The Evolution of Microbial Phosphonate Degradative Pathways

Effects of 17β-Estradiol Pollution on Microbial Communities and Methane Emissions in Aerobic Water Bodies

17β-Estradiol (E2) is a widely present trace pollutant in aquatic environments. However, its impact on microbial communities in aerobic lake waters, which are crucial for methane (CH4) production, remains unclear. This study conducted an E2 contamination experiment by constructing laboratory-simulated aerobic microecosystems. Using 16S rRNA high-throughput sequencing, the effects of E2 on bacterial and archaeal communities were systematically examined. Combined with gas chromatography, the patterns and mechanisms of E2's impact on CH4 emissions in aerobic aquatic systems were uncovered for the first time. Generally, E2 contamination increased the randomness of bacterial and archaeal community assemblies and weakened microbial interactions. Furthermore, changes occurred in the composition and ecological functions of bacterial and archaeal communities under E2 pollution. Specifically, two days after exposure to E2, the relative abundance of Proteobacteria in the low-concentration (L) and high-concentration (H) groups decreased by 6.99% and 4.01%, respectively, compared to the control group (C). Conversely, the relative abundance of Planctomycetota was 1.81% and 1.60% higher in the L and H groups, respectively. E2 contamination led to an increase in the relative abundance of the methanogenesis functional group and a decrease in that of the methanotrophy functional group. These changes led to an increase in CH4 emissions. This study comprehensively investigated the ecotoxicological effects of E2 pollution on microbial communities in aerobic water bodies and filled the knowledge gap regarding aerobic methane production under E2 contamination.

Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics

Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life's origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS; <1 µM) appeared around the same time or in the Mesoarchean depending on the reconstruction method. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising pathways and hypophosphite-oxidising pathways. CP-lyases are particularly abundant in dissolved phosphate concentrations below 0.1 µM. Our results thus indicate at least local regions of declining phosphate levels through the Archean, possibly linked to phosphate-scavenging Fe(III), which may have limited productivity. However, reduced phosphorus species did not become widely used until after the Paleoproterozoic Great Oxidation Event (2.3 Ga), possibly linked to expansion of the biosphere at that time.

Response of bacterial community structure to different phosphorus additions in a tobacco-growing soil

Introduction

Phosphorus (P), which plays a vital role in plant growth, is continually added to soil to maximize biomass production, leading to excessive P accumulation and water eutrophication.

Results

In this study, a pot experiment using a subtropical tobacco-growing soil fertilized with four P levels-no P, low P, medium P, and high P-was conducted and rhizosphere and bulk soils were analyzed.

Results

P addition significantly increased tobacco biomass production (except under low P input) and total soil P and available P content (P<0.05), whereas total nitrogen content decreased in the rhizosphere soils, although this was only significant with medium P application. P fertilization also significantly altered the bacterial communities of rhizosphere soils (P<0.05), but those of bulk soils were unchanged (P>0.05). Moreover, a significant difference was found between rhizosphere soils with low (LR) and high (HR) P inputs (P<0.05). Additionally, compared with rhizosphere soils with no P (CKR), Shannon diversity showed a declining trend, which was significant with LR and HR (P<0.05), whereas an increasing tendency was observed for Chao1 diversity except in LR (P>0.05). Functional prediction revealed that P application significantly decreased the total P and N metabolism of microorganisms in rhizosphere soils (P<0.05).

Discussion

Collectively, our results indicate that maintaining sustainable agricultural ecosystems under surplus P conditions requires more attention to be directed toward motivating the potential of soil functional microbes in P cycling, rather than just through continual P input.

Biodegradation of selected aminophosphonates by the bacterial isolate Ochrobactrum sp. BTU1

Aminophosphonates, like glyphosate (GS) or metal chelators such as ethylenediaminetetra(methylenephosphonic acid) (EDTMP), are released on a large scale worldwide. Here, we have characterized a bacterial strain capable of degrading synthetic aminophosphonates. The strain was isolated from LC/MS standard solution. Genome sequencing indicated that the strain belongs to the genus Ochrobactrum. Whole-genome classification using pyANI software to compute a pairwise ANI and other metrics between Brucella assemblies and Ochrobactrum contigs revealed that the bacterial strain is designated as Ochrobactrum sp. BTU1. Degradation batch tests with Ochrobactrum sp. BTU1 and the selected aminophosphonates GS, EDTMP, aminomethylphosphonic acid (AMPA), iminodi(methylene-phosphonic) (IDMP) and ethylaminobis(methylenephosphonic) acid (EABMP) showed that the strain can use all phosphonates as sole phosphorus source during phosphorus starvation. The highest growth rate was achieved with AMPA, while EDTMP and GS were least supportive for growth. Proteome analysis revealed that GS degradation is promoted by C-P lyase via the sarcosine pathway, i.e., initial cleavage at the C-P bond. We also identified C-P lyase to be responsible for degradation of EDTMP, EABMP, IDMP and AMPA. However, the identification of the metabolite ethylenediaminetri(methylenephosphonic acid) via LC/MS analysis in the test medium during EDTMP degradation indicates a different initial cleavage step as compared to GS. For EDTMP, it is evident that the initial cleavage occurs at the C-N bond. The detection of different key enzymes at regulated levels, form the bacterial proteoms during EDTMP exposure, further supports this finding. This study illustrates that widely used and structurally more complex aminophosphonates can be degraded by Ochrobactrum sp. BTU1 via the well-known degradation pathways but with different initial cleavage strategy compared to GS.

