Methane emissions and the microbial community in flooded paddies affected by the application of Fe-stabilized natural organic matter.

Redox chemistry involving the quinone/phenol cycling of natural organic matter (NOM) is known to modulate microbial respiration. Complexation with metals or minerals can also affect NOM solubilization and stability. Inspired by these natural phenomena, a new soil amendment approach was suggested to effectively decrease methane emissions in flooded rice paddies. Structurally stable forms of NOM such as lignin and humic acids (HAs) were shown to decrease methane gas emissions in a vial experiment using different soil types and rice straw as a methanogenic substrate, and this inhibitory behavior was likely enhanced by ferric ion-NOM complexation. A mechanistic study using HAs revealed that complexation facilitated the slow release of the humic components. Interestingly, borohydride-based reduction, which transformed quinone moieties into phenols, caused the HAs to lose their inhibitory capacity, suggesting that the electron-accepting ability of HAs is vital for their inhibitory effect. In rice field tests, the humic-metal complexes were shown to successfully mitigate methane generation, while carbon dioxide emissions were relatively unchanged. Microbial community analysis of the rice fields by season revealed a decrease in specific cellulose-metabolizing and methanogenic genera associated with methane emissions. In contrast, the relative abundance of Thaumarchaeota and Actinomycetota, which are associated with NOM and recalcitrant organics, was higher in the presence of Fe-stabilized HAs. These microbial dynamics suggest that the slow release of humic components is effective in modulating the anoxic soil microbiome, possibly due to their electron-accepting ability. Given the simplicity, cost-effectiveness, and soil-friendly nature of complexation processes, Fe-stabilized NOM represents a promising approach for the mitigation of methane emissions from flooded rice paddies.

Humic-like crop stimulatory activities of coffee waste induced by incorporation of phytotoxic phenols in melanoidins during coffee roasting: Linking the Maillard reaction to humification.

Here we showed that the water-soluble components of fresh green coffee beans inhibit the growth of lettuce in hydroponic systems, whereas those of roasted coffee waste facilitate it. The growth enhancement was hardly related to hydroponic parameters (i.e., pH and electric conductivity) or the nitrogen contents of the extracts. Rather, the presence of chromogenic polymeric melanoidins in the coffee waste was found to be crucial for the crop growth acceleration. The quantitative comparison of low-molecular-weight organics including phytotoxic phenolics between the extracts suggested that Maillard reactions occurring during coffee roasting transform the phenolics into polymeric melanoidin products. The identification of humic-like molecular compositions in the roasted coffee waste and the restoration of crop-stimulating activity by the addition of a phenol oxidase to the fresh coffee bean extract also supported that the low-molecular-weight phenols are oxidatively coupled during the roasting, which was consistent with the bottom-up synthesis of crop-stimulatory humic substances.

Lignin Metabolism by Selected Fungi and Microbial Consortia for Plant Stimulation: Implications for Biologically Active Humus Genesis.

Plant lignin is regarded as an important source for soil humic substances (HSs). Nonetheless, it remains unclear whether microbial metabolism on lignin is related to the genesis of unique HS biological activities (e.g., direct plant stimulation). Here, selected white-rot fungi (i.e., Ganoderma lucidum and Irpex lacteus) and plant litter- or mountain soil-derived microbial consortia were exploited to structurally modify lignin, followed by assessing the plant-stimulatory activity of the lignin-derived products. Parts solubilized by microbial metabolism on lignin were proven to exhibit organic moieties of phenol, carboxylic acid, and aliphatic groups and the enhancement of chromogenic features (i.e., absorbance at 450 nm), total phenolic contents, and radical-scavenging capacities with the cultivation times. In addition, high-resolution mass spectrometry revealed the shift of lignin-like molecules toward those showing either more molar oxygen-to-carbon or more hydrogen-to-carbon ratios. These results support the findings that the microbes involved, solubilize lignin by fragmentation, oxygenation, and/or benzene ring opening. This notion was also substantiated by the detection of related exoenzymes (i.e., peroxidases, copper radical oxidases, and hydrolases) in the selected fungal cultures, while the consortia treated with antibacterial agents showed that the fungal community is a sufficient condition to induce the lignin biotransformation. Major families of fungi (e.g., Nectriaceae, Hypocreaceae, and Saccharomycodaceae) and bacteria (e.g., Burkholderiaceae) were identified in the lignin-enriched cultures. All the microbially solubilized lignin products were likely to stimulate plant root elongation in the order selected white-rot fungi > microbial consortia > antibacterial agent-treated microbial consortia. Overall, this study supports the idea that microbial transformation of lignin can contribute to the formation of biologically active organic matter. IMPORTANCE Structurally stable humic substances (HSs) in soils are tightly associated with soil fertility, and it is thus important to understand how soil HSs are naturally formed. It is believed that microbial metabolism on plant matter contributes to natural humification, but detailed microbial species and their metabolisms inducing humic functionality (e.g., direct plant stimulation) need to be further investigated. Our findings clearly support that microbial metabolites of lignin could contribute to the formation of biologically active humus. This research direction appears to be meaningful not only for figuring out the natural processes, but also for confirming natural microbial resources useful for artificial humification that can be linked to the development of high-quality soil amendments.

Microbial Volatile Organic Compound (VOC)-Driven Dissolution and Surface Modification of Phosphorus-Containing Soil Minerals for Plant Nutrition: An Indirect Route for VOC-Based Plant-Microbe Communications.

We investigated the ability of microbial volatile organic compounds (MVOCs) emitted by Bacillus megaterium (a well-known MVOC producer) to modify the dissolution kinetics and surface of hydroxyapatite, a natural soil mineral. Facilitated phosphate release was induced by the airborne MVOCs in a time-dependent manner. Use of each standard chemical of the MVOCs then revealed that acetic and oxalic acids are crucial for the phenomenon. In addition, the ability of such MVOCs to engineer the apatite surfaces was evidenced by FT-IR spectra showing the COO- band variation with incubation time and the prolonged acceleration of phosphate release during the negligible acidification of the hydroxyapatite-containing solutions. The formation of calcium oxalate was revealed through SEM-EDS and XRD analyses, suggesting that MVOC oxalic acid interacts with calcium ions, leading to the precipitation of calcium oxalate, thus preventing the recrystallization of calcium phosphates. Gel- and soil-based plant cultivation tests employing Arabidopsis thaliana and solid calcium phosphates (i.e., nano- and microsized hydroxyapatites and calcium phosphate dibasic) demonstrated that these MVOC mechanisms facilitate plant growth by ensuring the prolonged supply of plant-available phosphate. The relationship between the growth enhancement and the particle size of the calcium phosphates also substantiated the MVOC sorption onto soil minerals related to plant growth. Given that most previous studies have assumed that MVOCs are a molecular lexicon directly detected by the dedicated sensing machinery of plants, our approach provides a new mechanistic view of the presence of abiotic mediators in the interaction between plants and microbes via MVOCs.