Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes

Sulfur assimilation using gaseous carbonyl sulfide by the soil fungus Trichoderma harzianum

Fungi have the capacity to assimilate a diverse range of both inorganic and organic sulfur compounds. It has been recognized that all sulfur sources taken up by fungi are in soluble forms. In this study, we present evidence that fungi can utilize gaseous carbonyl sulfide (COS) for the assimilation of a sulfur compound. We found that the filamentous fungus Trichoderma harzianum strain THIF08, which has constitutively high COS-degrading activity, was able to grow with COS as the sole sulfur source. Cultivation with 34S-labeled COS revealed that sulfur atom from COS was incorporated into intracellular metabolites such as glutathione and ergothioneine. COS degradation by strain THIF08, in which as much of the moisture derived from the agar medium as possible was removed, indicated that gaseous COS was taken up directly into the cell. Escherichia coli transformed with a COS hydrolase (COSase) gene, which is clade D of the β-class carbonic anhydrase subfamily enzyme with high specificity for COS but low activity for CO2 hydration, showed that the COSase is involved in COS assimilation. Comparison of sulfur metabolites of strain THIF08 revealed a higher relative abundance of reduced sulfur compounds under the COS-supplemented condition than the sulfate-supplemented condition, suggesting that sulfur assimilation is more energetically efficient with COS than with sulfate because there is no redox change of sulfur. Phylogenetic analysis of the genes encoding COSase, which are distributed in a wide range of fungal taxa, suggests that the common ancestor of Ascomycota, Basidiomycota, and Mucoromycota acquired COSase at about 790-670 Ma.IMPORTANCEThe biological assimilation of gaseous CO2 and N2 involves essential processes known as carbon fixation and nitrogen fixation, respectively. In this study, we found that the fungus Trichoderma harzianum strain THIF08 can grow with gaseous carbonyl sulfide (COS), the most abundant and ubiquitous gaseous sulfur compound, as a sulfur source. When the fungus grew in these conditions, COS was assimilated into sulfur metabolites, and the key enzyme of this assimilation process is COS hydrolase (COSase), which specifically degrades COS. Moreover, the pathway was more energy efficient than the typical sulfate assimilation pathway. COSase genes are widely distributed in Ascomycota, Basidiomycota, and Mucoromycota and also occur in some Chytridiomycota, indicating that COS assimilation is widespread in fungi. Phylogenetic analysis of these genes revealed that the acquisition of COSase in filamentous fungi was estimated to have occurred at about 790-670 Ma, around the time that filamentous fungi transitioned to a terrestrial environment.

Root and rhizosphere contribution to the net soil COS exchange

Background and aims

Partitioning the measured net ecosystem carbon dioxide (CO2) exchange into gross primary productivity (GPP) and ecosystem respiration remains a challenge, which scientists try to tackle by using the properties of the trace gas carbonyl sulfide (COS). Its similar pathway into and within the leaf makes it a potential photosynthesis proxy. The application of COS as an effective proxy depends, among other things, on a robust inventory of potential COS sinks and sources within ecosystems. While the soil received some attention during the last couple of years, the role of plant roots is mostly unknown. In our study, we investigated the effects of live roots on the soil COS exchange.

Methods

An experimental setup was devised to measure the soil and the belowground plant parts of young beech trees observed over the course of 9 months.

Results

During the growing season, COS emissions were significantly lower when roots were present compared to chambers only containing soil, while prior to the growing season, with photosynthetically inactive trees, the presence of roots increased COS emissions. The difference in the COS flux between root-influenced and uninfluenced soil was fairly constant within each month, with diurnal variations in the COS flux driven primarily by soil temperature changes rather than the presence or absence of roots.

Conclusion

While the mechanisms by which roots influence the COS exchange are largely unknown, their contribution to the overall ground surface COS exchange should not be neglected when quantifying the soil COS exchange.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11104-023-06438-0.