Aerobic methane production by phytoplankton as an important methane source of aquatic ecosystems: Reconsidering the global methane budget

Biological methane, a major source of global methane budget, is traditionally thought to be produced in anaerobic environments. However, the recent reports about methane supersaturation occurring in oxygenated water layer, termed as "methane paradox", have challenged this prevailing paradigm. Significantly, growing evidence has indicated that phytoplankton including prokaryotic cyanobacteria and eukaryotic algae are capable of generating methane under aerobic conditions. In this regard, a systematic review of aerobic methane production by phytoplankton is expected to arouse the public attention, contributing to the understanding of methane paradox. Here, we comprehensively summarize the widespread phenomena of methane supersaturation in oxic layers. The remarkable correlation relationships between methane concentration and several key indicators (depth, chlorophyll a level and organic sulfide concentration) indicate the significance of phytoplankton in in-situ methane accumulation. Subsequently, four mechanisms of aerobic methane production by phytoplankton are illustrated in detail, including photosynthesis-driven metabolism, reactive oxygen species (ROS)-driven demethylation of methyl donors, methanogenesis catalyzed by nitrogenase and demethylation of phosphonates catalyzed by CP lyase. The first two pathways occur in various phytoplankton, while the latter two have been specially discovered in cyanobacteria. Additionally, the effects of four crucial factors on aerobic methane production by phytoplankton are also discussed, including phytoplankton species, light, temperature and crucial nutrients. Finally, the measures to control global methane emissions from phytoplankton, the precise intracellular mechanisms of methane production and a more complete global methane budget model are definitely required in the future research on methane production by phytoplankton. This review would provide guidance for future studies of aerobic methane production by phytoplankton and emphasize the potential contribution of aquatic ecosystems to global methane budget.

On the potential roles of phosphorus in the early evolution of energy metabolism

Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.

Transformation mechanism of methylphosphonate to methane by Burkholderia sp: Insight from multi-labeled water isotope probing and transcriptomic

Methylphosphonate (MPn), has been identified as a likely source of methane in aerobic ocean and may be responsible for the "ocean methane paradox", that is oversaturation of dissolved methane in oxic sea waters. However, the mechanism underlying the cleavage of C-P bonds during microbial degradation is not well understood. Using multi-labeled water isotope probing (MLWIP) and transcriptome analysis, we investigated the phosphate oxygen isotope systematics and mechanisms of microbial-mediated degradation of MPn in this study. In the aerobic culture containing MPn as the only phosphorus source, there was a significant release of inorganic phosphate (149.4 μmol/L) and free methane (268.3 mg/L). The oxygen isotopic composition of inorganic phosphorus (δ¹⁸O_P) of accumulated released phosphate was 4.50‰, 23.96‰, and 40.88‰, respectively, in the corresponding ¹⁸O-labeled waters of -10.3‰, 9.9‰, and 30.6‰, and the slope obtained in plots of δ¹⁸O_P versus the oxygen isotopic composition of water (δ¹⁸O_W) was 0.89. Consequently, 89% of the oxygen atoms (Os) in phosphate (PO₄) were exchanged with ¹⁸O-labeled waters in the medium, while the rest were exchanged with intracellular metabolic water. It has been confirmed that the C-P bond cleavage of MPn occurs in the cell with both ambient and metabolic water participation. Moreover, phn gene clusters play significant roles to cleave the C-P bond of MPn for Burkholderia sp. HQL1813, in which phnJ, phnM and phnI genes are significantly up-regulated during MPn decomposition to methane. In conclusion, the aerobic biotransformation of MPn to free methane by Burkholderia sp. HQL1813 has been elucidated, providing new insights into the mechanism that bio-cleaves C-P bonds to produce methane aerobically in aqueous environments for representative phosphonates.

Insights into the microbial degradation and resistance mechanisms of glyphosate

Glyphosate, as one of the broad-spectrum herbicides for controlling annual and perennial weeds, is widely distributed in various environments and seriously threatens the safety of human beings and ecology. Glyphosate is currently degraded by abiotic and biotic methods, such as adsorption, photolysis, ozone oxidation, and microbial degradation. Of these, microbial degradation has become the most promising method to treat glyphosate because of its high efficiency and environmental protection. Microorganisms are capable of using glyphosate as a phosphorus, nitrogen, or carbon source and subsequently degrade glyphosate into harmless products by cleaving C-N and C-P bonds, in which enzymes and functional genes related to glyphosate degradation play an indispensable role. There have been many studies on the abiotic and biotic treatment technologies, microbial degradation pathways and intermediate products of glyphosate, but the related enzymes and functional genes involved in the glyphosate degradation pathways have not been further discussed. There is little information on the resistance mechanisms of bacteria and fungi to glyphosate, and previous investigations of resistance mechanisms have mainly focused on how bacteria resist glyphosate damage. Therefore, this review explores the microorganisms, enzymes and functional genes related to the microbial degradation of glyphosate and discusses the pathways of microbial degradation and the resistance mechanisms of microorganisms to glyphosate. This review is expected to provide reference for the application and improvement of the microbial degradation of glyphosate in microbial remediation.

Phosphorus Recycling, Biocontrol, and Growth Promotion Capabilities of Soil Bacterial Isolates from Mexican Oak Forests: An Alternative to Reduce the Use of Agrochemicals in Maize Cultivation

Six bacteria (Bacillus velezensis 13, Bacillus subtillis 42, Pseudomonas fluorescens E221, Pseudomonas Poae EE12, Rahnella sp. EM1, and Serratia sp. EM2) isolated from the soil and litter of Mexican oak forests were characterized by identifying their ability to acquire phosphorus from different sources, analyzed for their biocontrol capabilities against two different phytopathogenic fungi, and finally tested for their ability to stimulate the germination of maize seeds and promotion of maize seedling growth. The greatest capacity to biocontrol the mycelial growth of phytopathogenic fungi Botrytis cinerea and Fusarium oxysporum was found in B. velezensis 13 and B. subtillis 42. P. poae EE12 and P. fluorescens E221 significantly promoted germination and the length of the primary root in Zea mays. Rahnella sp. EM1 and Serratia sp. EM2 could produce indole compounds related to auxin synthesis and increased the fresh weight of the maize seedlings. Together, these isolates represent an alternative to reduce the use of agrochemicals in maize cultivation. In general, soil microorganisms from Mexican oak forests represent a source of genetic resources for the sustainable management and conservation of soils for agricultural use.

