Ecological Aerobic Ammonia and Methane Oxidation Involved Key Metal Compounds, Fe and Cu

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.

A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli

Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.

Iron and nitrogen regulate carbon transformation in a methanotroph-microalgae system

Nutrient supply is important for maintaining a methanotroph and microalgae (MOB-MG) system for biogas valorization. However, there is a lack of understanding regarding how key elements regulate the growth of a MOB-MG coculture. In this study, a MOB-MG coculture with high protein content (0.47 g/g biomass) was established from waste activated sludge using synthetic biogas. An increase in iron availability substantially stimulated the specific growth rate (from 0.18 to 0.62 day-1) and biogas conversion rate (from 26.81 to 106.57 mg-C L-1 day-1) of the coculture. Moreover, the protein content remained high (0.51 g/g biomass), and the total lipid content increased (from 0.09 to 0.14 g/g biomass). Nitrogen limitation apparently constrained the specific growth rate (from 0.64 to 0.28 day-1) and largely reduced the protein content (from 0.51 to 0.31 g/g biomass) of the coculture. Intriguingly, the lipid content remained unchanged after nitrogen was depleted. The eukaryotic community was consistently dominated by MG belonging to Chlorella, while the populations of MOB shifted from Methylococcus/Methylosinus to Methylocystis due to iron and nitrogen amendment. In addition, diverse non-methanotrophic heterotrophs were present in the community. Their presence neither compromised the performance of the coculture system nor affected the protein content of the biomass. However, these heterotrophs may contribute to high carbon conversion efficiency by utilizing the dissolved organic carbon released by MOB and MG. Overall, the findings highlight the vital roles of iron and nitrogen in achieving efficient conversion of biogas, fast growth of cells, and optimal biomass composition in a MOB-MG coculture system.

Untapped talents: insight into the ecological significance of methanotrophs and its prospects

The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.

Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift

Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.

Nitrification rate in dairy cattle urine patches can be inhibited by changing soil bioavailable Cu concentration

Ammonia oxidation to hydroxylamine is catalyzed by the ammonia monooxygenase enzyme and copper (Cu) is a key element for this process. We investigated the effect of soil bioavailable Cu changes induced through the application of Cu-complexing compounds on nitrification rate, ammonia-oxidizing bacteria (AOB) and archaea (AOA) amoA gene abundance, and mineral nitrogen (N) leaching in urine patches using the Manawatu Recent soil. Further, evaluated the combination of organic compound calcium lignosulphonate (LS) with a growth stimulant Gibberellic acid (GA). Treatments were applied in May 2021 as late-autumn treatments: control (no urine), urine-only at 600 kg N ha^-1, urine + dicyandiamide (DCD), urine + co-poly-acrylic-maleic acid (PA-MA), urine + LS, urine + split-application of LS (2LS), and urine + combination of GA plus LS (GA + LS). In addition, another four treatments were applied in July 2021 as mid-winter treatments: control, urine-only at 600 kg N ha^-1, urine + GA, and urine + GA + LS. Soil bioavailable Cu and mineral N leaching were examined during the experimental period. The AOB/AOA amoA genes were quantified using quantitative polymerase chain reaction. Changes in soil bioavailable Cu across treatments correlated with nitrification rate and AOB amoA abundance in late-autumn while the AOA amoA abundance did not change. The reduction in soil bioavailable Cu induced by the PA-MA and 2LS was linked to significant (P < 0.05) reduction in mineral N leaching of 16 and 30%, respectively, relative to the urine-only. The LS did not induce a significant effect on either bioavailable Cu or mineral N leaching relative to urine-only. The GA + LS reduced mineral N leaching by 10% relative to LS in late-autumn, however, there was no significant effect in mid-winter. This study demonstrated that reducing soil bioavailable Cu can be a potential strategy to reduce N leaching from urine patches.