Combined application of arbuscular mycorrhizal fungi and selenium fertilizer increased wheat biomass under cadmium stress and shapes rhizosphere soil microbial communities.

BACKGROUND: Selenium (Se) fertilizer and arbuscular mycorrhizal fungi (AMF) are known to modulate cadmium (Cd) toxicity in plants. However, the effects of their co-application on wheat growth and soil microbial communities in Cd-contaminated soil are unclear. RESULTS: A pot experiment inoculation with two types of AMF and the application of Se fertilizer under Cd stress in wheat showed that inoculation AMF alone or combined with Se fertilizer significantly increased wheat biomass. Se and AMF alone or in combination significantly reduced available Cd concentration in wheat and soil, especially in the Se combined with Ri treatment. High throughput sequencing of soil samples indicated that Se and AMF application had stronger influence on bacterial community compared to fungal community and the bacterial network seemed to have more complex interconnections than the fungal network, and finally shaped the formation of specific microflora to affect Cd availability. CONCLUSION: These results indicate that the application of Se and AMF, particularly in combination, could successfully decrease soil Cd availability and relieve the harm of Cd in wheat by modifying rhizosphere soil microbial communities.

Responses of soil and rhizosphere microbial communities to Cd-hyperaccumulating willows and Cd contamination.

BACKGROUND: The pollution of soil by heavy metals, particularly Cd, is constitutes a critical international environmental concern. Willow species are renowned for their efficacy in the phytoremediation of heavy metals owing to their high Cd absorption rate and rapid growth. However, the mechanisms underlying microbial regulation for high- and low-accumulating willow species remain poorly understood. Therefore, we investigated the responses of soil and rhizosphere microbial communities to high- and low-Cd-accumulating willows and Cd contamination. We analyzed soil properties were analyzed in bulk soil (SM) and rhizosphere soil (RM) planted with high-accumulating (H) and low-accumulating (L) willow species. RESULTS: Rhizosphere soil for different willow species had more NH4+ than that of bulk soil, and RM-H soil had more than RM-L had. The available phosphorus content was greater in hyper-accumulated species than it was in lower-accumulated species, especially in RM-H. Genome sequencing of bacterial and fungal communities showed that RM-L exhibited the highest bacterial diversity, whereas RM-H displayed the greatest richness than the other groups. SM-L exhibited the highest diversity and richness of fungal communities. Ralstonia emerged as the predominant bacterium in RM-H, whereas Basidiomycota and Cercozoa were the most enriched fungi in SM-H. Annotation of the N and C metabolism pathways revealed differential patterns: expression levels of NRT2, NarB, nirA, nirD, nrfA, and nosZ were highest in RM-H, demonstrating the effects of NO3-and N on the high accumulation of Cd in RM-H. The annotated genes associated with C metabolism indicated a preference for the tricarboxylic pathway in RM-H, whereas the hydroxypropionate-hydroxybutyrate cycle was implicated in C sequestration in SM-L. CONCLUSIONS: These contribute to elucidation of the mechanism underlying high Cd accumulation in willows, particularly in respect of the roles of microbes and N and C utilization. This will provide valuable insights for repairing polluted soil using N and employing organic acids to improve heavy metal remediation efficiency.

Microbiome analysis reveals the differences in gut fungal community between Dutch Warmblood and Mongolian horses.

Similar to gut bacterial community, gut fungal community are also an important part of the gut microbiota and play crucial roles in host immune regulation and metabolism. However, most studies have focused on the gut bacterial community, and research on the gut fungal community has been limited. Dutch Warmblood (DWH) and Mongolian horses (MGH) are important equine breeds, but little research has been done on their gut fungal community. Here, we assessed differences in gut fungal community between two horse species. Results showed that a total of 2159 OTUs were found in the Dutch Warmblood and Mongolian horses, of which 308 were common. Between-group analyzes of microbial diversity showed no differences in the alpha and beta diversity of gut fungal community between the two horse species. Microbiological taxonomic surveys showed that the dominant fungal phyla (Neocallimastigomycota and Ascomycota) and genera (unclassified_Neocallimastigaceae and Anaeromyces) were the same without being affected by species. Although the types of dominant fungal phyla did not change, the abundances of some fungal genera changed significantly. Results of Metastats analysis showed that there were a total of 206 fungal genera that were significantly different between the two horses, among which 78 genera showed an increase and 127 genera significantly decreased in Dutch Warmblood horses compared with Mongolian horses. In conclusion, this study investigated the composition and structure of the gut fungal community of Dutch Warmblood and Mongolian horses and found significant differences in gut fungal community between both breeds. Notably, this is the first exploration of the differences in the gut fungal community of both breeds, which may help to understand the distribution characteristics of the gut fungal community of different breeds of horses and reveal the differences in the traits of different horses.