Comparative Metagenomics Highlight a Widespread Pathway Involved in Catabolism of Phosphonates in Marine and Terrestrial Serpentinizing Ecosystems

Serpentinizing hydrothermal systems result from water circulating into the subsurface and interacting with mantle-derived rocks notably near mid-ocean ridges or continental ophiolites. Serpentinization and associated reactions produce alkaline fluids enriched in molecular hydrogen, methane, and small organic molecules that are assumed to feed microbial inhabitants. In this study, we explored the relationships linking serpentinization to associated microbial communities by comparative metagenomics of serpentinite-hosted systems, basalt-hosted vents, and hot springs. The shallow Prony bay hydrothermal field (PBHF) microbiome appeared to be more related to those of ophiolitic sites than to the Lost City hydrothermal field (LCHF) microbiome, probably because of the meteoric origin of its fluid, like terrestrial alkaline springs. This study emphasized the ubiquitous importance of a set of genes involved in the catabolism of phosphonates and highly enriched in all serpentinizing sites compared to other ecosystems. Because most of the serpentinizing systems are depleted in inorganic phosphate, the abundance of genes involved in the carbon-phosphorus lyase pathway suggests that the phosphonates constitute a source of phosphorus in these ecosystems. Additionally, hydrocarbons such as methane, released upon phosphonate catabolism, may contribute to the overall budget of organic molecules in serpentinizing systems.

IMPORTANCE This first comparative metagenomic study of serpentinite-hosted environments provides an objective framework to understand the functioning of these peculiar ecosystems. We showed a taxonomic similarity between the PBHF and other terrestrial serpentinite-hosted ecosystems. At the same time, the LCHF microbial community was closer to deep basalt-hosted hydrothermal fields than continental ophiolites, despite the influence of serpentinization. This study revealed shared functional capabilities among serpentinite-hosted ecosystems in response to environmental stress, the metabolism of abundant dihydrogen, and the metabolism of phosphorus. Our results are consistent with the generalized view of serpentinite environments but provide deeper insight into the array of factors that may control microbial activities in these ecosystems. Moreover, we show that metabolism of phosphonate is widespread among alkaline serpentinizing systems and could play a crucial role in phosphorus and methane biogeochemical cycles. This study opens a new line of investigation of the metabolism of reduced phosphorus compounds in serpentinizing environments.

Microbiomes and glyphosate biodegradation in edaphic and aquatic environments: recent issues and trends

Glyphosate (N-(phosphonomethyl)glycine) has emerged as the top-selling herbicide worldwide because of its versatility in controlling annual and perennial weeds and the extensive use of glyphosate-resistant crops. Concerns related to the widespread use of glyphosate and its ubiquitous presence in the environment has led to a large number of studies and reviews, which examined the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid (AMPA) in the environment. Because the biological breakdown of glyphosate is most likely the main elimination process, the biodegradation of glyphosate has also been the object of abundant experimental work. Importantly, glyphosate biodegradation in aquatic and soil ecosystems is affected not only by the composition and the activity of microbial communities, but also by the physical environment. However, the interplay between microbiomes and glyphosate biodegradation in edaphic and aquatic environments has rarely been considered before. The proposed minireview aims at filling this gap. We summarize the most recent work exploring glyphosate biodegradation in natural aquatic biofilms, the biological, chemical and physical factors and processes playing on the adsorption, transport and biodegradation of glyphosate at different levels of soil organization and under different agricultural managements, and its impact on soil microbial communities.

Molecular mechanisms underlying glyphosate resistance in bacteria

Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.

Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries

Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.

Primer design to assess bacterial degradation of glyphosate and other phosphonates

Phosphonates are organic phosphorous (P) compounds frequently detected in the environment due to a very stable CP bond that render them relatively recalcitrant. Glyphosate [N-phosphonomethyl glycine] is the most widely used and best-known synthetic phosphonate, and one of the most concerning herbicides in the world today. Microbial degradation of glyphosate and organophosphonates in general, is the main dissipation mechanism operating in most environments. One microbial metabolic pathway in this process is the CP lyase pathway, entailing an enzymatic complex encoded by about 14 genes (the Phn operon). Our goal was to develop a quantitative polymerase chain reaction (qPCR) assay for a key enzyme, the CP lyase that breaks down the CP bond, via quantification of the codifying phnJ gene. The primers designed in this study fulfill the requirements for a successful qPCR assay, with high efficiency and sensitivity, as well as specific detection of the target sequence in a wide range of taxonomic groups. This is, to our knowledge, the first report of primers designed to target phnJ in both pure cultures and metagenomic DNA from different environmental sources. Direct quantification of phnJ may be a cost-effective proxy to determine glyphosate degradation potential in different matrixes.

Fresh Ideas Bloom in Gut Healthcare to Cross-Fertilize Lake Management

Harmful bacteria may be the most significant threat to human gut and lake ecosystem health, and they are often managed using similar tools, like poisoning with antibiotics or algicides. Out-of-the-box thinking in human microbiome engineering is leading to novel methods, like engineering bacteria to kill pathogens, "persuade" them not to produce toxins, or "mop up" their toxins. The bacterial agent can be given a competitive edge via an exclusive nutrient, and they can be engineered to commit suicide once their work is done. Viruses can kill pathogens with specific DNA sequences or knock out their antibiotic resistance genes using CRISPR technology. Some of these ideas may work for lakes. We critically review novel methods for managing harmful bacteria in the gut from the perspective of managing toxic cyanobacteria in lakes, and discuss practical aspects such as modifying bacteria using genetic engineering or directed evolution, mass culturing and controlling the agents. A key knowledge gap is in the ecology of strains, like toxigenic vs nontoxigenic Microcystis, including allelopathic and Black Queen interactions. Some of the "gut methods" may have future potential for lakes, but there presently is no substitute for established management approaches, including reducing N and P nutrient inputs, and mitigating climate change.

