A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions - Identifying knowledge gaps

Organophosphonates (OPs) are a unique group of natural and synthetic compounds, characterised by the presence of a stable, hard-to-cleave bond between the carbon and phosphorus atoms. OPs exhibit high resistance to abiotic degradation, excellent chelating properties and high biological activity. Despite the huge and increasing scale of OP production and use worldwide, little is known about their transportation and fate in the environment. Available data are dominated by information concerning the most recognised organophosphonate - the herbicide glyphosate - while other OPs have received little attention. In this paper, a comprehensive review of the current state of knowledge about natural and artificial OPs is presented (including glyphosate). Based on the available literature, a number of knowledge gaps have been identified that need to be filled in order to understand the environmental effects of these abundant compounds. Special attention has been given to GHG-related processes, with a particular focus on CH4. This stems from the recent discovery of OP-dependent CH4 production in aqueous environments under aerobic conditions. The process has changed the perception of the biogeochemical cycle of CH4, since it was previously thought that biological methane formation was only possible under anaerobic conditions. However, there is a lack of knowledge on whether OP-associated methane is also formed in soils. Moreover, it remains unclear whether anthropogenic OPs affect the CH4 cycle, a concern of significant importance in the context of the increasing rate of global warming. The literature examined in this review also calls for additional research into the date of OPs in waste and sewage and in their impact on environmental microbiomes.

Bacterial aerobic methane cycling by the marine sponge-associated microbiome

BACKGROUND

Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane-oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed.

RESULTS

Here, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methane synthesis occurring in fully oxygenated shallow-water habitats. Specifically, we suggest methane generation occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C₁-metabolic loop that involves both the sponge host and specific members of the associated microbial community.

CONCLUSION

Given the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge-hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methane production and consumption, sponges may serve as marine sources or sinks of this potent greenhouse gas. Video Abstract.

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.

Microplastic accelerate the phosphorus-related metabolism of bacteria to promote the decomposition of methylphosphonate to methane

Microplastic (MP) contaminants in marine water have become a global public health concern because of their persistence and potentially adverse effects on organisms. MP can affect the growth and metabolism of marine microorganisms and further impact the microbial environmental functions. The molecular impact mechanisms of MP on specific functional microbes with the capability of decomposing methylphosphonate (MPn) to release methane (CH₄) in oxygenated water have rarely been reported upon. Herein, we investigated the effects of MP on microbes and concomitant methanogenesis via the microbial degradation of MPn. Furthermore, the specific perturbation was revealed at the molecular level combined with transcriptomics and metabolomics. The results showed that intracellular phosphorus utilization by MPn-degrading strain Burkholderia sp. HQL1813 was enhanced by accelerating the catabolism of MPn. Phosphorus transport-related genes (phnG-M, pstSCAB, phnCDE) were upregulated in the MP exposure groups. Amino acid metabolism, the phosphotransferase system and nucleotide metabolism were also perturbed after MP exposure. Notably, released CH₄ increased by 24 %, 29 % and 14 % in the exposure group. In addition, the responses of the strain were dose-independent with increasing MP doses. These findings are beneficial for clarifying the effect of MP on specific functional microbes at the molecular level and their degradation of CH₄ by MPn.

Phosphate oxygen isotope evidence for methylphosphonate sources of methane and dissolved inorganic phosphate

The ocean is an important source of methane, however, the sources of oceanic methane and mechanisms of its release to the atmosphere have only recently begun to be understood. Recent studies have identified methylphosphonate (MPn) as a previously unknown and likely source of methane in the aerobic ocean (Karl et al., 2008), as well as shown the biosynthesis of methylphosphonic acid to be a widespread trait in marine microbes (Metcalf et al., 2012). The mechanisms and reaction pathways from MPn to free methane, however, have not been well studied. Here we present results of laboratory studies on the photo-degradation of MPn, a likely mechanism of methane release to the atmosphere and phosphate release to the surface oceans. Phosphonoacetic acid was also studied as an additional model compound for comparison. We used the multi-labeled water isotope probing (MLWIP) approach, involving ¹⁸O-labeled waters to probe the photolytic mechanism of CP bond cleavage in phosphates through analysis of P released from MPn as PO₄. These studies identified distinct reaction pathways involving phosphates compared with other common organophosphorus compounds (e.g., phosphoesters), as well as suggest the involvement of both ambient water and atmospheric oxygen in CP bond cleavage. There is only a small amount of water oxygen incorporated into product PO₄ after cleavage of the CP bond in MPn, suggesting atmospheric O₂ or radicals formed from O₂ under Ultra Violet Radiation (UVR), as the primary source of O that replaces C in the CP bond of MPn. Model calculations suggest that the δ¹⁸O_P signature of phosphate released via UV-degradation of phosphates is largely (75%) inherited from the original phosphate substrate. This opens up the possibility of tracing and differentiating specific phosphate sources of dissolved phosphate from other organophosphorus (Porg) sources (e.g., phosphoesters) used in primary production, as well as for tracing specific MPn sources of atmospheric methane.

Organophosphonates utilization by soil strains of Ochrobactrum anthropi and Achromobacter sp

Four bacterial strains from glyphosate- or alkylphosphonates-contaminated soils were tested for ability to utilize different organophosphonates. All studied strains readily utilized methylphosphonic acid and a number of other phosphonates, but differed in their ability to degrade glyphosate. Only strains Ochrobactrum anthropi GPK 3 and Achromobacter sp. Kg 16 utilized this compound after isolation from enrichment cultures with glyphosate. Achromobacter sp. MPK 7 from the same enrichment culture, similar to Achromobacter sp. MPS 12 from methylphosphonate-polluted source, required adaptation to growth on GP. Studied strains varied significantly in their growth parameters, efficiency of phosphonates degradation and characteristic products of this process, as well as in their energy metabolism. These differences give grounds to propose a possible model of interaction between these strains in microbial consortium in phosphonate-contaminated soils.

Chemical synthesis of RNA with site-specific methylphosphonate modifications

Methylphosphonate(mP)-modified RNA serves as valuable probe to evaluate biomolecular interactions between the nucleic acid backbone and binding partners, such as proteins or small molecules. Here, we describe an efficient workflow for the synthesis of RNA with a single mP modification in diastereomerically pure form. While the automated assembly of mP-modified RNA is straightforward, its deprotection under basic conditions is challenging; a carefully optimized step-by-step procedure is provided. In addition, we demonstrate purification and separation strategies for the R_P and S_P-configurated RNA diastereomers using a combination of anion-exchange and reversed-phase HPLC, and comment on troubleshooting if their separation appears difficult. Furthermore, we demonstrate the stereochemical assignment of short R_P and S_P mP-modified RNA diastereomers based on 2D ROESY NMR spectroscopy and we report on the impact of the mP modification on thermal and thermodynamic stabilities of RNA-DNA hybrid and RNA-RNA duplexes.

Chemical modifications of DNA for study of helicase mechanisms

Helicases are ubiquitous enzymes that are required for virtually all processes in DNA and RNA metabolism including replication, repair, recombination, transcription, and translation. The mechanisms for helicase-catalyzed unwinding of double-stranded DNA or remodeling of RNA have been the subject of intense investigation for more than two decades. The central function of these enzymes is to transduce the energy available from ATP binding and hydrolysis to alter the conformation of nucleic acids. Specific interactions between helicases and nucleic acids have been investigated by chemical approaches in which the nucleic acid substrate has been modified in order to provide specific insight into the enzymatic mechanism.