Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean

Multifunctionality of alkaline phosphatase in ecology and biotechnology

Multifunctional enzymes can significantly impact biotechnological applications by performing activities beyond their primary functions. This review explores the role of the multifunctionality of alkaline phosphatase, a key enzyme in the phosphorus cycle, focusing on the molecular mechanisms influencing its activity and its biotechnological potential. We argue that understanding these aspects can enhance the utility of alkaline phosphatase in research and industry, fostering innovations in enzyme engineering, environmental biotechnology, and metabolic engineering. By exploring enzyme promiscuity, we highlight alkaline phosphatase's versatility, paving the way for advancements in sustainable agriculture, environmental remediation, and clinical diagnostics. Further research will unlock new applications and catalytic efficiencies, driving forward ecological and biotechnological progress.

Unveiling the P-solubilizing potential of bacteria enriched from natural colonies of Red Sea Trichodesmium spp

Phosphorus (P) is pivotal for all organisms, yet its availability is, particularly in the marine habitat, limited. Natural, puff-shaped colonies of Trichodesmium, a genus of diazotrophic cyanobacteria abundant in the Red Sea, have been demonstrated to capture and centre dust particles. While this particle mining strategy is considered to help evade nutrient limitation, details behind the mechanism remain elusive. This study explores P-solubilizing bacteria (PSB) residing within Trichodesmium's associated microbial community, their potential contribution to the host, and the possible implications for P cycling in marine ecosystems. Bacterial enrichment on YBCII medium resulted in 28 enrichment cultures, primarily comprising bacterial families such as Rhodobacteraceae, Alteromonadaceae and Burkholderiaceae. Five enrichment cultures were further grown on hydroxyapatite, revealing their ability to consume and release Nitrogen and P while forming strong physical interactions with the mineral. A drop in pH was observed, indicating acid production as the primary P-solubilizing pathway. Co-cultivation experiments confirmed a positive effect on Trichodesmium erythraeum strain IMS101 growth by the presence of putative PSBs. These results reveal that the enriched bacteria exhibit significant P-solubilizing activity, thus potentially increasing the bioavailability of P in seawater. Thus, PSB could play a vital role in maintaining the P balance in the Red Sea, supporting the growth of Trichodesmium spp. and other marine organisms. Overall, our results contribute to a deeper understanding of the P cycle in the Red Sea and have implications for developing novel strategies for P management in marine ecosystems.

Beyond Meta-Omics: Functional Genomics in Future Marine Microbiome Research

When President Bill Clinton and Francis Collins, then the director of the National Human Genome Research Institute, celebrated the near completion of the human genome sequence at the White House in the summer of 2000, it is unlikely that they or anyone else could have predicted the blossoming of meta-omics in the following two decades and their applications in modern human microbiome and environmental microbiome research. This transformation was enabled by the development of high-throughput sequencing technologies and sophisticated computational biology tools and bioinformatics software packages. Today, environmental meta-omics has undoubtedly revolutionized our understanding of ocean ecosystems, providing the genetic blueprint of oceanic microscopic organisms. In this review, I discuss the importance of functional genomics in future marine microbiome research and advocate a position for a gene-centric, bottom-up approach in modern oceanography. I propose that a synthesis of multidimensional approaches is required for a better understanding of the true functionality of the marine microbiome.

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.

In Silico Prediction of Alkaline Phosphatase Interaction with the Natural Inhibitory 5-Azaindoles Guitarrin C and D

The natural 5-azaindoles, marine sponge guitarrin C and D, were observed to exert inhibitory activity against a highly active alkaline phosphatase (ALP) CmAP of the PhoA family from the marine bacterium Cobetia amphilecti, with IC50 values of 8.5 and 110 µM, respectively. The superimposition of CmAP complexes with p-nitrophenyl phosphate (pNPP), a commonly used chromogenic aryl substrate for ALP, and the inhibitory guitarrins C, D, and the non-inhibitory guitarrins A, B, and E revealed that the presence of a carboxyl group at C6 together with a hydroxyl group at C8 is a prerequisite for the inhibitory effect of 5-azaindoles on ALP activity. The 10-fold more active guitarrin C could compete with pNPP for binding sites in the ALP active site due to similarities in size, three-dimensional structure, and the orientation of the COOH group along the phosphate group. However, the inhibition of CmAP and calf intestinal ALP (CIAP) by guitarrin C was observed to occur via a non-competitive mode of action, as evidenced by a twofold decrease in Vmax and an unchanged Km. In contrast, the kinetic model with guitarrin D, with an additional OH group at C7, reflected a mixed type of inhibition, with a decrease in both values. The sensitivity of CIAP to guitarrins C and D was shown to be slightly lower than that of CmAP, with IC50 values of 195 and 230 µM, respectively. Nevertheless, these findings prompted the prediction of complexes of human ALP isoenzymes with guitarrins C and D.

