Impacts of size reduction and alkaline-soaking pretreatments on microbial community and organic matter decomposition during wheat straw composting

The effects of small geographical resolution and age on the phyllosphere microbial diversity of Castanopsis eyrei in subtropical forest

Our understanding of the mechanisms that maintain phyllosphere microbial diversity in natural systems remains far less developed than our understanding of belowground microbiomes. This knowledge gap hinders our comprehension of growth dynamics in the Fagaceae, a predominant tree family in subtropical regions, and the critical role it plays as a major forest community assembly. Here, we tested leaves from Castanopsis eyrei, a widespread subtropical Fagaceae species in south-eastern China, sampled across multiple ages within a forest dynamics plot on Mt. Huangshan. Using third-generation sequencing of full-length bacterial 16S rRNA genes and fungal ITS regions, we characterized the associated phyllosphere microbiota. We found that phyllosphere fungal diversity was high, dominated by Teratosphaeriaceae, Trimorphomycetaceae, and Bulleribasidiaceae, while bacterial diversity was lower and primarily comprised Beijerinckiaceae, Isosphaeraceae, and Acidobacteriaceae. Habitat, rather than host age, emerged as the principal factor influencing fungal and pathogen diversity. Linear mixed-effects models revealed a negative relationship between C. eyrei biomass and phyllosphere pathogen diversity. Co-occurrence network analysis showed that C. eyrei saplings supported the most complex network structure, with Recuromyces acting as a key pathogenic fungus, serving as both a module hub and a connector across all age classes. Overall, these findings highlight the ecological importance of habitat in shaping phyllosphere microbial diversity and underscore the interplay between host function and the maintenance of microbial diversity.

IMPORTANCE

Plant surfaces host diverse microbial communities that significantly impact host health and overall forest productivity. However, mechanisms maintaining phyllosphere microbial diversity and their consequences for host plants remain poorly understood. Employing a three-generation high-throughput sequencing approach, we investigated the phyllosphere fungal and bacterial diversity across different microhabitats and ages of Castanopsis eyrei, a common species in subtropical forest, China. Our results underscore the presence of exceptionally high microbial diversity on the plant surface, elucidating the taxonomic composition at the family level of key host microorganisms. Furthermore, our observation of a negative correlation between host performance and phyllosphere pathogens underscores the potential self-limiting ability of plants.

Comparative transcriptomics and metabolomics provide insight into degeneration-related physiological mechanisms of Morchella importuna after long-term preservation

Ascomycetes fungi are often prone to degeneration. Agricultural production of the prized ascomycete mushroom Morchella importuna (black morel) typically suffers from reduced yield and malformed ascocarps owing to culture degeneration. This study compared M. importuna cultures subjected to five different long-term preservation treatments, using transcriptomics and metabolomics. Avoiding repeated subculturing in combination with nutrient-limited conditions was found to be the most beneficial method for maintaining the fruiting capability of morels. The expression of the gene sets involved in cysteine and methionine metabolism and nucleocytoplasmic transport was upregulated under nutrient-limited and nutrient-rich conditions, respectively. This increased expression was accompanied by differential accumulation of metabolites involved in nucleobase metabolism. Repeated subculturing triggered dissimilar changes in the functional modules under nutrient-rich and nutrient-limited conditions. A diverse set of cellular biochemical processes related to carbon metabolism were altered by repeated subculturing under nutrient-rich conditions, whereas glycerophospholipid and purine metabolism were key functions affected by repeated subculturing under nutrient-limited conditions. Altogether, metabolic alterations related to sulfur-containing amino-acid biosynthesis, DNA repair, and cellular structural maintenance contributed to improved preservation outcomes in terms of morel fruiting capability. Our findings contribute to a more detailed understanding of the molecular mechanisms related to subculturing and fruiting of ascomycete macrofungi after long-term preservation.

Physicochemical property and microbial community characteristics of the casing soil for cultivating Oudemansiella raphanipes

Background

Casing soil is critical for the cultivation process of Oudemansiella raphanipes and promotes the formation of mushroom fruiting bodies. Therefore, reliable casing soil indicators are crucial for obtaining high yields of high-quality mushrooms.

