Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media

Magnetic biochar accelerates microbial succession and enhances assimilatory nitrate reduction during pig manure composting

Biochar promotes microbial metabolic activities and reduces N2O on aerobic composting. However, the effects of magnetic biochar (MBC) on the microbial succession and N2O emissions during pig manure composting remain unclear. Herein, a 42-day composting experiment was conducted with five treatment regimes: pig manure without biochar (CK), 5 % pig manure-based biochar (5 % PBC), 2 % MBC (2 % MBC), 5 % MBC (5 % MBC) and 7.5 % MBC (7.5 % MBC)), to clarify the variation in functional microorganisms and genes associated with nitrogen and direct interspecies electron transfer via metagenomics. Fourier-transform infrared spectroscopy showed that MBC possessed more stable aromatic structures than pig manure-based biochar (PBC), indicating its greater potential for nitrous oxide reduction. MBC treatments were more effective in composting organic matter and improving the carbon/nitrogen ratio than PBC. The microbial composition during composting varied significantly, with the dominant phyla shifting from Firmicutes to Proteobacteria, Actinobacteria, and Bacteroidota. Network and hierarchical clustering analyses showed that the MBC treatment enhanced the interactions of dominant microbes (Proteobacteria and Bacteroidota) and accelerated the composting process. The biochar addition accelerated assimilatory nitrate reduction and slowed dissimilatory nitrate reduction and denitrification. The Mantel test demonstrated that magnetic biochar potentially helped regulate composting nutrients and affected functional nitrogen genes. These findings shed light on the role of MBC in mitigating greenhouse gas emissions during aerobic composting.

Oxygen uptake rate versus CO2 based respiration rate for assessment of the biological stability of peat, plant fibers and woody materials with high C:N ratio versus composts

The biological stability of organic materials predicts their performance when used as either a soil improver or as an ingredient in growing media. CO₂ release in a static measurement and O₂ consumption rate (OUR) were compared for seven groups of growing media components. The ratio between CO₂ release and OUR was matrix-specific. This ratio was highest for plant fibers high in C:N and with a high risk of N immobilization, intermediate for wood fiber and woody composts, and lowest for peat and other compost types. The effect of variable test conditions in the OUR setup was assessed for plant fibers, where addition of mineral N and/or nitrification inhibitor had no effect on the OUR measurements. Testing at 30 °C instead of 20 °C resulted in higher OUR values as expected, but did not change the effect of mineral N dose. A strong increase in the CO₂ flux was measured when plant fibers were mixed with mineral fertilizer; in contrast, addition of mineral N or fertilizer before or during the OUR test had no effect. The present experimental setup did not allow for differentiation between a higher CO₂ release as a result of increased microbial respiration after adding mineral N versus an underestimation of stability due to N limitation in the dynamic OUR setup. Results indicate that type of material, C:N ratio and risk of N immobilization all appear to affect the OUR results. The OUR criteria may therefore require clear differentiation based on the different materials used in horticultural substrates.

Rare alkaline phosphatase-harboring bacteria mediate organic phosphorus mineralization during swine manure composting

Deciphering ecological functions of alkaline phosphatase (phoD)-harboring bacteria in composting systems is crucial but poorly understood. High-throughput sequencing, gene quantification, and statistical analyses were applied to investigate effects of abundance and diversity of phoD-harboring bacteria (PHB) on phosphorus availability during swine manure composting. Results showed that available phosphorus notably increased from 0.5 to 1.43 g kg^-1, and physicochemical properties and enzyme activities affected PHB community composition. Phylogenetic signals of PHB responded notably to temperature and phosphorus components, and stochasticity (94.2 %) dominated community assembly. Abundance and diversity of PHB directly and indirectly influenced phosphorus availability, and rare PHB mediated organic phosphorus mineralization. A phosphate-solubilizing bacterium (PSB) Pseudomonas sp. WWJ-22 isolated from compost displayed good efficiency in mineralizing lecithin, demonstrating the highest phosphorus-solubilizing level of 116.3 mg L^-1. This study highlights ecological roles of PHB on phosphorus availability and provides a potential PSB candidate for composting.

Changes in Soil Characteristics, Microbial Metabolic Pathways, TCA Cycle Metabolites and Crop Productivity following Frequent Application of Municipal Solid Waste Compost

The benefit sof municipal solid waste (MSW) compost on soil health and plant productivity are well known, but not its long-term effect on soil microbial and plant metabolic pathways. A 5-year study with annual (AN), biennial (BI) and no (C, control) MSW compost application were carried out to determine the effect on soil properties, microbiome function, and plantgrowth and TCA cycle metabolites profile of green beans (Phaseolus vulgaris), lettuce (Latuca sativa) and beets (Beta vulgaris). MSW compost increased soil nutrients and organic matter leading to a significant (p < 0.05) increase in AN-soil water-holding capacity followed by BI-soil compared to C-soil. Estimated nitrogen release in the AN-soil was ca. 23% and 146% more than in BI-soil and C-soil, respectively. Approximately 44% of bacterial community due to compost. Deltaproteobacteria, Bacteroidetes Bacteroidia, and Chloroflexi Anaerolineae were overrepresented in compost amended soils compared to C-soil. A strong positive association existed between AN-soil and 18 microbial metabolic pathways out of 205. Crop yield in AN-soil were increased by 6−20% compared to the BI-soil, and by 35−717% compared to the C-soil. Plant tricarboxylic acid cycle metabolites were highly (p < 0.001) influenced by compost. Overall, microbiome function and TCA cycle metabolites and crop yield were increased in the AN-soil followed by the BI-soil and markedly less in C-soil. Therefore, MSW compost is a possible solution to increase soil health and plants production in the medium to long term. Future study must investigate rhizosphere metabolic activities.