The initial composition and structure of microbial community determined the yield and quality of Baijiu during the spontaneous fermentation.

The microbiota during pit mud fermentation is a crucial factor in Baijiu brewing since it determines the yield and flavor. However, the impact of the microbial community during the initial fermentation stage on Baijiu quality remains uncertain. Herein, high-throughput sequencing was employed to investigate the microbial diversities and distribution during Baijiu fermentation in individual pit mud workshops at both initial and late stages. During the initial fermentation stage, the bacterial community exerted a more pronounced effect on Baijiu quality than the fungal community. And the high-yield pit mud workshop exhibited lower richness and evenness, as well as greater Bray-Curtis dissimilarity during Baijiu fermentation. Lactobacillus was the dominant genus and biomarker in high-yield pit mud, and it constituted the only genus within the bacterial association network during the late fermentation stage. Fungal communities tended to maintain a simple association network with selected core species. Based on the correlation network, Rhizopus and Trichosporon were identified as biomarkers in Baijiu fermentation process. Together, Lactobacillus and Rhizopus could serve as bio-indicators for Baijiu quality during the initial fermentation stage. Therefore, these findings provided novel insights into microbiota interactions during fermentation and the impact of initial microbiota on final Baijiu quality.

How host species and body part determine the microbial communities of five ambrosia beetle species.

The ambrosia beetles are farming insects that feed mainly on their cultivated fungi, which in some occasions are pathogens from forest and fruit trees. We used a culture-independent approach based on 16S and 18S rRNA gene metabarcoding analysis to investigate the diversity and composition of the bacterial and fungal communities associated with five ambrosia beetle species: four species native to America (Monarthrum dimidiatum, Dryocoetoides capucinus, Euwallacea discretus, Corthylus consimilis) and an introduced species (Xylosandrus morigerus). For the bacterial community, the beetle species hosted a broad diversity with 1,579 amplicon sequence variants (ASVs) and 66 genera, while for the fungal community they hosted 288 ASVs and 39 genera. Some microbial groups dominated the community within a host species or a body part (Wolbachia in the head-thorax of E. discretus; Ambrosiella in the head-thorax and abdomen of X. morigerus). The taxonomic composition and structure of the microbial communities appeared to differ between beetle species; this was supported by beta-diversity analysis, which indicated that bacterial and fungal communities were clustered mainly by host species. This study characterizes for the first time the microbial communities associated with unexplored ambrosia beetle species, as well as the factors that affect the composition and taxonomic diversity per se, contributing to the knowledge of the ambrosia beetle system.

Facilitating Effects of Reductive Soil Disinfestation on Soil Health and Physiological Properties of Panax ginseng.

Chemical soil fumigation (CSF) and reductive soil disinfestation (RSD) have been proven to be effective agricultural strategies to improve soil quality, restructure microbial communities, and promote plant growth in soil degradation remediation. However, it is still unclear how RSD and CSF ensure soil and plant health by altering fungal communities. Field experiments were conducted to investigate the effects of CSF with chloropicrin, and RSD with animal feces on soil properties, fungal communities and functional composition, and plant physiological characteristics were evaluated. Results showed that RSD and CSF treatment improved soil properties, restructured fungal community composition and structure, enhanced fungal interactions and functions, and facilitated plant growth. There was a significant increase in OM, AN, and AP contents in the soil with both CSF and RSD treatments compared to CK. Meanwhile, compared with CK and CSF, RSD treatment significantly increased biocontrol Chaetomium relative abundance while reducing pathogenic Neonectria relative abundance, indicating that RSD has strong inhibition potential. Furthermore, the microbial network of RSD treatment was more complex and interconnected, and the functions of plant pathogens, and animal pathogen were decreased. Importantly, RSD treatment significantly increased plant SOD, CAT, POD activity, SP, Ca, Zn content, and decreased MDA, ABA, Mg, K, and Fe content. In summary, RSD treatment is more effective than CSF treatment, by stimulating the proliferation of probiotic communities to further enhance soil health and plant disease resistance.

Dynamic Changes of Soil Microbial Communities During the Afforestation of Pinus Armandii in a Karst Region of Southwest China.

Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the "space instead of time" approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.

Response of microbial communities to the changes in grazing intensity and season in a typical steppe.

