Rethinking the biotic and abiotic remineralization of complex phosphate molecules in soils and sediments

Photolysis triggers multiple microbial responses: New insights of phosphorus compensation for algal blooms

Photolysis and microbial degradation enabling the rapid mineralization of organic phosphorus constitute the crucial mechanism for phosphorus compensation during algal bloom outbreaks in shallow lakes. This study explored the key pathways of microbial degradation of algae-derived organic phosphorus (ADOP) exacerbated by photolysis through molecular biology techniques. The results showed that photolysis could exacerbate microbial degradation, and the effects on microbial degradation were multifaceted. The photolysis process changes the composition of dissolved organic matter (DOM) in the environment and generates DOM components required for microbial activity, among which the saturated compounds significantly promote the increase of microbial biomass. Differential analysis showed that the photolysis process mainly affected the distribution of bacteria and fungi. The saturated compounds and highly aromatic compounds accompanying the photolysis process stimulated the increase of the abundance of phosphorus-cycling functional bacteria and related functional genes. Simultaneously, photolysis also promoted the growth of extracellular reactive oxygen species (ROS)-producing bacteria, and enhanced biological metabolism by stimulating the significant upregulation and differentiation of multiple enzyme protein subunits in cells. In summary, various changes in microorganisms caused by photolysis enhanced their mineralization of ADOP. These results bring new insights into the mechanism of the persistence of algal blooms.

Quantitative Benchmarking of Catalytic Parameters for Enzyme-Mimetic Ribonucleotide Dephosphorylation by Iron Oxide Minerals

Iron oxides, which are documented phosphorus (P) sinks as adsorbents, have been shown to catalyze organic P dephosphorylation, implicating these minerals as catalytic traps in P cycling. However, quantitative evaluation of this abiotic catalysis is lacking. Here, we investigated the dephosphorylation kinetics of eight ribonucleotides, with different nucleobase structures and P stoichiometry, reacting with common iron oxides. X-ray absorption spectroscopy determined that 0-98% of mineral-bound P was recycled inorganic P (Pi). Matrix-assisted laser desorption/ionization with mass spectrometry demonstrated short-lived triphosphorylated and monophosphorylated ribonucleotides bound to goethite. Based on Michaelis-Menten type modeling of the kinetic evolution of both dissolved and mineral-bound Pi, maximal Pi production rates from triphosphorylated ribonucleotides reacted with goethite (1.9-16.1 μmol Pi h-1 ggoethite-1) were >5-fold higher than with hematite and ferrihydrite; monophosphorylated ribonucleotides generated only mineral-bound Pi at similar rates (0.0-12.9 μmol Pi h-1 gmineral-1) across minerals. No clear distinction was observed between purine-based and pyrimidine-based ribonucleotides. After normalization to mineral-dependent Pi binding capacity, resulting catalytic turnover rates implied surface chemistry-controlled reactivity. Ribonucleotide-mineral complexation mechanisms were identified with infrared spectroscopy and molecular modeling. We estimated iron oxide-catalyzed rates in soil (0.01-5.5 μmol Pi h-1 gsoil) comparable to reported soil phosphatase rates, highlighting both minerals and enzymes as relevant catalysts in P cycling.

Expression and Characterization of Alkaline Phosphatase from Cobetia amphilecti KMM 296 in Transiently Transformed Tobacco Leaves and Transgenic Calli

Alkaline phosphatase (ALP) of the PhoA family is an important enzyme in mammals, microalgae, and certain marine bacteria. It plays a crucial role in the dephosphorylation of lipopolysaccharides (LPS) and nucleotides, which overstimulate cell signaling pathways and cause tissue inflammation in animals and humans. Insufficient ALP activity and expression levels have been linked to various disorders. This study aims to produce recombinant ALP from the marine bacterium Cobetia amphilecti KMM 296 (CmAP) in transformed leaves and calli of Nicotiana tabacum and to elucidate the influence of the plant host on its physical and chemical properties. N. tabacum has proven to be versatile and is extensively used as a heterologous host in molecular farming. The alp gene encoding for CmAP was cloned into the binary vectors pEff and pHREAC and transformed into N. tabacum leaves through agroinfiltration and the leaf disc method for callus induction using Agrobacterium tumefaciens strain EHA105. Transformed plants were screened for recombinant CmAP (rCmAP) production by its enzymatic activity and protein electrophoresis, corresponding to 55 kDa of mature CmAP. A higher rCmAP activity (14.6 U/mg) was detected in a homogenate of leaves bearing the pEFF-CmAP construct, which was further purified 150-fold using metal affinity, followed by anion exchange chromatography. Enzymatic activity and stability were assessed at different temperatures (15-75 °C) and exposure times (≤1 h), with different buffers, pHs, divalent metal ions, and salt concentrations. The results show that rCmAP is relatively thermostable, retaining its activity at 15-45 °C for up to 1 h. Its activity is highest in Tris HCl (pH 9.0-11.0) at 35 °C for 40 min. rCmAP shows higher salt-tolerance and divalent metal-dependence than obtained in Escherichia coli. This can be further explored for cost-effective and massively scalable production of LPS-free CmAP for possible biomedical and agricultural applications.