Role of subterranean microbiota in the carbon cycle and greenhouse gas dynamics

Subterranean ecosystems play an active role in the global carbon cycle, yet only a few studies using indirect methods have focused on the role of the cave microbiota in this critical cycle. Here we present pioneering research based on in situ real-time monitoring of CO₂ and CH₄ diffusive fluxes and concurrent δ¹³C geochemical tracing in caves, combined with 16S microbiome analysis. Our findings show that cave sediments are promoting continuous CH₄ consumption from cave atmosphere, resulting in a significant removal of 65% to 90%. This research reveals the most effective taxa and metabolic pathways in consumption and uptake of greenhouse gases. Methanotrophic bacteria were the most effective group involved in CH₄ consumption, namely within the families Methylomonaceae, Methylomirabilaceae and Methylacidiphilaceae. In addition, Crossiella and Nitrosococcaceae wb1-P19 could be one of the main responsible of CO₂ uptake, which occurs via the Calvin-Benson-Bassham cycle and reversible hydration of CO₂. Thus, syntrophic relationships exist between Crossiella and nitrifying bacteria that capture CO₂, consume inorganic N produced by heterotrophic ammonification in the surface of sediments, and induce moonmilk formation. Moonmilk is found as the most evolved phase of the microbial processes in cave sediments that fixes CO₂ as calcite and intensifies CH₄ oxidation. From an ecological perspective, cave sediments act qualitatively as soils, providing fundamental ecosystem services (e.g. nutrient cycling and carbon sequestration) with direct influence on greenhouse gas emissions.

Fungal Carbonyl Sulfide Hydrolase of Trichoderma harzianum Strain THIF08 and Its Relationship with Clade D β-Carbonic Anhydrases

Carbonyl sulfide (COS) is the most abundant and long-lived sulfur-containing gas in the atmosphere. Soil is the main sink of COS in the atmosphere and uptake is dominated by soil microorganisms; however, biochemical research has not yet been conducted on fungal COS degradation. COS hydrolase (COSase) was purified from Trichoderma harzianum strain THIF08, which degrades COS at concentrations higher than 10,000 parts per million by volume from atmospheric concentrations, and its gene cos (492 bp) was cloned. The recombinant protein purified from Escherichia coli expressing the cos gene converted COS to H₂S. The deduced amino acid sequence of COSase (163 amino acids) was assigned to clade D in the phylogenetic tree of the β-carbonic anhydrase (β-CA) family, to which prokaryotic COSase and its structurally related enzymes belong. However, the COSase of strain THIF08 differed from the previously known prokaryotic COSase and its related enzymes due to its low reactivity to CO₂ and inability to hydrolyze CS₂. Sequence comparisons of the active site amino acids of clade D β-CA family enzymes suggested that various Ascomycota, particularly Sordariomycetes and Eurotiomycetes, possess similar enzymes to the COSase of strain THIF08 with >80% identity. These fungal COSase were phylogenetically distant to prokaryotic clade D β-CA family enzymes. These results suggest that various ascomycetes containing COSase contribute to the uptake of COS by soil.

Enumeration of Chemoorganotrophic Carbonyl Sulfide (COS)-degrading Microorganisms by the Most Probable Number Method

Carbonyl sulfide (COS) is the most abundant sulfur compound in the atmosphere, and, thus, is important in the global sulfur cycle. Soil is a major sink of atmospheric COS and the numerical distribution of soil microorganisms that degrade COS is indispensable for estimating the COS-degrading potential of soil. However, difficulties are associated with counting COS-degrading microorganisms using culture-dependent approaches, such as the most probable number (MPN) method, because of the chemical hydrolysis of COS by water. We herein developed a two-step MPN method for COS-degrading microorganisms: the first step for chemoorganotrophic growth that supported a sufficient number of cells for COS degradation in the second step. Our new MPN analysis of various environmental samples revealed that the cell density of COS-degrading microorganisms in forest soils ranged between 10⁶ and 10⁸ MPN (g dry soil)^–1, which was markedly higher than those in volcanic deposit and water samples, and strongly correlated with the rate of COS degradation in environmental samples. Numerically dominant COS degraders that were isolated from the MPN-positive culture were related to bacteria in the orders Bacillales and Actinomycetales. The present results provide numerical evidence for the ubiquity of COS-degrading microbes in natural environments.