Livestock grazing is an influencing factor playing a key role in shaping the plant community, microbial community, and soil properties in grassland ecosystems. Northern China's Loess Plateau has been used for livestock grazing for centuries and is a vulnerable ecosystem. In this study, the fates of bacterial and fungal communities of the typical steppe of the Loess Plateau were investigated under increasing grazing intensities practiced in summer and winter seasons. The results revealed changes in soil physiochemical properties, plant community properties, and microbial diversity in response to alterations in the grazing intensity. The alpha diversity of microbial communities (including bacteria and fungi) exhibited an uneven trend during summer grazing due to an increase in grazing intensity, but it decreased during winter grazing; however, the observed changes were not significant. The beta diversity of the bacterial community was highly influenced by grazing intensity, the summer community clustered near nongrazing, and the winter community presented significantly different results. The beta diversity of the fungal community was not influenced by grazing intensity or season. Grazing induced the growth of fast-growing bacteria (such as Actinobacteria and Firmicutes) and saprophytic fungi and a reduction in overall pathogenic traits. Co-occurrence network analysis and a structural equation model revealed changes in soil and plant properties (such as soil nitrogen level, soil organic carbon level, aboveground biomass, and litter biomass), with an increase in grazing intensity contributing to alterations in bacterial and fungal diversities. This finding demonstrates that grazing intensity can directly affect soil microbes and play an indirect role by modifying soil nutrients and reducing plant biomass, which eventually contributes to changes in microbial communities. Overall, implementing low grazing intensity is suggested for maintaining the microbial community structure the same as that of the native microbiome (ungrazed) in the steppe ecosystems.

Fungi play a crucial role in sustaining microbial networks and accelerating organic matter mineralization and humification during thermophilic phase of composting.

Fungi play an important role in the mineralization and humification of refractory organic matter such as lignocellulose during composting. However, limited research on the ecological role of fungi in composting system hindered the development of efficient microbial agents. In this study, six groups of lab-scale composting experiments were conducted to reveal the role of fungal community in composting ecosystems by comparing them with bacterial community. The findings showed that the thermophilic phase was crucial for organic matter degradation and humic acid formation. The Richness index of the fungal community peaked at 1165 during this phase. PCoA analysis revealed a robust thermal stability in the fungal community. Despite temperature fluctuations, the community structure, predominantly governed by Pichia and Candida, remained largely unaltered. The stability of fungal community and the complexity of ecological networks were 1.26 times and 5.15 times higher than those observed in bacterial community, respectively. Fungi-bacteria interdomain interaction markedly enhanced network complexity, contributing to maintain microbial ecological functions. The core fungal species belonging to the family Saccharomycetaceae drove interdomain interaction during thermophilic phase. This study demonstrated the key role of fungi in the composting system, which would provide theoretical guidance for the development of high efficiency composting agents to strengthen the mineralization and humification of organic matter.

Community composition of phytopathogenic fungi significantly influences ectomycorrhizal fungal communities during subtropical forest succession.

Ectomycorrhizal fungi (EMF) can form symbiotic relationships with plants, aiding in plant growth by providing access to nutrients and defense against phytopathogenic fungi. In this context, factors such as plant assemblages and soil properties can impact the interaction between EMF and phytopathogenic fungi in forest soil. However, there is little understanding of how these fungal interactions evolve as forests move through succession stages. In this study, we used high-throughput sequencing to investigate fungal communities in young, intermediate, and old subtropical forests. At the genus level, EMF communities were dominated by Sebacina, Russula, and Lactarius, while Mycena was the most abundant genus in pathogenic fungal communities. The relative abundances of EMF and phytopathogenic fungi in different stages showed no significant difference with the regulation of different factors. We discovered that interactions between phytopathogenic fungi and EMF maintained a dynamic balance under the influence of the differences in soil quality attributed to each forest successional stage. The community composition of phytopathogenic fungi is one of the strong drivers in shaping EMF communities over successions. In addition, the EMF diversity was significantly related to plant diversity, and these relationships varied among successional stages. Despite the regulation of various factors, the positive relationship between the diversity of phytopathogenic fungi and EMF remained unchanged. However, there is no significant difference in the ratio of the abundance of EMF and phytopathogenic fungi over the course of successions. These results will advance our understanding of the biodiversity-ecosystem functioning during forest succession. KEY POINTS: •Community composition of both EMF and phytopathogenic fungi changed significantly over forest succession. •Phytopathogenic fungi is a key driver in shaping EMF community. •The effect of plant Shannon's diversity on EMF communities changed during the forest aging process.