Suppression treatment differentially influences the microbial community and the occurrence of broad host range plasmids in the rhizosphere of the model cover crop Avena sativa L

Cover crop suppression with glyphosate-based herbicides (GBHs) represents a common agricultural practice. The objective of this study was to compare rhizospheric microbial communities of A. sativa plants treated with a GBH relative to the mechanical suppression (mowing) in order to assess their differences and the potential implications for soil processes. Samples were obtained at 4, 10, 17 and 26 days post-suppression. Soil catabolic profiling and DNA-based methods were applied. At 26 days, higher respiration responses and functional diversity indices (Shannon index and catabolic evenness) were observed under glyphosate suppression and a neat separation of catabolic profiles was detected in multivariate analysis. Sarcosine and Tween 20 showed the highest contribution to this separation. Metabarcoding revealed a non-significant effect of suppression method on either alpha-diversity metrics or beta-diversity. Conversely, differences were detected in the relative abundance of specific bacterial taxa. Mesorhizobium sequences were detected in higher relative abundance in glyphosate-treated plants at the end of the experiment while the opposite trend was observed for Gaiella. Quantitative PCR of amoA gene from ammonia-oxidizing archaea showed a lower abundance under GBH suppression again at 26 days, while ammonia-oxidizing bacteria remained lower at all sampling times. Broad host range plasmids IncP-1β and IncP-1ε were exclusively detected in the rhizosphere of glyphosate-treated plants at 10 days and at 26 days, respectively. Overall, our study demonstrates differential effects of suppression methods on the abundance of specific bacterial taxa, on the physiology and mobile genetic elements of microbial communities while no differences were detected in taxonomic diversity.

Comparative genomics of Bifidobacterium species isolated from marmosets and humans

The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.

Phosphate-limited ocean regions select for bacterial populations enriched in the carbon-phosphorus lyase pathway for phosphonate degradation

In tropical and subtropical oceanic surface waters phosphate scarcity can limit microbial productivity. However, these environments also have bioavailable forms of phosphorus incorporated into dissolved organic matter (DOM) that microbes with the necessary transport and hydrolysis metabolic pathways can access to supplement their phosphorus requirements. In this study we evaluated how the environment shapes the abundance and taxonomic distribution of the bacterial carbon–phosphorus (C–P) lyase pathway, an enzyme complex evolved to extract phosphate from phosphonates. Phosphonates are organophosphorus compounds characterized by a highly stable C–P bond and are enriched in marine DOM. Similar to other known bacterial adaptions to low phosphate environments, C–P lyase was found to become more prevalent as phosphate concentrations decreased. C–P lyase was particularly enriched in the Mediterranean Sea and North Atlantic Ocean, two regions that feature sustained periods of phosphate depletion. In these regions, C–P lyase was prevalent in several lineages of Alphaproteobacteria (Pelagibacter, SAR116, Roseobacter and Rhodospirillales), Gammaproteobacteria, and Actinobacteria. The global scope of this analysis supports previous studies that infer phosphonate catabolism via C–P lyase is an important adaptive strategy implemented by bacteria to alleviate phosphate limitation and expands the known geographic extent and taxonomic affiliation of this metabolic pathway in the ocean.

Integrated interrogation of causes of membrane fouling in a pilot-scale anoxic-oxic membrane bioreactor treating oil refinery wastewater

Studies on membrane fouling during treatment of oil refinery wastewater (ORW) via membrane bioreactor (MBR) are currently lacking, and associated fouling challenges are largely undocumented. Using advanced chemical and Illumina sequencing approach, we investigated the complex bio-physiochemical interactions responsible for foulant-membrane interactions during treatment of ORW. After nearly 2 months of the MBR operation, COD removal reached maximal of 97.15 ± 1.85%, while oil and grease removal was maintained at 96.6 ± 2.6%, during the treatment duration. Most of the less or non-biodegradable oil moieties (>0.5 μm) progressively accumulated on the membrane as the influent oil concentration increased. Presence of relatively higher unsaturated extracellular polymers (100.6 mg/g VSS) like fulvic acid and aromatic-like compounds at high volumetric loading (~18.7 kg COD/m³/d), enhanced the adsorption of chemical elements (Fe = 88.9, Al = 63.4, and Ce = 0.56 mg/g dry-sludge, respectively). Moreover, shift in microbial community structure to hydrocarbon-utilizing and metals-tolerating genera, as Comamonas and Rhodanobacter, respectively, uncovers major membrane colonizers in ORW treatment via MBR.

Genome analysis of two novel Pseudomonas strains exhibiting differential hypersensitivity reactions on tobacco seedlings reveals differences in nonflagellar T3SS organization and predicted effector proteins

Multilocus sequence analysis (MLSA) of two new biological control strains (S1E40 and S3E12) of Pseudomonas was performed to assess their taxonomic position relative to close lineages, and comparative genomics employed to investigate whether these strains differ in key genetic features involved in hypersensitivity responses (HRs). Strain S3E12, at high concentration, incites HRs on tobacco and corn plantlets while S1E40 does not. Phylogenies based on individual genes and 16S rRNA-gyrB-rpoB-rpoD concatenated sequence data show strains S1E40 and S3E12 clustering in distinct groups. Strain S3E12 consistently clustered with Pseudomonas marginalis, a bacterium causing soft rots on plant tissues. MLSA data suggest that strains S1E40 and S3E12 are novel genotypes. This is consistent with the data of genome-based DNA-DNA homology values that are below the proposed cutoff species boundary. Comparative genomics analysis of the two strains revealed major differences in the type III secretion systems (T3SS) as well as the predicted T3SS secreted effector proteins (T3Es). One nonflagellar (NF-T3SS) and two flagellar T3SSs (F-T3SS) clusters were identified in both strains. While F-T3SS clusters in both strains were relatively conserved, the NF-T3SS clusters differed in the number of core components present. The predicted T3Es also differed in the type and number of CDSs with both strains having unique predicted protease-related effectors. In addition, the T1SS organization of the S3E12 genome has protein-coding sequences (CDSs) encoding for key factors such as T1SS secreted agglutinin repeats-toxins (a group of cytolysins and cytotoxins), a membrane fusion protein (LapC), a T1SS ATPase of LssB family (LapB), and T1SS-associated transglutaminase-like cysteine proteinase (LapP). In contrast, strain S1E40 has all CDSs for the seven-gene operon (pelA-pelG) required for Pel biosynthesis but not S3E12, suggesting that biofilm formation in these strains is modulated differently. The data presented here provide an insight of the genome organization of these two phytobacterial strains.