Phytophthora zoospores: From perception of environmental signals to inoculum formation on the host-root surface

To explore moist soils and to target host plants, phytopathogenic Phytophthora species utilize the sensory and propulsion capabilities of the biflagellate unicellular zoospores they produce. Zoospore motion and interactions with the microenvironment are of primary importance for Phytophthora physiology. These are also of critical significance for plant pathology in early infection sequential events and their regulation: the directed zoospore migration toward the host, the local aggregation and adhesion at the host penetration site. In the soil, these early events preceding the root colonization are orchestrated by guidance factors, released from the soil particles in water films, or emitted within microbiota and by host plants. This signaling network is perceived by zoospores and results in coordinated behavior and preferential localization in the rhizosphere. Recent computational and structural studies suggest that rhizospheric ion and plant metabolite sensing is a key determinant in driving zoospore motion, orientation and aggregation. To reach their target, zoospores respond to various molecular, chemical and electrical stimuli. However, it is not yet clear how these signals are generated in local soil niches and which gene functions govern the sensing and subsequent responses of zoospores. Here we review studies on the soil, microbial and host-plant factors that drive zoospore motion, as well as the adaptations governing zoospore behavior. We propose several research directions that could be explored to characterize the role of zoospore microbial ecology in disease.

Soil carbonyl sulfide exchange in relation to microbial community composition: insights from a managed grassland soil amendment experiment

The viability of carbonyl sulfide (COS) measurements for partitioning ecosystem-scale net carbon dioxide (CO2) fluxes into photosynthesis and respiration critically depends on our knowledge of non-leaf sinks and sources of COS in ecosystems. We combined soil gas exchange measurements of COS and CO2 with next-generation sequencing technology (NGS) to investigate the role of soil microbiota for soil COS exchange. We applied different treatments (litter and glucose addition, enzyme inhibition and gamma sterilization) to soil samples from a temperate grassland to manipulate microbial composition and activity. While untreated soil was characterized by consistent COS uptake, other treatments reduced COS uptake and even turned the soil into a net COS source. Removing biotic processes through sterilization led to positive or zero fluxes. We used NGS to link changes in the COS response to alterations in the microbial community composition, with bacterial data having a higher explanatory power for the measured COS fluxes than fungal data. We found that the genera Arthrobacter and Streptomyces were particularly abundant in samples exhibiting high COS emissions. Our results indicate co-occurring abiotic production and biotic consumption of COS in untreated soil, the latter linked to carbonic anhydrase activity, and a strong dependency of the COS flux on the activity, identity, abundance of and substrate available to microorganisms.

Nitrogen Fertilization Reduces the Capacity of Soils to Take up Atmospheric Carbonyl Sulphide

Soils are an important carbonyl sulphide (COS) sink. However, they can also act as sources of COS to the atmosphere. Here we demonstrate that variability in the soil COS sink and source strength is strongly linked to the available soil inorganic nitrogen (N) content across a diverse range of biomes in Europe. We revealed in controlled laboratory experiments that a one-off addition of ammonium nitrate systematically decreased the COS uptake rate whilst simultaneously increasing the COS production rate of soils from boreal and temperate sites in Europe. Furthermore, we found strong links between variations in the two gross COS fluxes, microbial biomass, and nitrate and ammonium contents, providing new insights into the mechanisms involved. Our findings provide evidence for how the soil–atmosphere exchange of COS is likely to vary spatially and temporally, a necessary step for constraining the role of soils and land use in the COS mass budget.