Identifying environmental factors affecting the microbial community composition on outdoor structural timber.

Timber wood is a building material with many positive properties. However, its susceptibility to microbial degradation is a major challenge for outdoor usage. Although many wood-degrading fungal species are known, knowledge on their prevalence and diversity causing damage to exterior structural timber is still limited. Here, we sampled 46 decaying pieces of wood from outdoor constructions in the area of Hamburg, Germany; extracted their DNA; and investigated their microbial community composition by PCR amplicon sequencing of the fungal ITS2 region and partial bacterial 16S rRNA genes. In order to establish a link between the microbial community structure and environmental factors, we analysed the influence of wood species, its C and N contents, the effect of wood-soil contact, and the importance of its immediate environment (city, forest, meadow, park, respectively). We found that fungal and bacterial community composition colonising exterior timber was similar to fungi commonly found in forest deadwood. Of all basidiomycetous sequences retrieved, some, indicative for Perenniporia meridionalis, Dacrymyces capitatus, and Dacrymyces stillatus, were more frequently associated with severe wood damage. Whilst the most important environmental factor shaping fungal and bacterial community composition was the wood species, the immediate environment was important for fungal species whilst, for the occurrence of bacterial taxa, soil contact had a high impact. No influence was tangible for variation of the C or N content. In conclusion, our study demonstrates that wood colonising fungal and bacterial communities are equally responsive in their composition to wood species, but respond differently to environmental factors. KEY POINTS: • Perenniporia meridionalis and Dacrymyces are frequently associated with wood damage • Fungal community composition on timber is affected by its surrounding environment • Bacterial community composition on structural timber is affected by soil contact.

Changes in the soil fungal communities of steppe grasslands at varying degradation levels in North China.

The grasslands in North China are rich in fungal resources. However, the knowledge of the structure and function of fungal communities and the role of microbial communities in vegetation restoration and succession are limited. Thus, we used an Illumina HiSeq PE250 high-throughput sequencing platform to study the changing characteristics of soil fungal communities in degraded grasslands, which were categorized as non-degraded (ND), lightly degraded, moderately degraded, and severely degraded (SD). Moreover, a correlation analysis between soil physical and chemical properties and fungal communities was completed. The results showed that the number of plant species, vegetation coverage, aboveground biomass, and diversity index decreased significantly with increasing degradation, and there were significant differences in the physical and chemical properties of the soil among the different degraded grasslands. The dominant fungal phyla in the degraded grassland were as follows: Ascomycota, 44.88%-65.03%; Basidiomycota, 12.68%-29.91%; and unclassified, 5.51%-16.91%. The dominant fungi were as follows: Mortierella, 6.50%-11.41%; Chaetomium, 6.71%-11.58%; others, 25.95%-36.14%; and unclassified, 25.56%-53.0%. There were significant differences in the microbial Shannon-Wiener and Chao1 indices between the ND and degraded meadows, and the composition and diversity of the soil fungal community differed significantly as the meadows continued to deteriorate. The results showed that pH was the most critical factor affecting soil microbial and fungal communities in SD grasslands, whereas soil microbial and fungal communities in ND grasslands were mainly affected by water content and other environmental factors.

Community composition of the entomopathogenic fungal genus Metarhizium in soils of tropical and temperate conventional and organic strawberry fields.

Studies on community composition and population structure of entomopathogenic fungi are imperative to link ecosystem functions to conservation biological control. We studied the diversity and abundance of Metarhizium spp. from soil of conventionally and organically farmed strawberry crops and from the adjacent field margins in two different climatic zones: Brazil (tropical) and Denmark (temperate), using the same isolating methods. In Brazilian strawberry soil, Metarhizium robertsii (n = 129 isolates) was the most abundant species, followed by M. humberi (n = 16); M. anisopliae (n = 6); one new taxonomically unassigned lineage Metarhizium sp. indet. 5 (n = 4); M. pingshaense (n = 1) and M. brunneum (n = 1). In Denmark, species composition was very different, with M. brunneum (n = 33) being isolated most commonly, followed by M. flavoviride (n = 6) and M. pemphigi (n = 5), described for the first time in Denmark. In total, 17 haplotypes were determined based on MzFG543igs sequences, four representing Danish isolates and 13 representing Brazilian isolates. No overall difference between the two climatic regimes was detected regarding the abundance of Metarhizium spp. in the soil in strawberry fields and the field margins. However, we found a higher Shannon's diversity index in organically managed soils, confirming a more diverse Metarhizium community than in soils of conventionally managed agroecosystems in both countries. These findings contribute to the knowledge of the indigenous diversity of Metarhizium in agricultural field margins with the potential to contribute to pest regulation in strawberry cropping systems.