The microbial phosphorus cycle in aquatic ecosystems

Phosphorus is an essential element for life, and phosphorus cycling is crucial to planetary habitability. In aquatic environments, microorganisms are a major component of phosphorus cycling and rapidly transform the diverse chemical forms of phosphorus through various uptake, assimilation and release pathways. Recent discoveries have revealed a more dynamic and complex aquatic microbial phosphorus cycle than previously understood. Some microorganisms have been shown to use and produce new phosphorus compounds, including those in reduced forms. New findings have also raised numerous unanswered questions that warrant further investigation. There is an expanding influence of human activity on aquatic ecosystems. Advancements in understanding the phosphorus biogeochemistry of evolving aquatic environments offer a unique opportunity to comprehend, anticipate and mitigate the effect of human activities. In this Review, I discuss the wealth of new aquatic phosphorus cycle research, spanning disciplines from omics and physiology to global biogeochemical modelling, with a focus on the current comprehension of how aquatic microorganisms sense, transport, assimilate, store, produce and release phosphorus. Of note, I delve into cellular phosphorus allocation, an underexplored topic with wide-ranging implications for energy and element flux in aquatic ecosystems.

Peptide-Driven Assembly of Magnetic Beads for Potentiometric Sensing of Bacterial Enzyme at a Subcellular Level

Bacterial enzymes with different subcellular localizations play a critical ecological role in biogeochemical processing. However, precisely quantifying enzymes localized at certain subcellular levels, such as extracellular enzymes, has not yet been fully realized due to the complexity and dynamism of the bacterial outer membrane. Here we present a magneto-controlled potentiometric sensing platform for the specific detection of extracellular enzymatic activity. Alkaline phosphatase (ALP), which is one of the crucial hydrolytic enzymes in the ocean, was selected as the target enzyme. Magnetic beads functionalized with an ALP-responsive self-assembled peptide (GGGGGFFFpYpYEEE, MBs-peptides) prevent negatively charged peptides from entering the bacterial outer membrane, thereby enabling direct potentiometric sensing of extracellular ALP both attached to the bacterial cell surface and released into the surrounding environment. The dephosphorylation-triggered assembly of peptide-coupled magnetic beads can be directly and sensitively measured by using a magneto-controlled sensor. In this study, extracellular ALP activity of Pseudomonas aeruginosa at concentrations ranging from 10 to 1.0 × 105 CFU mL-1 was specifically and sensitively monitored. Moreover, this magneto-controlled potentiometric method enabled a simple and accurate assay of ALP activity across different subcellular localizations.

Dissolved organic phosphorus bond-class utilization by Synechococcus

Dissolved organic phosphorus (DOP) contains compounds with phosphoester, phosphoanhydride, and phosphorus-carbon bonds. While DOP holds significant nutritional value for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by Synechococcus strains from open and coastal oceans. Both strains exhibited comparable growth rates when provided phosphate, a phosphoanhydride [3-polyphosphate and 45-polyphosphate], or a DOP compound with both phosphoanhydride and phosphoester bonds (adenosine 5'-triphosphate). Growth rates on phosphoesters [glucose-6-phosphate, adenosine 5'-monophosphate, bis(4-methylumbelliferyl) phosphate] were variable, and neither strain grew on selected phosphorus-carbon compounds. Both strains hydrolyzed 3-polyphosphate, then adenosine 5'-triphosphate, and lastly adenosine 5'-monophosphate, exhibiting preferential enzymatic hydrolysis of phosphoanhydride bonds. The strains' exoproteomes contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of phosphoanhydride bonds by these exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity toward the phosphoanhydride 3-polyphosphate, with varying affinities between strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition and highlight varied growth and enzymatic responses to molecular diversity within DOP bond-classes, thereby expanding our understanding of microbially mediated DOP cycling in marine ecosystems.