Glyphosate Shapes a Dinoflagellate-Associated Bacterial Community While Supporting Algal Growth as Sole Phosphorus Source

Glyphosate is a widely used herbicide that can potentially be a phosphorus (P) source for phytoplankton and microbes when discharged into the coastal ocean. In contrast to bacteria, few eukaryotic phytoplankton species appear capable of directly utilizing glyphosate. In this study, we observed, after a long delay (>60 days), Prorocentrum donghaiense, a dinoflagellate known to cause major harmful algal blooms in the East China Sea, could grow in a medium with glyphosate as the sole P source; suggesting that P. donghaiense growth was through bacterial mediation. To understand how the bacteria community might respond to glyphosate, we analyzed the 16S rRNA genes of the microbial community present in P. donghaiense cultures when grown under lower (36 μM) and higher (360 μM) glyphosate concentrations. Based on both Sanger and Illumina high throughput sequencing, we obtained more than 55,323 good-quality sequences, which were classified into six phyla. As the concentration of glyphosate rose, our results showed a significant increase in the phyla Proteobacteria and Firmicutes and a decrease in the phylum Bacteroidetes. Further qPCR (Quantitative PCR) analysis showed higher abundances of two specific phylotypes in the higher-glyphosate P. donghaiense cultures when compared to the lower-glyphosate and no-glyphosate cultures. Correspondingly, qPCR displayed the same trend for the abundance of a gammaproteobacterial type of phnJ, a gene encoding Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase, which is responsible for phosphonate degradation. In addition, Tax4Fun analysis based on our 16S rRNA gene sequences results in higher predicted abundances of phosphonate metabolizing genes in glyphosate-treated cultures. This study demonstrates that glyphosate could selectively promote the growth of particular groups of bacteria within an algal culture and in glyphosate enriched coastal waters, this interaction may potentially further facilitate the growth of alga.

Full-scale evaluation of methane production under oxic conditions in a mesotrophic lake

Oxic lake surface waters are frequently oversaturated with methane (CH₄). The contribution to the global CH₄ cycle is significant, thus leading to an increasing number of studies and stimulating debates. Here we show, using a mass balance, on a temperate, mesotrophic lake, that ~90% of CH₄ emissions to the atmosphere is due to CH₄ produced within the oxic surface mixed layer (SML) during the stratified period, while the often observed CH₄ maximum at the thermocline represents only a physically driven accumulation. Negligible surface CH₄ oxidation suggests that the produced 110 ± 60 nmol CH₄ L^-1 d^-1 efficiently escapes to the atmosphere. Stable carbon isotope ratios indicate that CH₄ in the SML is distinct from sedimentary CH₄ production, suggesting alternative pathways and precursors. Our approach reveals CH₄ production in the epilimnion that is currently overlooked, and that research on possible mechanisms behind the methane paradox should additionally focus on the lake surface layer.

Phosphonate Biochemistry

Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.

Differential impact of Limnoperna fortunei-herbicide interaction between Roundup Max® and glyphosate on freshwater microscopic communities

Multiple anthropogenic stressors act simultaneously on the environment, with consequences different from those caused by single-stressor exposure. We investigated how the combination of the invasive mussel Limnoperna fortunei and a widely applied herbicide, Roundup Max®, affected freshwater microscopic communities and water quality. Further, we compared these results with those induced by the combination of the mussel and technical-grade glyphosate. We carried out a 34-day experiment in outdoor mesocosms, applying the following six treatments: 6 mg L(-1) of technical-grade glyphosate (G), the equivalent concentration of glyphosate in Roundup Max® (R), 100 mussels (M), the combination of mussels and herbicide either in the technical-grade or formulated form (MG and MR, respectively), and control (C). Herbicides significantly increased total phosphorus in water; R and MR showed greater initial total nitrogen and ammonium. R increased picoplankton abundance and caused an eightfold increase in phytoplankton, with high turbidity values; G had a lower effect on these variables. Herbicide-mussel combination induced an accelerated dissipation of glyphosate in water (MG 6.36 ± 0.83 mg G g DW(-1) day(-1) and MR 5.16 ± 1.26 mg G g DW(-1) day(-1)). A synergistic effect on ammonium was observed in MR but not in MG. MR and MG had an antagonistic effect on phytoplankton, which showed a drastic reduction due to grazing, as revealed by M. We provide evidence of differential effects of Roundup Max® and technical-grade glyphosate over water quality and microscopic communities, and in combination with mussels. However, in the combination of mussels and herbicides, mussels seem to play a leading role. In the presence of L. fortunei, the effects of higher nutrient availability provided by herbicides addition were counteracted by the filtration activity of mussels, which released nutrients, grazed on picoplankton and phytoplankton, and boosted the development of other primary producers, periphyton and metaphyton.