Phylogeny and Fungal Community Structures of Helotiales Associated with Sclerotial Disease of Mulberry Fruits in China.

Mulberry fruit sclerotiniose is a prevalent disease caused by the fungal species Ciboria shiraiana, C. carunculoides, and Scleromitrula shiraiana of the order Helotiales, and severely affects the production of mulberry. However, these species have only been identified using morphological and rDNA-ITS sequence analyses, and their genetic variation is unclear. To address this, morphological and two-locus (ITS and RPB2) phylogenetic analyses were conducted using culture-dependent and independent methods for 49 samples from 31 orchards across four provinces in China. Illumina MiSeq sequencing was used to assess the fungal communities obtained from fruits varying in disease severity and color from an orchard in Wuhan. Conidial suspensions of C. shiraiana and C. carunculoides isolated from diseased fruits, diseased fruits affected with hypertrophy and pellet sorosis sclerotiniose, and mycelia of Sclerotinia sclerotiorum were determined to be pathogenic to the mulberry cultivar YSD10. However, fruits inoculated with S. sclerotiorum mycelia exhibited nontypical disease symptoms, and mycelia and conidia obtained from C. carunculoides and S. shiraiana strains were not pathogenic. Maximum parsimony and Bayesian analyses using the sequences of the assessed loci indicated species variability with no evidence of geographic specialization. Metagenomic analysis revealed that the diversity of fungal communities was reduced with disease progression. Furthermore, within a single fruit, the presence of two Ciboria spp. was detected. These results provide novel insights into Ciboria spp., revealing the secondary infections caused by conidia in diseased fruits, genetic variations of the pathogens, and the occurrence of coinfection. This improved understanding of fungal pathogens will aid in developing effective disease control strategies.

Long-term Consequences on Soil Fungal Community Structure: Monoculture Planting and Natural Regeneration.

Understanding the regeneration and succession of belowground communities, particularly in forests, is vital for maintaining ecosystem health. Despite its importance, there is limited knowledge regarding how fungal communities change over time during ecosystem development, especially under different forest restoration strategies. In this study, we focused on two restoration methods used in northern Japan: monoculture planting and natural regeneration. We examined the responses of the fungal community to monoculture plantations (active tree planting) and naturally regenerated (passive regeneration) forests over a 50-year chronosequence, using natural forests as a reference. Based on DNA metabarcoding, we assessed the richness of fungal Operational Taxonomic Units (OTUs) and their dissimilarity. Our findings revealed that soil fungal richness remained stable after natural regeneration but declined in monoculture plantations, from 354 to 247 OTUs. While the compositional dissimilarity of fungal assemblages between monoculture plantations and natural forests remained consistent regardless of the time since tree planting, it significantly decreased after natural regeneration, suggesting recovery to a state close to the reference level. Notably, the composition of key functional fungal groups-saprotrophic and ectomycorrhizal- has increasingly mirrored that of natural forests over time following passive natural regeneration. In summary, our study suggests that monoculture plantations may not be effective for long-term ecosystem function and service recovery because of their limited support for soil fungal diversity. These results underscore the importance of natural regeneration in forest restoration and management strategies.

Interactions among the composition changes in fungal communities and the main mycotoxins in simulated stored wheat grains.

BACKGROUND: There are significant food safety risks associated with wheat spoilage due to fungal growth and mycotoxin contamination. Nevertheless, a few studies have examined how stored wheat grain microbial communities and mycotoxins vary in different storage conditions. In this study, changes in deoxynivalenol (DON) and deoxynivalenol-3-glucoside (D3G) content were measured with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and an amplicon sequence analysis of fungi was performed on stored wheat grains from different storage conditions using high-throughput sequencing. The detailed interactions among the composition changes in the fungal community and the DON content of simulated stored wheat grains were also analyzed. RESULTS: Alternaria, Fusarium, Mrakia, and Aspergillus were the core fungal taxa, and the fungal communities of samples stored under different conditions were observed to be different. Aspergillus relative abundances increased, whereas Fusarium decreased. This led to an increase in the content of DON. The content of DON increased about 67% with 12% moisture and at 25 °C after 2 months of storage, which was influenced by the stress response of Fusarium. Correlations in fungal and mycotoxins changes were observed. There may be potential value in these findings for developing control strategies to prevent mildew infestations and mycotoxins contamination during grain storage. CONCLUSION: In storage, the more the fungal community composition and the relative abundance of Fusarium change, the more mycotoxins will be produced. We should therefore reduce competition between fungal communities through pre-storage treatment and through measures during storage. © 2023 Society of Chemical Industry.