Identification and characterization of a promiscuous metallohydrolase in metallo-β-lactamase superfamily from a locally isolated organophosphate-degrading Bacillus sp. strain S3wahi

In this present study, characteristics and structure-function relationship of an organophosphate-degrading enzyme from Bacillus sp. S3wahi were described. S3wahi metallohydrolase, designated as S3wahi-MH (probable metallohydrolase YqjP), featured the conserved αβ/βα metallo-β-lactamase-fold (MBL-fold) domain and a zinc bimetal at its catalytic site. The metal binding site of S3wahi-MH also preserves the H-X-H-X-D-H motif, consisting of specific amino acids at Zn1 (Asp69, His70, Asp182, and His230) and Zn2 (His65, His67, and His137). The multifunctionality of S3wahi-MH was demonstrated through a steady-state kinetic study, revealing its highest binding affinity (KM) and catalytic efficiency (kcat/KM) for OP compound, paraoxon, with values of 8.09 × 10-6 M and 4.94 × 105 M-1 s-1, respectively. Using OP compound, paraoxon, as S3wahi-MH native substrate, S3wahi-MH exhibited remarkable stability over a broad temperature range, 20 °C - 60 °C and a broad pH tolerance, pH 6-10. Corresponded to S3wahi-MH thermal stability characterization, the estimated melting temperature (Tm) was found to be 72.12 °C. S3wahi-MH was also characterized with optimum catalytic activity at 30 °C and pH 8. Additionally, the activity of purified S3wahi-MH was greatly enhanced in the presence of 1 mM and 5 mM of manganese (Mn2+), showing relative activities of 1323.68 % and 2073.68 %, respectively. The activity of S3wahi-MH was also enhanced in the presence of DMSO and DMF, showing relative activities of 270.37 % and 307.41 %, respectively. The purified S3wahi-MH retained >60 % residual activity after exposure to non-ionic Tween series surfactants. Nevertheless, the catalytic activity of S3wahi-MH was severely impacted by the treatment of SDS, even at low concentrations. Considering its enzymatic properties and promiscuity, S3wahi-MH emerges as a promising candidate as a bioremediation tool in wide industrial applications, including agriculture industry.

A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity. We demonstrate that Psip1 has undergone convergent evolution with PhoX, requiring both iron and calcium for activity and likely possessing identical key residues around the active site, despite generally very low sequence homology. Interrogation of metagenomes and transcriptomes from TARA oceans and an Atlantic Meridional transect shows that psip1 is abundant and highly expressed in picocyanobacterial populations from the Mediterranean Sea and north Atlantic gyre, regions well recognized to be phosphorus (P)-deplete. Together, this identifies psip1 as an important oligotrophy-specific gene for P recycling in these organisms. Furthermore, psip1 is not restricted to picocyanobacteria and is abundant and highly transcribed in some α-proteobacteria and eukaryotic algae, suggesting that such a high-affinity phosphatase is important across the microbial taxonomic world to occupy low-P environments.

Mechanism of organic phosphorus transformation and its impact on the primary production in a deep oligotrophic plateau lake during stratification

Global warming is leading to extended stratification in deep lakes, which may exacerbate phosphorus (P) limitation in the upper waters. Conversion of labile dissolved organic P (DOP) is a possible adaptive strategy to maintain primary production. To test this, the spatiotemporal distributions of various soluble P fractions and phosphomonesterase (PME)/phosphodiesterase (PDE) activities were investigated in Lake Fuxian during the stratification period and the transition capacity of organic P and its impact on primary productivity were evaluated. The results indicated that the DOP concentration (mean 0.20 ± 0.05 μmol L-1) was significantly higher than that of dissolved inorganic P (DIP) (mean 0.08 ± 0.03 μmol L-1) in the epilimnion and metalimnion, which were predominantly composed of orthophosphate monoester (monoester-P) and orthophosphate diesters (diester-P). The low ratio of diester-P / monoester-P and high activities of PME and PDE indicate DOP mineralization in the epilimnion and metalimnion. We detected a DIP threshold of approximately 0.19 μmol L-1, corresponding to the highest total PME activity in the lake. Meta-analysis further demonstrated that DIP thresholds of PME activities were prevalent in oligotrophic (0.19 μmol L-1) and mesotrophic (0.74 μmol L-1) inland waters. In contrast to the phosphate-sensitive phosphatase PME, dissolved PDE was expressed independent of phosphate availability and its activity invariably correlated with chlorophyll a, suggesting the involvement of phytoplankton in DOP utilization. This study provides important field evidence for the DOP transformation processes and the strategy for maintaining primary productivity in P-deficient scenarios, which contributes to the understanding of P cycles and the mechanisms of system adaptation to future long-term P limitations in stratified waters.