Compost from willow biomass (Salix viminalis L.) as a horticultural substrate alternative to peat in the production of vegetable transplants

Willow (Salix viminalis L.) is a species well adapted to the environment conditions of central Europe. It is mainly cultivated for energy purposes as solid fuel. In this study, an evaluation of its suitability for other purposes was made using a 4-year old short rotation coppice (SRC) willow regrowth to produce chipped biomass which was composted. Four composting methods were used: without additives (WC), with the addition of nitrogen to narrow the C:N ratio (WN), with the addition of mycelium (WPG) and with the addition of mycelium and nitrogen (WPGN). A mixture of WC and WPGN composts was also prepared at 75:25% and 50:50% by volume. Composts, different proportion (25, 50 and 75%) of peat (SM) were evaluated for suitability as a substrate for tomato and cucumber transplant production. Tomato transplants produced in the medium were prepared from mixtures of willow composts (WPGN + WC(1) and WPGN + WC(2) and these mixtures with peat (WPGN + WC(1):SM and WPGN + WC(2):SM) were characterised as having the best parameters: plant height, lateral leaf span and number of leaves. Similarly, for cucumber transplants, better growth conditions than in peat substrate were obtained in the variant WPGN + WC(1) and WPGN + WC(1):SM. The addition of nitrogen to the composted biomass positively influenced the composting process. N concentration in the substrate was too high and toxic for the growth of tomato and cucumber transplants. At the end of the tomato and cucumber experiment, the nitrate content was 1510 and 2260 mg dm^-3, respectively, in the WN substrate. Similarly, the high N-NO₃^- content in the composted willow substrate with the addition of nitrogen and mycelium did not promote the growth of tomato and cucumber. Based on this research at least 25% of the mass of the peat can be replaced by different willow composts without having an adverse impact on seedling growth and with some of the willow compost mixtures this could be as high as 50%.

Elucidating the microbiome of the sustainable peat replacers composts and nature management residues

Sustainable peat alternatives, such as composts and management residues, are considered to have beneficial microbiological characteristics compared to peat-based substrates. Studies comparing microbiological characteristics of these three types of biomass are, however, lacking. This study examined if and how microbiological characteristics of subtypes of composts and management residues differ from peat-based substrates, and how feedstock and (bio)chemical characteristics drive these characteristics. In addition, microbiome characteristics were evaluated that may contribute to plant growth and health. These characteristics include: genera associated with known beneficial or harmful microorganisms, microbial diversity, functional diversity/activity, microbial biomass, fungal to bacterial ratio and inoculation efficiency with the biocontrol fungus Trichoderma harzianum. Bacterial and fungal communities were studied using 16S rRNA and ITS2 gene metabarcoding, community-level physiological profiling (Biolog EcoPlates) and PLFA analysis. Inoculation with T. harzianum was assessed using qPCR. Samples of feedstock-based subtypes of composts and peat-based substrates showed similar microbial community compositions, while subtypes based on management residues were more variable in their microbial community composition. For management residues, a classification based on pH and hemicellulose content may be relevant for bacterial and fungal communities, respectively. Green composts, vegetable, fruit and garden composts and woody composts show the most potential to enhance plant growth or to suppress pathogens for non-acidophilic plants, while grass clippings, chopped heath and woody fractions of compost show the most potential for blends for calcifuge plants. Fungal biomass was a suitable predictor for inoculation efficiency of composts and management residues.

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.

Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells

The mycotoxin deoxynivalenol (DON), produced in wheat, barley and maize by Fusarium graminearum and Fusarium culmorum, is threatening the health of humans and animals. With its worldwide high incidence in food and feed, mitigation strategies are needed to detoxify DON, maintaining the nutritional value and palatability of decontaminated commodities. A promising technique is biological degradation, where microorganisms are used to biotransform mycotoxins into less toxic metabolites. In this study, bacterial enrichment cultures were screened for their DON detoxification potential, where DON and its potential derivatives were monitored. The residual phytotoxicity was determined through a bioassay using the aquatic plant Lemna minor L. Two bacterial enrichment cultures were found to biotransform DON into a still highly toxic metabolite for plants. Furthermore, a cytotoxic effect was observed on the cellular viability of intestinal porcine epithelial cells. Through liquid chromatography high-resolution mass spectrometry analysis, an unknown compound was detected, and tentatively characterized with a molecular weight of 30.0 Da (i.e., CH₂O) higher than DON. Metabarcoding of the subsequently enriched bacterial communities revealed a shift towards the genera Sphingopyxis, Pseudoxanthomonas, Ochrobactrum and Pseudarthrobacter. This work describes the discovery of a novel bacterial DON-derived metabolite, toxic to plant and porcine cells.