Upgrade from aerated static pile to agitated bed systems promotes lignocellulose degradation in large-scale composting through enhanced microbial functional diversity.

Composting presents a viable management solution for lignocellulose-rich municipal solid waste. However, our understanding about the microbial metabolic mechanisms involved in the biodegradation of lignocellulose, particularly in industrial-scale composting plants, remains limited. This study employed metaproteomics to compare the impact of upgrading from aerated static pile (ASP) to agitated bed (AB) systems on physicochemical parameters, lignocellulose biodegradation, and microbial metabolic pathways during large-scale biowaste composting process, marking the first investigation of its kind. The degradation rates of lignocellulose including cellulose, hemicellulose, and lignin were significantly higher in AB (8.21%-32.54%, 10.21%-39.41%, and 6.21%-26.78%) than those (5.72%-23.15%, 7.01%-33.26%, and 4.79%-19.76%) in ASP at three thermal stages, respectively. The AB system in comparison to ASP increased the carbohydrate-active enzymes (CAZymes) abundance and production of the three essential enzymes required for lignocellulose decomposition involving a mixture of bacteria and fungi (i.e., Actinobacteria, Bacilli, Sordariomycetes and Eurotiomycetes). Conversely, ASP primarily produced exoglucanase and ß-glucosidase via fungi (i.e., Ascomycota). Moreover, AB effectively mitigated microbial stress caused by acetic acid accumulation by regulating the key enzymes involved in acetate conversion, including acetyl-coenzyme A synthetase and acetate kinase. Overall, the AB upgraded from ASP facilitated the lignocellulose degradation and fostered more diverse functional microbial communities in large-scale composting. Our findings offer a valuable scientific basis to guide the engineering feasibility and environmental sustainability for large-scale industrial composting plants for treating lignocellulose-rich waste. These findings have important implications for establishing green sustainable development models (e.g., a circular economy based on material recovery) and for achieving sustainable development goals.

Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum.

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.

Metatranscriptomics and metabarcoding reveal spatiotemporal shifts in fungal communities and their activities in Chinese coastal waters.

Fungal communities are diverse and abundant in coastal waters, yet, their ecological roles and adaptations remain largely unknown. To address these gaps, ITS2 metabarcoding and metatranscriptomic analyses were used to capture the whole suite of fungal diversity and their metabolic potential in water column and sediments in the Yellow Sea during August and October 2019. ITS2 metabarcoding described successfully the abundance of Dikarya during August and October at the different examined habitats, but strongly underrepresented or failed to identify other fungal taxa, including zoosporic and early-diverging lineages, that were abundant in the mycobiome as uncovered by metatranscriptomes. Metatranscriptomics also revealed enriched expression of genes annotated to zoosporic fungi (e.g., chytrids) mainly in the surface water column in October. This enriched expression was correlated with the two-fold increase in chlorophyll-a intensity attributed to phytoplanktonic species which are known to be parasitized by chytrids. The concurrent high expression of genes related to calcium signalling and GTPase activity suggested that these metabolic traits facilitate the parasitic lifestyle of chytrids. Similarly, elevated expression of phagosome genes annotated to Rozellomycota, an early-diverging fungal phylum not fully detected with ITS2 metabarcoding, suggested that this taxon utilizes a suite of feeding modes, including phagotrophy in this coastal setting. Our data highlight the necessity of using combined approaches to accurately describe the community structure of coastal mycobiome. We also provide in-depth insights into the fungal ecological roles in coastal waters, and report potential metabolic mechanisms utilized by fungi to cope with environmental stresses that occur during distinct seasonal months in coastal ecosystems.

Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency.

Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine (i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and (ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs. high). Our results revealed that bacteria were associated with particular soil properties (such as base saturation) and both bacteria and fungi were associated with plant community composition across sites and within the majority of sites. Moreover, a discernible microbial community signal emerged, clearly distinguishing high and low-productivity soils across different grasslands independent of their location in the world. Hence, regional productivity differences may be typified by characteristic soil microbial communities across the grassland biome. These results could encourage future research aiming to predict the general effects of global changes on soil microbial community composition in grasslands and to discriminate fertile from infertile systems using generally applicable microbial indicators.