Enzymatic phosphatization of fish scales-a pathway for fish fossilization

Phosphatized fish fossils occur in various locations worldwide. Although these fossils have been intensively studied over the past decades they remain a matter of ongoing research. The mechanism of the permineralization reaction itself remains still debated in the community. The mineralization in apatite of a whole fish requires a substantial amount of phosphate which is scarce in seawater, so the origin of the excess is unknown. Previous research has shown that alkaline phosphatase, a ubiquitous enzyme, can increase the phosphate content in vitro in a medium to the degree of saturation concerning apatite. We applied this principle to an experimental setup where fish scales were exposed to commercial bovine alkaline phosphatase. We analyzed the samples with SEM and TEM and found that apatite crystals had formed on the remaining soft tissue. A comparison of these newly formed apatite crystals with fish fossils from the Solnhofen and Santana fossil deposits showed striking similarities. Both are made up of almost identically sized and shaped nano-apatites. This suggests a common formation process: the spontaneous precipitation from an oversaturated solution. The excess activity of alkaline phosphatase could explain that effect. Therefore, our findings could provide insight into the formation of well-preserved fossils.

Soil phosphorus transformation and plant uptake driven by phosphate-solubilizing microorganisms

Phosphorus (P) is an important nutrient for plants, and a lack of available P greatly limits plant growth and development. Phosphate-solubilizing microorganisms (PSMs) significantly enhance the ability of plants to absorb and utilize P, which is important for improving plant nutrient turnover and yield. This article summarizes and analyzes how PSMs promote the absorption and utilization of P nutrients by plants from four perspectives: the types and functions of PSMs, phosphate-solubilizing mechanisms, main functional genes, and the impact of complex inoculation of PSMs on plant P acquisition. This article reviews the physiological and molecular mechanisms of phosphorus solubilization and growth promotion by PSMs, with a focus on analyzing the impact of PSMs on soil microbial communities and its interaction with root exudates. In order to better understand the ability of PSMs and their role in soil P transformation and to provide prospects for research on PSMs promoting plant P absorption. PSMs mainly activate insoluble P through the secretion of organic acids, phosphatase production, and mycorrhizal symbiosis, mycorrhizal symbiosis indirectly activates P via carbon exchange. PSMs can secrete organic acids and produce phosphatase, which plays a crucial role in soil P cycling, and related genes are involved in regulating the P-solubilization ability. This article reviews the mechanisms by which microorganisms promote plant uptake of soil P, which is of great significance for a deeper understanding of PSM-mediated soil P cycling, plant P uptake and utilization, and for improving the efficiency of P utilization in agriculture.

New insights in bacterial organophosphorus cycling: From human pathogens to environmental bacteria

In terrestrial and aquatic ecosystems, phosphorus (P) availability controls primary production, with consequences for climate regulation and global food security. Understanding the microbial controls on the global P cycle is a prerequisite for minimising our reliance on non-renewable phosphate rock reserves and reducing pollution associated with excessive P fertiliser use. This recognised importance has reinvigorated research into microbial P cycling, which was pioneered over 75 years ago through the study of human pathogenic bacteria-host interactions. Immobilised organic P represents a significant fraction of the total P pool. Hence, microbes have evolved a plethora of mechanisms to transform this fraction into labile inorganic phosphate, the building block for numerous biological molecules. The 'genomics era' has revealed an extraordinary diversity of organic P cycling genes exist in the environment and studies going 'back to the lab' are determining how this diversity relates to function. Through this integrated approach, many hitherto unknown genes and proteins that are involved in microbial P cycling have been discovered. Not only do these fundamental discoveries push the frontier of our knowledge, but several examples also provide exciting opportunities for biotechnology and present possible solutions for improving the sustainability of how we grow our food, both locally and globally. In this review, we provide a comprehensive overview of bacterial organic P cycling, covering studies on human pathogens and how this knowledge is informing new discoveries in environmental microbiology.