How To Live with Phosphorus Scarcity in Soil and Sediment: Lessons from Bacteria

Phosphorus (P) plays a fundamental role in the physiology and biochemistry of all living things. Recent evidence indicates that organisms in the oceans can break down and use P forms in different oxidation states (e.g., +5, +3, +1, and -3); however, information is lacking for organisms from soil and sediment. The Cuatro Ciénegas Basin (CCB), Mexico, is an oligotrophic ecosystem with acute P limitation, providing a great opportunity to assess the various strategies that bacteria from soil and sediment use to obtain P. We measured the activities in sediment and soil of different exoenzymes involved in P recycling and evaluated 1,163 bacterial isolates (mainly Bacillus spp.) for their ability to use six different P substrates. DNA turned out to be a preferred substrate, comparable to a more bioavailable P source, potassium phosphate. Phosphodiesterase activity, required for DNA degradation, was observed consistently in the sampled-soil and sediment communities. A capability to use phosphite (PO3 (3-)) and calcium phosphate was observed mainly in sediment isolates. Phosphonates were used at a lower frequency by both soil and sediment isolates, and phosphonatase activity was detected only in soil communities. Our results revealed that soil and sediment bacteria are able to break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Different strategies for P utilization were distributed between and within the different taxonomic lineages analyzed, suggesting a dynamic movement of P utilization traits among bacteria in microbial communities.

IMPORTANCE

Phosphorus (P) is an essential element for life found in molecules, such as DNA, cell walls, and in molecules for energy transfer, such as ATP. The Valley of Cuatro Ciénegas, Coahuila (Mexico), is a unique desert characterized by an extreme limitation of P and a great diversity of microbial life. How do bacteria in this valley manage to obtain P? We measured the availability of P and the enzymatic activity associated with P release in soil and sediment. Our results revealed that soil and sediment bacteria can break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Even genetically related bacterial isolates exhibited different preferences for molecules, such as DNA, calcium phosphate, phosphite, and phosphonates, as substrates to obtain P, evidencing a distribution of roles for P utilization and suggesting a dynamic movement of P utilization traits among bacteria in microbial communities.

Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone

Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and denitrification to nitrogen loss seems to vary in different OMZs. In the Arabian Sea, both processes were reported. Here, we performed a metagenomics study of the upper and core zone of the Arabian Sea OMZ, to provide a comprehensive overview of the genetic potential for nitrogen and methane cycling. We propose that aerobic ammonium oxidation is carried out by a diverse community of Thaumarchaeota in the upper zone of the OMZ, whereas a low diversity of Scalindua-like anammox bacteria contribute significantly to nitrogen loss in the core zone. Aerobic nitrite oxidation in the OMZ seems to be performed by Nitrospina spp. and a novel lineage of nitrite oxidizing organisms that is present in roughly equal abundance as Nitrospina. Dissimilatory nitrate reduction to ammonia (DNRA) can be carried out by yet unknown microorganisms harbouring a divergent nrfA gene. The metagenomes do not provide conclusive evidence for active methane cycling; however, a low abundance of novel alkane monooxygenase diversity was detected. Taken together, our approach confirmed the genomic potential for an active nitrogen cycle in the Arabian Sea and allowed detection of hitherto overlooked lineages of carbon and nitrogen cycle bacteria.

Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation

Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México), to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo) biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with MGEs. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding alkaline phosphatase that revealed that in addition to gene gain and loss, regulation adjustment of gene expression also has contributed to the intraspecific diversity of B. coahuilensis.

Bacterial Mobilization of Nutrients From Biochar-Amended Soils

Soil amendments with biochar to improve soil fertility and increase soil carbon stocks have received some high-level attention. Physical and chemical analyses of amended soils and biochars from various feedstocks are reported, alongside some evaluations of plant growth promotion capabilities. Fewer studies investigated the soil microbiota and their potential to increase cycling and mobilization of nutrients in biochar-amended soils. This review is discussing the latest findings in the bacterial contribution to cycling and mobilizing nitrogen, phosphorus, and sulfur in biochar-amended soils and potential contributions to plant growth promotion. Depending on feedstock, pyrolysis, soil type, and plant cover, changes in the bacterial community structure were observed for a majority of the studies using amplicon sequencing or genetic fingerprinting methods. Prokaryotic nitrification largely depends on the availability of ammonium and can vary considerably under soil biochar amendment. However, denitrification to di-nitrogen and in particular, nitrous oxide reductase activity is commonly enhanced, resulting in reduced nitrous oxide emissions. Likewise, bacterial fixation of di-nitrogen appears to be regularly enhanced. A paucity of studies suggests that bacterial mobilization of phosphorus and sulfur is enhanced as well. However, most studies only tested for extracellular sulfatase and phosphatase activity. Further research is needed to reveal details of the bacterial nutrient mobilizing capabilities and this is in particular the case for the mobilization of phosphorus and sulfur.

Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase

After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. This is in contrast to the general phosphorus compounds utilized and metabolized by microorganisms. Here phosphorus is found as phosphoric acid or phosphate ion, phosphoric acid esters, or phosphoric acid anhydrides. The latter compounds contain phosphorus that is bound only to oxygen. Hydrolytic, oxidative, and radical-based mechanisms for carbon-phosphorus bond cleavage have been described. This review deals with the radical-based mechanism employed by the carbon-phosphorus lyase of the carbon-phosphorus lyase pathway, which involves reactions for activation of phosphonate, carbon-phosphorus bond cleavage, and further chemical transformation before a useful phosphate ion is generated in a series of seven or eight enzyme-catalyzed reactions. The phn genes, encoding the enzymes for this pathway, are widespread among bacterial species. The processes are described with emphasis on glyphosate as a substrate. Additionally, the catabolism of glyphosate is intimately connected with that of aminomethylphosphonate, which is also treated in this review. Results of physiological and genetic analyses are combined with those of bioinformatics analyses.