Methods

In this study, soil enzyme activity, physicochemical properties, and microorganisms at five cultivation stages [namely casing (A1), mycelial (A2), primordial (A3), fruiting (A4), and harvesting (A5)] of O. raphanipes cultivation were evaluated in casing soils.

Results

The results indicated that sucrase and catalase activities were significantly increased with increasing cultivation time (p < 0.01), and the activities peaked [16.67 and 0.25 g/(g·h), respectively] at A4. Urease activity peaked [1.56 g/(g·h)] at A1, and it decreased gradually (p < 0.01). Polyphenol oxidase activity was significantly higher at A2 [0.95 g/(g·h)] than at the other stages and was significantly lower at A1 [0.06 g/(g·h)]. Soil pH peaked at A1 (8.20) and decreased gradually (p = 0.003). Soil total organic carbon content increased significantly with increasing cultivation time (p < 0.001) and was the highest at A5 (8.40 g/kg). The available phosphorus at A1 (0.40 g/kg) was significantly higher than those at the other stages (p = 0.004), and the available nitrogen at A1 (0.28 g/kg) and A3 (0.26 g/kg) was significantly higher than those at the other stages (p < 0.001). The number and diversity of bacteria and fungi in soil increased gradually, and nine bacterial and four fungal genera were identified.

Conclusion

This study offers soil characteristic and microbial community data for O. raphanipes casing soil at different cultivation stages, which could facilitate sustainable cultivation of O. raphanipes and reduction of live contaminants.

Effect of substrate size reduction and periodic nutrient supplementation on biological wood oxidation

Biological wood oxidation (BWO) is a composting heat recovery system tailored for woody lignocellulose valorization, with the potential to generate sustainable and low-temperature heat. This study investigated the effects of feedstock particle sizing and periodic nutrient supplementation (PNS) on microbial activity and wood decomposition during BWO. Birch wood was processed into sawdust (<5 mm) and cubes of various diameters (5, 10, and 15 mm), incubated in batch-mode BWO reactors for 88 days, and periodically supplemented with a nutrient medium. Sawdust-BWO outperformed cubes-BWO and demonstrated greater sensitivity to PNS, exhibiting in total 207% higher cumulative oxygen consumption, 50%∼ higher nitrogen utilization efficiency, 217% higher wood dry matter (DM) loss, and 101% higher total carbohydrates removal. The use of human urine as a nutrient source, combined with sawdust and PNS, further enhanced the BWO performance and resulted in an unprecedented 34.2% DM loss and 45.5% total carbohydrate removal over a 60-day incubation period. As revealed by an overall energy balance analysis, the process of grinding wood cubes into sawdust consumes around 55-72 kWh/t DM of additional electricity but results in a potentially 10-fold increase in heat output (680.6-719.5 kWh/t DM). Hence, combining fine grinding of wood with PNS emerges as an effective and energy-efficient strategy to elevate the performance and heat generation potential of BWO.

Converting kitchen waste into value-added fertilizer using thermophilic semi-continuous composting-biofiltration two-stage process with minimized NH3 emission

Thermophilic semi-continuous composting (TSC) is effective for kitchen waste (KW) treatment, but large amounts of NH3-rich odorous gas are generated. This study proposes a TSC-biofiltration (BF) two-stage process. Compost from the front-end TSC was used as the packing material in the BF to remove NH3 from the exhaust gas. The BF process was effective in removing up to 83.7 % of NH3, and the NH3 content was reduced to < 8 ppm. Seven days of BF improved the quality of the product from TSC by enhancing the germination index to 134.6 %, 36.5 % higher than that in the aerated-only group. Microbial community analysis revealed rapid proliferation and eventual dominance in the BF of members related to compost maturation and the nitrogen cycle from Actinobacteria, Proteobacteria, Chloroflexi, and Bacteroidetes. The results suggest that the TSC-BF two-stage process is effective in reducing NH3 emissions from TSC and improving compost quality.