Rapid analysis of dichlorvos via releasing the phosphate core

Monitoring the residual dichlorvos (O,O-dimethyl-O-2,2-dichlorovinylphosphate, DDVP) in food has received extensive attention owing to its large consumption in agriculture. However, the previous sensing methods are not time-efficient enough due to the long incubation time for enzyme inhibition (tens of minutes to hours) or bottlenecked by the complicated procedures for senor fabrication. Herein, a novel sensing strategy is proposed based on the hydrolysis of DDVP into PO43-. By using alkaline phosphatase for hydrolysis, a certain portion of DDVP was transformed to PO43- within only 8 min. Then, the released PO43- was detected by a fluorescent terbium metal-organic framework (Tb-MOF). The coordination of the naked P-O groups to the metal nodes of the Tb-MOF disturbed the antenna effects of its ligands. Thus, DDVP was quantified by the decrease of the fluorescence of Tb ions. Based on this method, DDVP residues on plum surfaces were collected by swabs and successfully detected. The recovery of DDVP was determined in the range from 105 % to 115 %, demonstrating the quantification accuracy of this method. The detection limit reached 4.7 μM, which was lower than the restricted amount in fruit set by the National Standard of China. The present method provides an efficient and user-friendly way for the detection of DDVP and many other organophosphorus pesticides in food.

Influence of Salinity on the Extracellular Enzymatic Activities of Marine Pelagic Fungi

Even though fungi are ubiquitous in the biosphere, the ecological knowledge of marine fungi remains rather rudimentary. Also, little is known about their tolerance to salinity and how it influences their activities. Extracellular enzymatic activities (EEAs) are widely used to determine heterotrophic microbes' enzymatic capabilities and substrate preferences. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). Due to their sensitivity and specificity, fluorogenic substrate analogues were used to determine hydrolytic activity on carbohydrates (β-glucosidase, β-xylosidase, and N-acetyl-β-D-glucosaminidase); peptides (leucine aminopeptidase and trypsin); lipids (lipase); organic phosphorus (alkaline phosphatase), and sulfur compounds (sulfatase). Afterwards, kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were calculated. All fungal species investigated cleaved these substrates, but some species were more efficient than others. Moreover, most enzymatic activities were reduced in the saline medium, with some exceptions like sulfatase. In non-saline conditions, the average Vmax ranged between 208.5 to 0.02 μmol/g biomass/h, and in saline conditions, 88.4 to 0.02 μmol/g biomass/h. The average Km ranged between 1553.2 and 0.02 μM with no clear influence of salinity. Taken together, our results highlight a potential tolerance of marine fungi to freshwater conditions and indicate that changes in salinity (due to freshwater input or evaporation) might impact their enzymatic activities spectrum and, therefore, their contribution to the oceanic elemental cycles.

Release of cell-free enzymes by marine pelagic fungal strains

Fungi are ubiquitous organisms that secrete different enzymes to cleave large molecules into smaller ones so that can then be assimilated. Recent studies suggest that fungi are also present in the oceanic water column harboring the enzymatic repertoire necessary to cleave carbohydrates and proteins. In marine prokaryotes, the cell-free fraction is an important contributor to the oceanic extracellular enzymatic activities (EEAs), but the release of cell-free enzymes by marine fungi remains unknown. Here, to study the cell-free enzymatic activities of marine fungi and the potential influence of salinity on them, five strains of marine fungi that belong to the most abundant pelagic phyla (Ascomycota and Basidiomycota), were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). The biomass was separated from the medium by filtration (0.2 μm), and the filtrate was used to perform fluorogenic enzymatic assays with substrate analogues of carbohydrates, lipids, organic phosphorus, sulfur moieties, and proteins. Kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were obtained. The species studied were able to release cell-free enzymes, and this represented up to 85.1% of the respective total EEA. However, this differed between species and enzymes, with some of the highest contributions being found in those with low total EEA, with some exceptions. This suggests that some of these contributions to the enzymatic pool might be minimal compared to those with higher total EEA. Generally, in the saline medium, the release of cell-free enzymes degrading carbohydrates was reduced compared to the non-saline medium, but those degrading lipids and sulfur moieties were increased. For the remaining substrates, there was not a clear influence of the salinity. Taken together, our results suggest that marine fungi are potential contributors to the oceanic dissolved (i.e., cell-free) enzymatic pool. Our results also suggest that, under salinity changes, a potential effect of global warming, the hydrolysis of organic matter by marine fungal cell-free enzymes might be affected and hence, their potential contribution to the oceanic biogeochemical cycles.

Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils

Grassland biomes provide valuable ecosystem services, including nutrient cycling. Organic phosphorus (Po) represents more than half of the total P in soils. Soil microorganisms release organic P through enzymatic processes, with alkaline phosphatases, acid phosphatases and phytases being the key P enzymes involved in the cycling of organic P. This study analysed 74 soil metagenomes from 17 different grassland biomes worldwide to evaluate the distribution and abundance of eight key P enzymes (PhoD, PhoX, PhoA, Nsap-A, Nsap-B, Nsap-C, BPP and CPhy) and their relationship with environmental factors. Our analyses showed that alkaline phosphatase phoD was the dataset's most abundant P-enzyme encoding genes, with a wide phylogenetic distribution. Followed by the acid phosphatases Nsap-A and Nsap-C showed similar abundance but a different distribution in their respective phylogenetic trees. Multivariate analyses revealed that pH, Tmax , SOC and soil moisture were associated with the abundance and diversity of all genes studied. PhoD and phoX genes strongly correlated with SOC and clay, and the phoX gene was more common in soils with low to medium SOC and neutral pH. In particular, P-enzyme genes tended to respond in a positively correlated manner among them, suggesting a complex relationship of abundance and diversity among them.

Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles

In marine systems, the availability of inorganic phosphate can limit primary production leading to bacterial and phytoplankton utilization of the plethora of organic forms available. Among these are phospholipids that form the lipid bilayer of all cells as well as released extracellular vesicles. However, information on phospholipid degradation is almost nonexistent despite their relevance for biogeochemical cycling. Here, we identify complete catabolic pathways for the degradation of the common phospholipid headgroups phosphocholine (PC) and phosphorylethanolamine (PE) in marine bacteria. Using Phaeobacter sp. MED193 as a model, we provide genetic and biochemical evidence that extracellular hydrolysis of phospholipids liberates the nitrogen-containing substrates ethanolamine and choline. Transporters for ethanolamine (EtoX) and choline (BetT) are ubiquitous and highly expressed in the global ocean throughout the water column, highlighting the importance of phospholipid and especially PE catabolism in situ. Thus, catabolic activation of the ethanolamine and choline degradation pathways, subsequent to phospholipid metabolism, specifically links, and hence unites, the phosphorus, nitrogen, and carbon cycles.

A dataset of global ocean alkaline phosphatase activity

Utilisation of dissolved organic phosphorus (DOP) by marine microbes as an alternative phosphorus (P) source when phosphate is scarce can help sustain non-Redfieldian carbon:nitrogen:phosphorus ratios and efficient ocean carbon export. However, global spatial patterns and rates of microbial DOP utilisation are poorly investigated. Alkaline phosphatase (AP) is an important enzyme group that facilitates the remineralisation of DOP to phosphate and thus its activity is a good proxy for DOP-utilisation, particularly in P-stressed regions. We present a Global Alkaline Phosphatase Activity Dataset (GAPAD) with 4083 measurements collected from 79 published manuscripts and one database. Measurements are organised into four groups based on substrate and further subdivided into seven size fractions based on filtration pore size. The dataset is globally distributed and covers major oceanic regions, with most measurements collected in the upper 20 m of low-latitude oceanic regions during summer since 1997. This dataset can help support future studies assessing global ocean P supply from DOP utilisation and provide a useful data reference for both field investigations and modelling activities.

Insights into the conversion of dissolved organic phosphorus favors algal bloom, arsenate biotransformation and microcystins release of Microcystis aeruginosa

Little information is available on influences of the conversion of dissolved organic phosphorus (DOP) to inorganic phosphorus (IP) on algal growth and subsequent behaviors of arsenate (As(V)) in Microcystis aeruginosa (M. aeruginosa). In this study, the influences factors on the conversion of three typical DOP types including adenosine-5-triphosphate disodium salt (ATP), β-glycerophosphate sodium (βP) and D-glucose-6-phosphate disodium salt (GP) were investigated under different extracellular polymeric secretions (EPS) ratios from M. aeruginosa, and As(V) levels. Thus, algal growth, As(V) biotransformation and microcystins (MCs) release of M. aeruginosa were explored in the different converted DOP conditions compared with IP. Results showed that the three DOP to IP without EPS addition became in favor of algal growth during their conversion. Compared with IP, M. aeruginosa growth was thus facilitated in the three converted DOP conditions, subsequently resulting in potential algal bloom particularly at arsenic (As) contaminated water environment. Additionally, DOP after conversion could inhibit As accumulation in M. aeruginosa, thus intracellular As accumulation was lower in the converted DOP conditions than that in IP condition. As(V) biotransformation and MCs release in M. aeruginosa was impacted by different converted DOP with their different types. Specifically, DMA concentrations in media and As(III) ratios in algal cells were promoted in converted βP condition, indicating that the observed dissolved organic compositions from βP conversion could enhance As(V) reduction in M. aeruginosa and then accelerate DMA release. The obtained findings can provide better understanding of cyanobacteria blooms and As biotransformation in different DOP as the main phosphorus source.

