byppkin the plants have the ability of chelating heavy metals, so the potential hazards of the new elite rice variety have raised concerns. In the study, we planted ETR and wild-type Nipponbare (WT) in paddy fields in southern China. After harvest, the concentrations of eight heavy metals in rice tissues were measured, and health risks assessments were performed. The field experiment showed that the ppkexpressions were detected in the roots and straws of ETR plants but did not increase the concentrations of As, Cd, Cr, Ni and Pb in rice tissues. The Hg concentration in the ETRD root was 1.70-fold higher than that in WT, but the abundant Hg bioaccumulation in ETRD only occurred in the root. The bioaccumulation factors (BAFs) of all the detected heavy metals in the ETRS were no different from WT except for Cu and Zn. The results of human health risks assessment of heavy metals in brown rice showed that the non-carcinogenic risks of Cu or Zn in ETRD were higher than that in WT, while there was no difference in the total noncarcinogenic risk of the eight heavy metals in ETR. The carcinogenic risks of heavy metals in ETR were also comparable to that in WT. The results of this study indicated that the ppk expression in rice did not increase human health risks of heavy metals by consuming brown rice, which would provide a safety guarantee for agricultural and environmental applications of ETR not only with single-copy line but also with double-copy line.

Effect of Varying Nitrate Concentrations on Denitrifying Phosphorus Uptake by DPAOs With a Molecular Insight Into Pho Regulon Gene Expression

Bacterial Pho regulon is a key regulator component in biological phosphorus-uptake. Poly-phosphate accumulating bacteria used in enhanced biological phosphorus removal (EBPR) system encounter negative regulation of the Pho regulon, resulting in reduced phosphorus-uptake from phosphorus-replete waste effluents. This study demonstrates possible trends of overcoming the PhoU negative regulation, resulting in excessive PO4 3--P uptake at varying concentrations of NO3 --N through denitrifying phosphorus removal process. We investigated the Pho regulon gene expression pattern and kinetic studies of P-removal by denitrifying phosphate accumulating organisms (DPAOs) which are able to remove both PO4 3--P and NO3 --N in single anoxic stage with the utilization of external carbon sources, without the use of stored polyhydroxyalkanoate (PHA) and without any anaerobic-aerobic or anaerobic-anoxic switches. Our study establishes that a minimum addition of 100 ppm NO3 --N leads to the withdrawal of the negative regulation of Pho regulon and results in ∼100% P-removal with concomitant escalated poly-phosphate accumulation by our established DPAO isolates and their artificially made consortium, isolated from sludge sample of PO4 3- -rich parboiled rice mill effluent, in a settling tank within 12 h of treatment. The same results were obtained when a phosphate rich effluent (stillage from distillery) mixed with a nitrate rich effluent (from explosive industry) was treated together in a single phase anoxic batch reactor, eliminating the need for alternating anaerobic/aerobic or anaerobic/anoxic switches for removing both the pollutants simultaneously. The highest poly-phosphate accumulation was observed to be more than 17% of cell dry weight. Our studies unequivocally establish that nitrate induction of Pho regulon is parallely associated with the repression of PhoU gene transcription, which is the negative regulator of Pho regulon. Based on earlier observations where similar nitrate mediated transcriptional repression was cited, we hypothesize the possible involvement of NarL/NarP transcriptional regulator proteins in PhoU repression. At present, we propose this denitrifying phosphorus removal endeavor as an innovative methodology to overcome the negative regulation of Pho regulon for accelerated unhindered phosphorus remediation from phosphate rich wastewater in India and the developing world where the stringency of EBPR and other reactors prevent their use due to financial reasons.

A Stringent Analysis of Polyphosphate Dynamics in Escherichia coli

During stress, bacterial cells activate a conserved pathway called the stringent response that promotes survival. Polyphosphates are long chains of inorganic phosphates that modulate this response in diverse bacterial species. In this issue, Michael J. Gray provides an important correction to the model of how polyphosphate accumulation is regulated during the stringent response in Escherichia coli (M. J. Gray, J. Bacteriol, 201:e00664-18, 2019, https://doi.org/10.1128/JB.00664-18). With other recent publications, this study provides a revised framework for understanding how bacterial polyphosphate dynamics might be exploited in infection control and industrial applications.

Mutations in Escherichia coli Polyphosphate Kinase That Lead to Dramatically Increased In Vivo Polyphosphate Levels

Bacteria synthesize inorganic polyphosphate (polyP) in response to a wide variety of stresses, and production of polyP is essential for stress response and survival in many important pathogens and bacteria used in biotechnological processes. However, surprisingly little is known about the molecular mechanisms that control polyP synthesis. We have therefore developed a novel genetic screen that specifically links growth of Escherichia coli to polyP synthesis, allowing us to isolate mutations leading to enhanced polyP production. Using this system, we have identified mutations in the polyP-synthesizing enzyme polyP kinase (PPK) that lead to dramatic increases in in vivo polyP synthesis but do not substantially affect the rate of polyP synthesis by PPK in vitro These mutations are distant from the PPK active site and found in interfaces between monomers of the PPK tetramer. We have also shown that high levels of polyP lead to intracellular magnesium starvation. Our results provide new insights into the control of bacterial polyP accumulation and suggest a simple, novel strategy for engineering bacteria with increased polyP contents.IMPORTANCE PolyP is an ancient, universally conserved biomolecule and is important for stress response, energy metabolism, and virulence in a remarkably broad range of microorganisms. PolyP accumulation by bacteria is also important in biotechnology applications. For example, it is critical to enhanced biological phosphate removal (EBPR) from wastewater. Understanding how bacteria control polyP synthesis is therefore of broad importance in both the fields of bacterial pathogenesis and biological engineering. Using Escherichia coli as a model organism, we have identified the first known mutations in polyP kinase that lead to increases in cellular polyP content.