Effects of initial corncob particle size on the short-term composting for preparation of cultivation substrates for Pleurotus ostreatus

The short-term composting based on corncob for preparing Pleurotus ostreatus cultivation medium originated from agricultural production practices and so lacked systematic investigation. In this study, the influences of a Dafen (15 mm, DFT) and Xiaofen (5 mm, XFT) initial particle size (IPS) of corncob on the microbial succession and compost quality were examined. Results demonstrated that XFT compost was better suited for mushroom cultivation due to its high biological efficiency of 70 % and the absence of contamination. The composting microbes differed significantly between the DFT and XFT composts. During composting, the genera of Bacillus, Acinetobacter, Lactobacillus, Streptomyces, and Paenibacillus were majorly found in the DFT compost, while Acinetobacter, Lactobacillus, Puccinia, Bacteroides, and Bacillus genera dominated the XFT compost. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that throughout the thermophilic phase, XFT compost had much greater relative abundances of sequences relevant to energy, carbohydrate, and amino acid metabolism than DFT compost. Analysis of network correlations and Mantel tests indicated that IPS reduction could increase microbial interactions. Overall, adjusting the IPS of corncob to 5 mm increased microbial interactions, improved compost quality, and thereby boosted the P. ostreatus yield. These findings will be pertinent in optimizing the composting process of cultivation medium for P. ostreatus.

Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots

IMPORTANCE

Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.

A review of additives use in straw composting

Straw composting is not only a process of decomposition and re-synthesis of organic matter, but also a process of harmless treatment, avoiding air pollution caused by straw burning. Many factors, including raw materials, humidity, C/N, and microbial structure, may determine the composting process and the quality of final product. In recent years, many researches have focused on composting quality improvement by adding one or more exogenous substances, including inorganic additives, organic additives, and microbial agents. Although a few review publications have compiled the research on the use of additives in composting, none of them has specifically addressed the composting of crop straw. Additives used in straw composting can increase degradation of recalcitrant substances and provide ideal living surroundings for microorganism, and thus reduce nitrogen loss and promote humus formation, etc. This review's objective is to critically evaluate the impact of various additives on straw composting process, and analyze how these additives enhance final quality of composting. Furthermore, a vision for future perspectives is provided. This paper can serve as a reference for straw composting process optimization and composting end-product improvement.

Valorizing kitchen waste to produce value-added fertilizer by thermophilic semi-continuous composting followed by static stacking: Performance and bacterial community succession analysis

To explore an effective decentralized kitchen waste (KW) treatment system, the performance and bacterial community succession of thermophilic semi-continuous composting (TSC) of KW followed by static stacking (SS) was studied. A daily feeding ratio of 10% ensured stable performance of TSC using an integrated automatic reactor; the efficiencies of organic matter degradation and seed germination index (GI) reached 80.88% and 78.51%, respectively. SS for seven days further promoted the quality of the compost by improving the GI to 91.58%. Alpha- and beta-diversity analyses revealed significant differences between the bacterial communities of TSC and SS. Firmicutes, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Myxococcota were dominant during the TSC of KW, whereas the members of Proteobacteria and Bacteroidetes responsible for product maturity rapidly proliferated during the subsequent SS and ultimately dominated the compost with Firmicutes and Actinobacteria. These results provide new perspectives for decentralized KW treatment using TSC for practical applications.