Utilization of diverse organophosphorus pollutants by marine bacteria

Anthropogenic organophosphorus compounds (AOPCs), such as phosphotriesters, are used extensively as plasticizers, flame retardants, nerve agents, and pesticides. To date, only a handful of soil bacteria bearing a phosphotriesterase (PTE), the key enzyme in the AOPC degradation pathway, have been identified. Therefore, the extent to which bacteria are capable of utilizing AOPCs as a phosphorus source, and how widespread this adaptation may be, remains unclear. Marine environments with phosphorus limitation and increasing levels of pollution by AOPCs may drive the emergence of PTE activity. Here, we report the utilization of diverse AOPCs by four model marine bacteria and 17 bacterial isolates from the Mediterranean Sea and the Red Sea. To unravel the details of AOPC utilization, two PTEs from marine bacteria were isolated and characterized, with one of the enzymes belonging to a protein family that, to our knowledge, has never before been associated with PTE activity. When expressed in Escherichia coli with a phosphodiesterase, a PTE isolated from a marine bacterium enabled growth on a pesticide analog as the sole phosphorus source. Utilization of AOPCs may provide bacteria a source of phosphorus in depleted environments and offers a prospect for the bioremediation of a pervasive class of anthropogenic pollutants.

Extracellular Enzymatic Activities of Oceanic Pelagic Fungal Strains and the Influence of Temperature

Although terrestrial and aquatic fungi are well-known decomposers of organic matter, the role of marine fungi remains largely unknown. Recent studies based on omics suggest that marine fungi potentially play a major role in elemental cycles. However, there is very limited information on the diversity of extracellular enzymatic activities performed by pelagic fungi in the ocean and how these might be affected by community composition and/or critical environmental parameters such as temperature. In order to obtain information on the potential metabolic activity of marine fungi, extracellular enzymatic activities (EEA) were investigated. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown at 5 °C and 20 °C, and fluorogenic enzymatic assays were performed using six substrate analogues for the hydrolysis of carbohydrates (β-glucosidase, β-xylosidase, and N-acetyl-β-D-glucosaminidase), amino acids (leucine aminopeptidase), and of organic phosphorus (alkaline phosphatase) and sulfur compounds (sulfatase). Remarkably, all fungal strains were capable of hydrolyzing all the offered substrates. However, the hydrolysis rate (Vmax) and half-saturation constant (Km) varied among the fungal strains depending on the enzyme type. Temperature had a strong impact on the EEAs, resulting in Q10 values of up to 6.1 and was species and substrate dependent. The observed impact of temperature on fungal EEA suggests that warming of the global ocean might alter the contribution of pelagic fungi in marine biogeochemical cycles.

A widely distributed phosphate-insensitive phosphatase presents a route for rapid organophosphorus remineralization in the biosphere

At several locations across the globe, terrestrial and marine primary production, which underpin global food security, biodiversity, and climate regulation, are limited by inorganic phosphate availability. A major fraction of the total phosphorus pool exists in organic form, requiring mineralization to phosphate by enzymes known as phosphatases prior to incorporation into cellular biomolecules. Phosphatases are typically synthesized in response to phosphate depletion, assisting with phosphorus acquisition. Here, we reveal that a unique bacterial phosphatase, PafA, is widely distributed in the biosphere and has a distinct functional role in carbon acquisition, releasing phosphate as a by-product. PafA, therefore, represents an overlooked mechanism in the global phosphorus cycle and a hitherto cryptic route for the regeneration of bioavailable phosphorus in nature.

