Cyanase-independent utilization of cyanate as a nitrogen source in ascomycete yeasts

Transcriptomic response of the picoalga Pelagomonas calceolata to nitrogen availability: new insights into cyanate lyase function

Cyanate (OCN-) is an organic nitrogen compound found in aquatic environments potentially involved in phytoplankton growth. Given the prevalence and activity of cyanate lyase genes in eukaryotic microalgae, cyanate has been suggested as an alternative source of nitrogen in the environment. However, the conditions under which cyanate lyase is expressed and the actual capacity of microalgae to assimilate cyanate remain largely underexplored. Here, we studied the nitrogen metabolism in the cosmopolitan open-ocean picoalga Pelagomonas calceolata (Pelagophyceae and Stramenopiles) in environmental metatranscriptomes and transcriptomes from culture experiments under different nitrogen sources and concentrations. We observed that cyanate lyase is upregulated in nitrate-poor oceanic regions, suggesting that cyanate is an important molecule contributing to the persistence of P. calceolata in oligotrophic environments. Non-axenic cultures of P. calceolata were capable of growing on various nitrogen sources, including nitrate, urea, and cyanate, but not ammonium. RNA sequencing of these cultures revealed that cyanate lyase was downregulated in the presence of cyanate, indicating that this gene is not involved in the catabolism of extracellular cyanate to ammonia. Based on environmental data sets and laboratory experiments, we propose that cyanate lyase is important in nitrate-poor environments to generate ammonia from cyanate produced by endogenous nitrogenous compound recycling rather than being used to metabolize imported extracellular cyanate as an alternative nitrogen source.IMPORTANCEVast oceanic regions are nutrient-poor, yet several microalgae thrive in these environments. While various acclimation strategies to these conditions have been discovered in a limited number of model microalgae, many important lineages remain understudied. Investigating nitrogen metabolism across different microalga lineages is crucial for understanding ecosystem functioning in low-nitrate areas, especially in the context of global ocean warming. This study describes the nitrogen metabolism of Pelagomonas calceolata, an abundant ochrophyte in temperate and tropical oceans. By utilizing both global scale in situ metatranscriptomes and laboratory-based transcriptomics, we uncover how P. calceolata adapts to low-nitrate conditions. Our findings reveal that P. calceolata can metabolize various nitrogenous compounds and relies on cyanate lyase to recycle endogenous nitrogen in low-nitrate conditions. This result paves the way for future investigations into the significance of cyanate metabolism within oceanic trophic webs.

Nitrogen recovery from low-value biogenic feedstocks via steam gasification to methylotrophic yeast biomass

Carbon and nitrogen are crucial elements for life and must be efficiently regenerated in a circular economy. Biomass streams at the end of their useful life, such as sewage sludge, are difficult to recycle even though they contain organic carbon and nitrogen components. Gasification is an emerging technology to utilize such challenging waste streams and produce syngas that can be further processed into, e.g., Fischer-Tropsch fuels, methane, or methanol. Here, the objective is to investigate if nitrogen can be recovered from product gas cleaning in a dual fluidized bed (DFB) after gasification of softwood pellets to form yeast biomass. Yeast biomass is a protein-rich product, which can be used for food and feed applications. An aqueous solution containing ammonium at a concentration of 66 mM was obtained and by adding other nutrients it enables the growth of the methylotrophic yeast Komagataella phaffii to form 6.2 g.L^-1 dry yeast biomass in 3 days. To further integrate the process, it is discussed how methanol can be obtained from syngas by chemical catalysis, which is used as a carbon source for the yeast culture. Furthermore, different gas compositions derived from the gasification of biogenic feedstocks including sewage sludge, bark, and chicken manure are evaluated for their ability to yield methanol and yeast biomass. The different feedstocks are compared based on their potential to yield methanol and ammonia, which are required for the generation of yeast biomass. It was found that the gasification of bark and chicken manure yields a balanced carbon and nitrogen source for the formation of yeast biomass. Overall, a novel integrated process concept based on renewable, biogenic feedstocks is proposed connecting gasification with methanol synthesis to enable the formation of protein-rich yeast biomass.

Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics

Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24-144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24-48 h (T1), 72-96 h (T2), and 120-144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products.