Phosphate-independent utilization of phosphonoacetic acid as sole phosphorus source by a psychrophilic strain of Geomyces pannorum P15

A psychrophilic fungal strain of Geomyces pannorum P15 was screened for its ability to utilize a range of synthetic and natural organophosphonate compounds as the sole source of phosphorus, nitrogen, or carbon. Only phosphonoacetic acid served as a phosphorus source for microbial growth in phosphate-independent manner. Substrate metabolism did not lead to extracellular release of inorganic phosphate. No phosphonate metabolizing enzyme activity was detectable in cell-free extracts prepared from Geomyces biomass pregrown on 2 mmol/L phosphonoacetic acid.

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria

Aerobic degradation of methylphosphonate (MPn) by marine bacterioplankton has been hypothesized to contribute significantly to the ocean's methane supersaturation, yet little is known about MPn utilization by marine microbes. To identify the microbial taxa and metabolic functions associated with MPn-driven methane production we performed parallel metagenomic, metatranscriptomic, and functional screening of microcosm perturbation experiments using surface water collected in the North Pacific Subtropical Gyre. In nutrient amended microcosms containing MPn, a substrate-driven microbial succession occurred. Initially, the addition of glucose and nitrate resulted in a bloom of Vibrionales and a transcriptional profile dominated by glucose-specific PTS transport and polyhydroxyalkanoate biosynthesis. Transcripts associated with phosphorus (P) acquisition were also overrepresented and suggested that the addition of glucose and nitrate had driven the community to P depletion. At this point, a second community shift occurred characterized by the increase in C-P lyase containing microbes of the Vibrionales and Rhodobacterales orders. Transcripts associated with C-P lyase components were among the most highly expressed at the community level, and only C-P lyase clusters were recovered in a functional screen for MPn utilization, consistent with this pathway being responsible for the majority, if not all, of the methane accumulation we observed. Our results identify specific bacterioplankton taxa that can utilize MPn aerobically under conditions of P limitation using the C-P lyase pathway, and thereby elicit a significant increase in the dissolved methane concentration.

Transport and attenuation of dissolved glyphosate and AMPA in a stormwater wetland

Glyphosate is an herbicide used widely and increasingly since the early 1990s in production of many crops and in urban areas. However, knowledge on the transport of glyphosate and its degradation to aminomethylphosphonic acid (AMPA) in ecosystems receiving urban or agricultural runoff is lacking. Here we show that transport and attenuation of runoff-associated glyphosate and AMPA in a stormwater wetland differ and largely vary over time. Dissolved concentrations and loads of glyphosate and AMPA in a wetland receiving runoff from a vineyard catchment were assessed during three consecutive seasons of glyphosate use (March to June 2009, 2010 and 2011). The load removal of glyphosate and AMPA by the wetland gradually varied yearly from 75% to 99%. However, glyphosate and AMPA were not detected in the wetland sediment, which emphasises that sorption on the wetland vegetation, which increased over time, and biodegradation were prevailing attenuation processes. The relative load of AMPA as a percentage of total glyphosate increased in the wetland and ranged from 0% to 100%, which indicates the variability of glyphosate degradation via the AMPA pathway. Our results demonstrate that transport and degradation of glyphosate in stormwater wetlands can largely change over time, mainly depending on the characteristics of the runoff event and the wetland vegetation. We anticipate our results to be a starting point for considering degradation products of runoff-associated pesticides during their transfer in wetlands, in particular when using stormwater wetlands as a management practice targeting pesticide attenuation.

The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment

Phosphonates are compounds that contain the chemically stable carbon–phosphorus (C–P) bond. They are widely distributed amongst more primitive life forms including many marine invertebrates and constitute a significant component of the dissolved organic phosphorus reservoir in the oceans. Virtually all biogenic C–P compounds are synthesized by a pathway in which the key step is the intramolecular rearrangement of phosphoenolpyruvate to phosphonopyruvate. However C–P bond cleavage by degradative microorganisms is catalyzed by a number of enzymes – C–P lyases, C–P hydrolases, and others of as-yet-uncharacterized mechanism. Expression of some of the pathways of phosphonate catabolism is controlled by ambient levels of inorganic P (Pi) but for others it is Pi-independent. In this report we review the enzymology of C–P bond metabolism in bacteria, and also present the results of an in silico investigation of the distribution of the genes that encode the pathways responsible, in both bacterial genomes and in marine metagenomic libraries, and their likely modes of regulation. Interrogation of currently available whole-genome bacterial sequences indicates that some 10% contain genes encoding putative pathways of phosphonate biosynthesis while ∼40% encode one or more pathways of phosphonate catabolism. Analysis of metagenomic data from the global ocean survey suggests that some 10 and 30%, respectively, of bacterial genomes across the sites sampled encode these pathways. Catabolic routes involving phosphonoacetate hydrolase, C–P lyase(s), and an uncharacterized 2-aminoethylphosphonate degradative sequence were predominant, and it is likely that both substrate-inducible and Pi-repressible mechanisms are involved in their regulation. The data we present indicate the likely importance of phosphonate-P in global biogeochemical P cycling, and by extension its role in marine productivity and in carbon and nitrogen dynamics in the oceans.

Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway

PhnP is a phosphodiesterase that plays an important role within the bacterial carbon-phosphorus lyase (CP-lyase) pathway by recycling a "dead-end" intermediate, 5-phospho-α-d-ribosyl 1,2-cyclic phosphate, that is formed during organophosphonate catabolism. As a member of the metallo-β-lactamase superfamily, PhnP is most homologous in sequence and structure to tRNase Z phosphodiesterases. X-ray structural analysis of PhnP complexed with orthovanadate to 1.5 Å resolution revealed this inhibitor bound in a tetrahedral geometry by the two catalytic manganese ions and the putative general acid residue H200. Guided by this structure, we probed the contributions of first- and second-sphere active site residues to catalysis and metal ion binding by site-directed mutagenesis, kinetic analysis, and ICP-MS. Alteration of H200 to alanine resulted in a 6-33-fold decrease in k(cat)/K(M) with substituted methyl phenylphosphate diesters with leaving group pK(a) values ranging from 4 to 8.4. With bis(p-nitrophenyl)phosphate as a substrate, there was a 10-fold decrease in k(cat)/K(M), primarily the result of a large increase in K(M). Moreover, the nickel ion-activated H200A PhnP displayed a bell-shaped pH dependence for k(cat)/K(M) with pK(a) values (pK(a1) = 6.3; pK(a2) = 7.8) that were comparable to those of the wild-type enzyme (pK(a1) = 6.5; pK(a2) = 7.8). Such modest effects are counter to what is expected for a general acid catalyst and suggest an alternate role for H200 in this enzyme. A Brønsted analysis of the PhnP reaction with a series of substituted phenyl methyl phosphate esters yielded a linear correlation, a β(lg) of -1.06 ± 0.1, and a Leffler α value of 0.61, consistent with a synchronous transition state for phosphoryl transfer. On the basis of these data, we propose a mechanism for PhnP.

Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake

We present the draft genome of Halorhabdus tiamatea, the first member of the Archaea ever isolated from a deep-sea anoxic brine. Genome comparison with Halorhabdus utahensis revealed some striking differences, including a marked increase in genes associated with transmembrane transport and putative genes for a trehalose synthase and a lactate dehydrogenase.

Divergence of chemical function in the alkaline phosphatase superfamily: structure and mechanism of the P-C bond cleaving enzyme phosphonoacetate hydrolase

Phosphonates constitute a class of natural products that mimic the properties of the more common organophosphate ester metabolite yet are not readily degraded owing to the direct linkage of the phosphorus atom to the carbon atom. Phosphonate hydrolases have evolved to allow bacteria to utilize environmental phosphonates as a source of carbon and phosphorus. The work reported in this paper examines one such enzyme, phosphonoacetate hydrolase. By using a bioinformatic approach, we circumscribed the biological range of phosphonoacetate hydrolase to a select group of bacterial species from different classes of Proteobacteria. In addition, using gene context, we identified a novel 2-aminoethylphosphonate degradation pathway in which phosphonoacetate hydrolase is a participant. The X-ray structure of phosphonoformate-bound phosphonoacetate hydrolase was determined to reveal that this enzyme is most closely related to nucleotide pyrophosphatase/diesterase, a promiscuous two-zinc ion metalloenzyme of the alkaline phosphatase enzyme superfamily. The X-ray structure and metal ion specificity tests showed that phosphonoacetate hydrolase is also a two-zinc ion metalloenzyme. By using site-directed mutagenesis and (32)P-labeling strategies, the catalytic nucleophile was shown to be Thr64. A structure-guided, site-directed mutation-based inquiry of the catalytic contributions of active site residues identified Lys126 and Lys128 as the most likely candidates for stabilization of the aci-carboxylate dianion leaving group. A catalytic mechanism is proposed which combines Lys12/Lys128 leaving group stabilization with zinc ion activation of the Thr64 nucleophile and the substrate phosphoryl group.

Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses

Phosphonates (Pn), compounds with a direct C-P bond instead of the more common C-O-P ester bond, constitute a significant fraction of marine dissolved organic phosphorus and recent evidence suggests that they may be an alternative source of P for marine microorganisms. To further characterize the microorganisms and pathways involved in Pn utilization, we screened bacterioplankton genomic libraries for their ability to complement an Escherichia coli strain unable to use Pns as a P source. Using this approach we identified a phosphonatase pathway as well as a novel pair of genes that allowed utilization of 2-aminoethylphosphonate (2-AEPn) as the sole P source. These pathways are present in diverse bacteria common in marine plankton including representatives of Proteobacteria, Planctomycetes and Cyanobacteria. Analysis of metagenomic databases for Pn utilization genes revealed that they are widespread and abundant among marine bacteria, suggesting that Pn metabolism is likely to play an important role in P-depleted surface waters, as well as in the more P-rich deep-water column.

Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation

Carbon-phosphorus lyase is a multienzyme system encoded by the phn operon that enables bacteria to metabolize organophosphonates when the preferred nutrient, inorganic phosphate, is scarce. One of the enzymes encoded by this operon, PhnP, is predicted by sequence homology to be a metal-dependent hydrolase of the beta-lactamase superfamily. Screening with a wide array of hydrolytically sensitive substrates indicated that PhnP is an enzyme with phosphodiesterase activity, having the greatest specificity toward bis(p-nitrophenyl)phosphate and 2',3'-cyclic nucleotides. No activity was observed toward RNA. The metal ion dependence of PhnP with bis(p-nitrophenyl)phosphate as substrate revealed a distinct preference for Mn(2+) and Ni(2+) for catalysis, whereas Zn(2+) afforded poor activity. The three-dimensional structure of PhnP was solved by x-ray crystallography to 1.4 resolution. The overall fold of PhnP is very similar to that of the tRNase Z endonucleases but lacks the long exosite module used by these enzymes to bind their tRNA substrates. The active site of PhnP contains what are probably two Mn(2+) ions surrounded by an array of active site residues that are identical to those observed in the tRNase Z enzymes. A second, remote Zn(2+) binding site is also observed, composed of a set of cysteine and histidine residues that are strictly conserved in the PhnP family. This second metal ion site appears to stabilize a structural motif.

Emission of methane from plants

It has been proposed that plants are capable of producing methane by a novel and unidentified biochemical pathway. Emission of methane with an apparently biological origin was recorded from both whole plants and detached leaves. This was the first report of methanogenesis in an aerobic setting, and was estimated to account for 10-45 per cent of the global methane source. Here, we show that plants do not contain a known biochemical pathway to synthesize methane. However, under high UV stress conditions, there may be spontaneous breakdown of plant material, which releases methane. In addition, plants take up and transpire water containing dissolved methane, leading to the observation that methane is released. Together with a new analysis of global methane levels from satellite retrievals, we conclude that plants are not a major source of the global methane production.