The interaction of soil phototrophs and fungi with pH and their impact on soil CO2, CO18O and OCS exchange

Improved assessment of the impacts of plant protection products on certain soil ecosystem services requires better consideration of terrestrial microalgae and cyanobacteria

There is growing scientific and societal consciousness that the environmental risks and impacts of plant protection products (PPPs) cannot be properly assessed without considering ecosystem services. However, the science on this issue remains incomplete and fragmented, as recently illustrated in a collective scientific assessment that pointed out the limited knowledge on the risks and impacts of PPPs on soil ecosystem services, which are clearly overlooked. Beside soil ecosystem services, certain key players involved in these services are largely overlooked in the scientific literature on the risks and impacts of PPPs, namely soil microbial photosynthetic communities. Here, we followed the principles of evidence-based logic chain approaches to show the importance of considering these microorganisms when studying the impacts of PPPs on certain services provided by soil ecosystems, with a focus on regulating and maintenance services that play a role in the regulation of baseline flows and extreme events. Terrestrial microalgae and cyanobacteria are ubiquitous photosynthetic microorganisms that, together with other soil micro- and macro-organisms, play key roles in the ecosystem functions that underpin these ecosystem services. There is an extensive literature on the ecotoxicological effects of PPPs on different organisms including soil microorganisms, but studies concerning soil microbial photosynthetic communities are very scarce. However, there is scientific evidence that herbicides can have both direct and indirect impacts on these microbial photosynthetic communities. Given that they play key functional roles, we argue that soil microbial photosynthetic communities warrant greater attention in efforts to assess the environmental risks and impacts of PPPs and, ultimately, help preserve or restore the regulating and maintenance services provided by soil ecosystems.

Straw return and nitrogen fertilization regulate soil greenhouse gas emissions and global warming potential in dual maize cropping system

Abundant nitrogen (N) fertilization is needed for maize (Zea mays L.) production in China because of its huge residual biomass return. However, excessive N fertilization has a negative impact on the soil ecosystem and environment, which contributes to climate change. Soil incorporation of maize residues is a well-known practice for reducing chemical N fertilization without compromising maize yield and soil fertility. Thus, residues incorporation has the capacity to minimize N fertilization uses and hence mitigate soil greenhouse gas emissions by improving plant N uptake and use efficiency. There is still a research gap regarding the effects of maize residues incorporation on maize yield, soil fertility, greenhouse gas emissions, and plant N and carbon (C) contents. Therefore, we conducted a field experiment during spring and autumn involving four different N fertilization rates (N0, N200, N250, and N300 kg N ha^-1), with and without maize residues incorporation, to evaluate grain yield, soil fertility, plant N and C contents, and greenhouse gas emissions (GHGs). Compared to N0, N fertilizer application at 300 kg N ha^-1 with residues incorporation significantly increased area-scaled global warming potential (GWP) compared to other N fertilization rates in both spring and autumn seasons, but soil nutrient contents and plant N and C contents were not statistically different from the N250 treatment. In contrast, the N recovery use efficiency (NRUE), physiological N use efficiency (PNUE), and agronomic N use efficiency (ANUE) were significantly lower in the N300 treatment than in the lower N treatment groups. Nitrous oxide (N₂O) and carbon dioxide (CO₂) fluxes, area-scaled GWP, and greenhouse gas intensity (GHGI) were significantly lower in the N200 treatment with straw incorporation than the N250 and N300 treatments of the traditional planting system. Thus, we concluded that N200 treatment with residues incorporation is optimal for improving grain yield, soil fertility, plant N uptake, and mitigating greenhouse gas emissions.