Synergistic metabolism of carbon and nitrogen: Cyanate drives nitrogen cycle to conserve nitrogen in composting system

In this study, HCO₃^- was used as a co-substrate for cyanate metabolism to investigate its effect on nitrogen cycle in composting. The results showed that the carbamate content in experimental group (T) with HCO₃^- added was higher than that in control group (CP) during cooling period. Actinobacteria and Proteobacteria were the dominant phyla for cyanate metabolism, and the process was mediated by cyanase gene (cynS). The cynS abundance was 16.6% higher in T than CP. In cooling period, the nitrification gene hao in T was 8.125% higher than CP. Denitrification genes narG, narH, nirK, norB, and nosZ were 25.64%, 35.33%, 45.93%, 36.62%, and 36.12% less than CP, respectively. The nitrogen fixation gene nifH in T was consistently higher than CP in the late composting period. Conclusively, cyanate metabolism drove the nitrogen cycle by promoting nitrification, nitrogen fixation, and inhibiting denitrification, which improved nitrogen retention and compost quality.

Comparative Proteomic Analysis of Rhizoctonia solani Isolates Identifies the Differentially Expressed Proteins with Roles in Virulence

Sheath blight of rice is a destructive disease that could be calamitous to rice cultivation. The significant objective of this study is to contemplate the proteomic analysis of the high virulent and less virulent isolate of Rhizoctonia solani using a quantitative LC-MS/MS-based proteomic approach to identify the differentially expressed proteins promoting higher virulence. Across several rice-growing regions in Odisha, Eastern India, 58 Rhizoctonia isolates were obtained. All the isolates varied in their pathogenicity. The isolate RS15 was found to be the most virulent and RS22 was identified as the least virulent. The PCR amplification confirmed that the RS15 and RS22 belonged to the Rhizoctonia subgroup of AG1-IA with a specific primer. The proteomic information generated has been deposited in the PRIDE database with PXD023430. The virulent isolate consisted of 48 differentially abundant proteins, out of which 27 proteins had higher abundance, while 21 proteins had lower abundance. The analyzed proteins acquired functionality in fungal development, sporulation, morphology, pathogenicity, detoxification, antifungal activity, essential metabolism and transcriptional activities, protein biosynthesis, glycolysis, phosphorylation and catalytic activities in fungi. A Quantitative Real-Time PCR (qRT-PCR) was used to validate changes in differentially expressed proteins at the mRNA level for selected genes. The abundances of proteins and transcripts were positively correlated. This study provides the role of the proteome in the pathogenicity of R. solani AG1-IA in rice and underpins the mechanism behind the pathogen’s virulence in causing sheath blight disease.

Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms

Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO₃ by the activity of nitrifying bacteria.

Bacterial non-specific nucleases of the phospholipase D superfamily and their biotechnological potential

Bacterial non-specific nucleases are ubiquitously distributed and involved in numerous intra- and extracellular processes. Although all nucleases share the basic chemistry for the hydrolysis of phosphodiester bonds in nucleic acid molecules, the catalysis comprises diverse modes of action, which offers great potential for versatile biotechnological applications. A major criterium for their differentiation is substrate specificity. Specific endonucleases are widely used as restriction enzymes in molecular biology approaches, whereas the main applications of non-specific nucleases (NSNs) are the removal of nucleic acids from crude extracts in industrial downstream processing and the prevention of cell clumping in microfabricated channels. In nature, the predominant role of NSNs is the acquisition of nutrient sources such as nucleotides and phosphates. The number of extensively characterized NSNs and available structures is limited. Moreover, their applicability is mostly challenged by the presence of metal chelators that impede the hydrolysis of nucleic acids in a metal ion-dependent manner. However, a few metal ion-independent NSNs that tolerate the presence of metal chelators have been characterized in recent years with none being commercially available to date. The classification and biotechnological potential of bacterial NSNs with a special focus on metal ion-independent nucleases are presented and discussed.Key Points • Bacterial phospholipases (PLD-family) exhibit nucleolytic activity. • Bacterial nucleases of the PLD-family are metal ion-independent. • NSNs can be used in downstream processing approaches.

Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area

Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.