The regeneration of bioavailable phosphate from immobilized organophosphorus represents a key process in the global phosphorus cycle and is facilitated by enzymes known as phosphatases. Most bacteria possess at least one of three phosphatases with broad substrate specificity, known as PhoA, PhoX, and PhoD, whose activity is optimal under alkaline conditions. The production and activity of these phosphatases is repressed by phosphate availability. Therefore, they are only fully functional when bacteria experience phosphorus-limiting growth conditions. Here, we reveal a previously overlooked phosphate-insensitive phosphatase, PafA, prevalent in Bacteroidetes, which is highly abundant in nature and represents a major route for the regeneration of environmental phosphate. Using the enzyme from Flavobacterium johnsoniae, we show that PafA is highly active toward phosphomonoesters, is fully functional in the presence of excess phosphate, and is essential for growth on phosphorylated carbohydrates as a sole carbon source. These distinct properties of PafA may expand the metabolic niche of Bacteroidetes by enabling the utilization of abundant organophosphorus substrates as C and P sources, providing a competitive advantage when inhabiting zones of high microbial activity and nutrient demand. PafA, which is constitutively synthesized by soil and marine flavobacteria, rapidly remineralizes phosphomonoesters releasing bioavailable phosphate that can be acquired by neighboring cells. The pafA gene is highly diverse in plant rhizospheres and is abundant in the global ocean, where it is expressed independently of phosphate availability. PafA therefore represents an important enzyme in the context of global biogeochemical cycling and has potential applications in sustainable agriculture.

Dissolved organic phosphorus utilization by the marine bacterium Ruegeria pomeroyi DSS-3 reveals chain length-dependent polyphosphate degradation

Dissolved organic phosphorus (DOP) is a critical nutritional resource for marine microbial communities. However, the relative bioavailability of different types of DOP, such as phosphomonoesters (P‐O‐C) and phosphoanhydrides (P‐O‐P), is poorly understood. Here we assess the utilization of these P sources by a representative bacterial copiotroph, Ruegeria pomeroyi DSS‐3. All DOP sources supported equivalent growth by R. pomeroyi, and all DOP hydrolysis rates were upregulated under phosphorus depletion (−P). A long‐chain polyphosphate (45polyP) showed the lowest hydrolysis rate of all DOP substrates tested, including tripolyphosphate (3polyP). Yet the upregulation of 45polyP hydrolysis under −P was greater than any other substrate analyzed. Proteomics revealed three common P acquisition enzymes potentially involved in polyphosphate utilization, including two alkaline phosphatases, PhoD and PhoX, and one 5′‐nucleotidase (5′‐NT). Results from DOP substrate competition experiments show that these enzymes likely have broad substrate specificities, including chain length‐dependent reactivity toward polyphosphate. These results confirm that DOP, including polyP, are bioavailable nutritional P sources for R. pomeroyi, and possibly other marine heterotrophic bacteria. Furthermore, the chain‐length dependent mechanisms, rates and regulation of polyP hydrolysis suggest that these processes may influence the composition of DOP and the overall recycling of nutrients within marine dissolved organic matter.

Structural and biochemical basis of a marine bacterial glycoside hydrolase family 2 β-glycosidase with broad substrate specificity

Uronic acids are commonly found in marine polysaccharides and increase structural complexity sanand intrinsic recalcitrance to enzymatic attack. The glycoside hydrolase family 2 (GH2) include proteins that target sugar conjugates with hexuronates and are involved in the catabolism and cycling of marine polysaccharides. Here, we reported a novel GH2, AqGalA from a marine algae-associated Bacteroidetes with broad-substrate specificity. Biochemical analyses revealed that AqGalA exhibits hydrolyzing activities against β-galacturonide, β-glucuronide, and β-galactopyranoside via retaining mechanisms. We solved the AqGalA crystal structure in complex with galacturonic acid (GalA) and showed (via mutagenesis) that charge characteristics at uronate-binding subsites controlled substrate selectivity for uronide hydrolysis. Additionally, conformational flexibility of the AqGalA active site pocket was proposed as a key component for broad substrate enzyme selectivity. Our AqGalA structural and functional data augments the current understanding of substrate recognition of GH2 enzymes and provided key insights into the bacterial use of uronic acid containing polysaccharides. IMPORTANCE The decomposition of algal glycans driven by marine bacterial communities represents one of the largest heterotrophic transformation of organic matter fueling marine food webs and global carbon cycling. However, our knowledge of the carbohydrate cycling is limited due to structural complexity of marine polysaccharides and the complicated enzymatic machinery of marine microbes. To degrade algal glycan, marine bacteria such as members of Bacteroidetes produce a complex repertoire of carbohydrate-active enzymes (CAZymes) matching the structural specificity of the different carbohydrates. In this study, we investigated an extracellular GH2 β-glycosidase, AqGalA from a marine Bacteroidetes to identify the key components responsible for glycuronides recognition and hydrolysis. The broad substrate specificity of AqGalA against glycosides with diverse stereochemical substitutions indicates its potential in processing complex marine polysaccharides. Our findings promote a better understanding of microbially-driven mechanisms of marine carbohydrate cycling.