Spatial and Temporal Variability and Driving Factors of Carbon Dioxide and Nitrous Oxide Fluxes in Alpine Wetland Ecosystems

Plants regulate greenhouse gas (GHG) fluxes in wetland ecosystems, but the mechanisms of plant removal and plant species that contribute to GHG emissions remain unclear. In this study, the fluxes of carbon dioxide (CO2) and nitrous oxide (N2O) were measured using the static chamber method from an island forest dominated by two different species, namely Betula platyphylla (BP) and Larix gmelinii (LG), in a marsh wetland in the Great Xing’an Mountains. Four sub-plots were established in this study: (1) bare soil after removing vegetation under BP (SBP); (2) bare soil after removing vegetation under LG (SLG); (3) soil with vegetation under BP (VSBP); and (4) soil with vegetation under LG (VSLG). Additionally, the contributions of the dark respiration from plant aerial parts under BP (VBP) and LG (VLG) to GHG fluxes were calculated. We found that the substantial spatial variability of CO2 fluxes ranged from −25.32 ± 15.45 to 187.20 ± 74.76 mg m−2 h−1 during the study period. The CO2 fluxes decreased in the order of SBP > VSLG > VSBP > SLG > VLG > VBP, indicating that vegetation species had a great impact on CO2 emissions. Particularly, the absence of vegetation promoted CO2 emission in both BP and LG. Additionally, CO2 fluxes showed dramatically seasonal variations, with high CO2 fluxes in late spring (May) and summer (June, July, and August), but low fluxes in late summer (August) and early autumn (September). Soil temperatures at 0−20 cm depth were better predictors of CO2 fluxes than deeper soil temperatures. N2O fluxes were varied in different treatments with the highest N2O fluxes in SLG and the lowest N2O fluxes in VBP. Meanwhile, no significant correlation was found between N2O fluxes and air or soil temperatures. Temporally, negative N2O fluxes were observed from June to October, indicating that soil N2O fluxes were reduced and emitted as N2, which was the terminal step of the microbial denitrification process. Most of the study sites were CO2 sources during the warm season and CO2 sinks in the cold season. Thus, soil temperature plays an important role in CO2 fluxes. We also found that the CO2 flux was positively related to pH in a 10 cm soil layer and positively related to moisture content (MC) in a 50 cm soil layer in VSBP and VSLG. However, the CO2 flux was negatively related to pH in a 30 cm soil layer in SBP and SLG. Our findings highlight the effects of vegetation removal on GHG fluxes, and aid in the scientific management of wetland plants.

Effects of different straw biochar combined with microbial inoculants on soil environment in pot experiment

Ginseng is an important cash crop. The long-term continuous cropping of ginseng causes the imbalance of soil environment and the exacerbation of soil-borne diseases, which affects the healthy development of ginseng industry. In this study, ginseng continuous cropping soil was treated with microbial inocula using broad-spectrum biocontrol microbial strain Frankia F1. Wheat straw, rice straw and corn straw were the best carrier materials for microbial inoculum. After treatment with microbial inoculum prepared with corn straw biochar, the soil pH value, organic matter, total nitrogen, available nitrogen, available phosphorus, and available potassium were increased by 11.18%, 55.43%, 33.07%, 26.70%, 16.40%, and 9.10%, the activities of soil urease, catalase and sucrase increased by 52.73%, 16.80% and 43.80%, respectively. A Metagenomics showed that after the application of microbial inoculum prepared with corn straw biochar, soil microbial OTUs, Chao1 index, Shannon index, and Simpson index increased by 19.86%, 16.05%, 28.83%, and 3.16%, respectively. Three classes (Alphaproteobacteria, Gammaproteobacteria and Sphingobacteria) were the dominant bacteria in ginseng soil, and their abundance increased by 7.87%, 9.81% and 1.24%, respectively, after treatment with microbial inoculum with corn straw biochar. Results indicated that the most effective treatment in ginseng soil would be the combined application of corn straw biochar and Frankia F1.

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.