From Gut to Blood: Spatial and Temporal Pathobiome Dynamics during Acute Abdominal Murine Sepsis

Abdominal sepsis triggers the transition of microorganisms from the gut to the peritoneum and bloodstream. Unfortunately, there is a limitation of methods and biomarkers to reliably study the emergence of pathobiomes and to monitor their respective dynamics. Three-month-old CD-1 female mice underwent cecal ligation and puncture (CLP) to induce abdominal sepsis. Serial and terminal endpoint specimens were collected for fecal, peritoneal lavage, and blood samples within 72 h. Microbial species compositions were determined by NGS of (cell-free) DNA and confirmed by microbiological cultivation. As a result, CLP induced rapid and early changes of gut microbial communities, with a transition of pathogenic species into the peritoneum and blood detected at 24 h post-CLP. NGS was able to identify pathogenic species in a time course-dependent manner in individual mice using cfDNA from as few as 30 microliters of blood. Absolute levels of cfDNA from pathogens changed rapidly during acute sepsis, demonstrating its short half-life. Pathogenic species and genera in CLP mice significantly overlapped with pathobiomes from septic patients. The study demonstrated that pathobiomes serve as reservoirs following CLP for the transition of pathogens into the bloodstream. Due to its short half-life, cfDNA can serve as a precise biomarker for pathogen identification in blood.

Influence of thermally activated peroxodisulfate pretreatment on gaseous emission, dissolved organic matter and maturity evolution during spiramycin fermentation residue composting

Aerobic composting combined with appropriate pretreatment is promising to achieve the utilization of antibiotics fermentation residues (AFRs). This research studied the effect of thermally activated peroxodisulfate (TAP) pretreatment on greenhouse gas (GHGs) emission, dissolved organic matter (DOM) and maturity evaluation during spiramycin fermentation residue (SFR) composting. Three treatments were conducted from co-composting of SFR and wheat straw, while 90% and 99.9% residual spirmycin removal pretreatment SFR by TAP were provided and compared with raw SFR. The cumulative CO₂ and NH₃ emissions increased by 17.2% and 30.8% after TAP pretreatment removed 99.9% residual spiramycin in SFR, while the cumulative CH₄ and N₂O emission decreased by 34.0% and 5.27%, respectively. The DOM, humic acid (HA)/fulvic acid (FA) and NH₄⁺/NO₃^- analysis confirmed that the composting maturity was improved with the increasing of HA and NO₃^- content by TAP pretreatment.

Changes of Arbuscular Mycorrhizal Fungal Community and Glomalin in the Rhizosphere along the Distribution Gradient of Zonal Stipa Populations across the Arid and Semiarid Steppe

Arbuscular mycorrhizal fungi (AMF) have been reported to have a wide distribution in terrestrial ecosystems and to play a vital role in ecosystem functioning and symbiosis with Stipa grasses. However, exactly how AMF communities in the rhizosphere change and are distributed along different Stipa population with substituted distribution and their relationships remain unclear. Here, the changes and distribution of the rhizosphere AMF communities and their associations between hosts and the dynamic differences in the glomalin-related soil protein (GRSP) in the rhizosphere soil of seven Stipa species with spatial substitution distribution characteristics in arid and semiarid grasslands were investigated. Along with the substituted distribution of the Stipa populations, the community structures, taxa, species numbers, and alpha diversity index values of AMF in the rhizosphere changed. Some AMF taxa appeared only in certain Stipa species, but there was no obvious AMF taxon turnover. When the Stipa baicalensis population was replaced by the Stipa gobica population, the GRSP tended to decline, whereas the carbon contribution of the GRSP tended to increase. Stipa grandis and Stipa krylovii had a great degree of network modularity of the rhizosphere AMF community and exhibited a simple and unstable network structure, while the networks of Stipa breviflora were complex, compact, and highly stable. Furthermore, with the succession of zonal populations, the plant species, vegetation coverage, and climate gradient facilitated the differentiation of AMF community structures and quantities in the rhizospheres of different Stipa species. These findings present novel insights into ecosystem functioning and dynamics correlated with changing environments. IMPORTANCE This study fills a gap in our understanding of the soil arbuscular mycorrhizal fungal community distribution, community composition changes, and diversity of Stipa species along different Stipa population substitution distributions and of their adaptive relationships; furthermore, the differences in the glomalin-related soil protein (GRSP) contents in the rhizospheres of different Stipa species and GRSP's contribution to the grassland organic carbon pool were investigated. These findings provide a theoretical basis for the protection and utilization of regional biodiversity resources and sustainable ecosystem development.