Investigating the genomic and metabolic abilities of PGPR Pseudomonas fluorescens in promoting plant growth and fire blight management

Pseudomonas fluorescens is commonly found in diverse environments and is well known for its metabolic and antagonistic properties. Despite its remarkable attributes, its potential role in promoting plant growth remains unexplored. This study examines these traits across 14 strains residing in diverse rhizosphere environments through pangenome and comparative genome analysis, alongside molecular docking studies against Erwinia amylovora to combat fire blight. Whole genome analysis revealed circular chromosome (6.01-7.07 Mb) with GC content averaging 59.95-63.39%. Predicted genes included 16S rRNA and protein-coding genes ranging from 4435 to 6393 bp and 1527 to 1541 bp, respectively. Pangenome analysis unveiled an open pangenome, shedding light on genetic factors influencing plant growth promotion and biocontrol, including nitrogen fixation, phosphorus solubilization, siderophore production, stress tolerance, flagella biosynthesis, and induced systemic resistance. Furthermore, pyrrolnitrin, phenazine-1-carboxylic acid, pyoluteorin, lokisin, 2,4-diacetylpholoroglucinol and pseudomonic acid were identified. Molecular docking against key proteins of E. amylovora highlighted the high binding affinities of 2,4-diacetylphloroglucinol, pseudomonic acid, and lokisin. These findings underscore the multifaceted role of P. fluorescens in plant growth promotion and biocontrol, with key biomolecules showing promising applications in plant growth and defense against pathogens.

Unraveling iron oxides as abiotic catalysts of organic phosphorus recycling in soil and sediment matrices

In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus. Dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this reaction. Evidence of this abiotic catalysis has relied on monitoring products in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Reactions of various organic phosphorus compounds with the different minerals identified in the environmental samples reveal up to ten-fold greater catalytic reactivities with iron oxides than with silicate and aluminosilicate minerals. Importantly, accounting for inorganic phosphate both in solution and mineral-bound, the dephosphorylarion rates of iron oxides were within reported enzymatic rates in soils. Our findings thus imply a missing abiotic axiom for organic phosphorus mineralization in phosphorus cycling.

Surface Passivation by Embedment of Polyphosphate Inhibits the Aragonite-to-Calcite Thermodynamic Pump

We monitored the conversion of aragonite to calcite in water by comparing single and mixed polymorph suspensions. We demonstrate that the enhanced aragonite-to-calcite conversion in mixed polymorph suspensions is dramatically inhibited by adding polyphosphate (sodium hexametaphosphate). 13C and 31P solid-state magic angle spinning (MAS) NMR and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectra allow us to follow quantitatively these effects as imparted by the dissolution-recrystallization processes. 31P{13C} and 13C{31P} rotational echo double resonance (REDOR)NMR experiments reveal coprecipitated phosphate that is embedded only within the surfaces of both polymorphs during the initial dissolution and recrystallization processes, causing passivation that arrests phase conversion.

Selectivity in Enzymatic Phosphorus Recycling from Biopolymers: Isotope Effect, Reactivity Kinetics, and Molecular Docking with Fungal and Plant Phosphatases

Among ubiquitous phosphorus (P) reserves in environmental matrices are ribonucleic acid (RNA) and polyphosphate (polyP), which are, respectively, organic and inorganic P-containing biopolymers. Relevant to P recycling from these biopolymers, much remains unknown about the kinetics and mechanisms of different acid phosphatases (APs) secreted by plants and soil microorganisms. Here we investigated RNA and polyP dephosphorylation by two common APs, a plant purple AP (PAP) from sweet potato and a fungal phytase from Aspergillus niger. Trends of δ¹⁸O values in released orthophosphate during each enzyme-catalyzed reaction in ¹⁸O-water implied a different extent of reactivity. Subsequent enzyme kinetics experiments revealed that A. niger phytase had 10-fold higher maximum rate for polyP dephosphorylation than the sweet potato PAP, whereas the sweet potato PAP dephosphorylated RNA at a 6-fold faster rate than A. niger phytase. Both enzymes had up to 3 orders of magnitude lower reactivity for RNA than for polyP. We determined a combined phosphodiesterase-monoesterase mechanism for RNA and terminal phosphatase mechanism for polyP using high-resolution mass spectrometry and ³¹P nuclear magnetic resonance, respectively. Molecular modeling with eight plant and fungal AP structures predicted substrate binding interactions consistent with the relative reactivity kinetics. Our findings implied a hierarchy in enzymatic P recycling from P-polymers by phosphatases from different biological origins, thereby influencing the relatively longer residence time of RNA versus polyP in environmental matrices. This research further sheds light on engineering strategies to enhance enzymatic recycling of biopolymer-derived P, in addition to advancing environmental predictions of this P recycling by plants and microorganisms.

What are the inorganic nanozymes? Artificial or inorganic enzymes!

The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...