Effects of long-term integrated agri-aquaculture on the soil fungal community structure and function in vegetable fields

The diversity and community structure of soil fungi play an important role in crop production and ecosystem balance, especially in paddy-upland vegetable field systems. High-throughput sequencing was used to study changes in the soil fungal community structure and function in paddy-upland vegetable field systems. The results showed that compared with traditional planting, the diversity and community structure of soil fungi were changed by the combination of flooding and drought, the Shannon index increased by 11.07%, and the proportion of the dominant species, Mortierella, decreased by 22.74%. Soil available nitrogen, total phosphorus, available phosphorus, total nitrogen and organic matter played a leading role in the initial stage of the experiment, while the dominant factor changed to total potassium 3 years later and then to soil pH and water content 6 years later. FUNGuild analysis showed that the proportion of three independent trophic modes of soil fungi were increased by the combined flooded-drought model, and there were multiple interaction factors, For example, nutrient supply, pH and planting pattern. This study showed that soil fertility, crop yield and economic benefits were better than the traditional model after three years of planting and breeding. The longer the time, the better the effect.

µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria

Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR2/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.

Synergistic effect of Klebsiella sp. FH-1 and Arthrobacter sp. NJ-1 on the growth of the microbiota in the black soil of Northeast China

The application of Atrazine in soil has always been a main problem in agriculture because its residuals may maintain in the soil for a long term. In this paper, two strains of Atrazine degrading bacteria (Klebsiella sp. FH-1 and Arthrobacter sp. NJ-1) were used to make biological compound microbial inoculum to repair the Atrazine contaminated typical black soil in Northeast China. Grain chaff was chosen as the optimal carrier material for microbial inoculum. The dynamic changes of Atrazine were detected by gas chromatography. The half-life of Atrazine in soil containing microbial inoculum was shortened from 9.8 d to 4.2 d. The Atrazine sensitive crops grown in the repaired soil showed increased stem length, root length, and emergence rate. The effects of microbial remediation on the original bacterial and fungal biota in the typical black soil in Northeast China were analyzed using the metagenomic approach. Results showed that Atrazine inhibited the original bacteria and fungi populations. The total numbers of bacterial and fungal species in the soil were partially recovered by adding the microbial inoculum. Two genera (Sphingosinicella and Sphingomonas) were the dominant bacteria. The beneficial bacterial biota was recovered and the number of species of the beneficial bacteria was higher than that in the original soil after adding the microbial inoculum. The dominant fungi included genera Guehomyces and Chaetomella. There was a total of 113 unclassified fungal genera (22.6% of 499), indicating the potential utility of the unclassified fungal species in the assessment of the soil contamination by Atrazine.

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.

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

Differentiating the contributions of photosynthesis and respiration to the global carbon cycle is critical for improving predictive climate models. Carbonic anhydrase (CA) activity in leaves is responsible for the largest biosphere-atmosphere trace gas fluxes of carbonyl sulfide (COS) and the oxygen-18 isotopologue of carbon dioxide (CO¹⁸O) that both reflect gross photosynthetic rates. However, CA activity also occurs in soils and will be a source of uncertainty in the use of COS and CO¹⁸O as carbon cycle tracers until process-based constraints are improved. In this study, we measured COS and CO¹⁸O exchange rates and estimated the corresponding CA activity in soils from a range of biomes and land use types. Soil CA activity was not uniform for COS and CO₂, and patterns of divergence were related to microbial community composition and CA gene expression patterns. In some cases, the same microbial taxa and CA classes catalyzed both COS and CO₂ reactions in soil, but in other cases the specificity towards the two substrates differed markedly. CA activity for COS was related to fungal taxa and β-D-CA expression, whereas CA activity for CO₂ was related to algal and bacterial taxa and α-CA expression. This study integrates gas exchange measurements, enzyme activity models, and characterization of soil taxonomic and genetic diversity to build connections between CA activity and the soil microbiome. Importantly, our results identify kinetic parameters to represent soil CA activity during application of COS and CO¹⁸O as carbon cycle tracers.