Fungal Phyla Research Articles

RETRACTED: Evaluation of fungal dynamics during sheep manure composting employing peach shell biochar

In this study, explored the influence of different proportion (0%, 2.5%, 5%, 7.5%, and 10%) peach shell biochar (PSB) with microbial agents (EM) on the carbon transformation, humification process and fungal community dynamics during sheep manure (SM) composting. And no additives were used as control. The results manifested that the CO2 and CH4 emissions were effectively reduced 8.23%∼13.10% and 17.92%∼33.71%. The degradation rate of fulvic acid increased by 17.12%∼23.08% and the humic acid contents were enhanced by 27.27%∼33.97% so that accelerated the composting. Besides, the dominant fungal phylum was Ascomycota (31.43%∼52.54%), Basidiomycota (3.12%∼13.85%), Mucoromycota (0.40%∼7.61%) and Mortierellomycota (0.97%∼2.39%). Pearson correlation analysis and network indicated that there were different correlations between physicochemical indexes and fungal community under different additive concentrations. In brief, the two modifiers application promoted the SM degradation and affected the fungal community structure.

The Relationship between Microbial Community Succession and Flavor Formation during the Natural Fermentation of Hongqu sufu.

To study the diversity of microbial flora in Hongqu sufu and analyze the characteristics of special flavor compounds, this study took self-made Hongqu sufu as the research object. Dynamic changes in sufu during fermentation were studied. High-throughput sequencing (HTS) was used to analyze changes in the diversity of fungal and bacterial communities during fermentation. The results showed that at the phylum level, the dominant fungal phyla were identified, Mucormyces and Ascomycetes. The dominant bacterial phyla were Proteobacteria and Firmicutes. At the genus level, the dominant fungal genera were identified as Actinomucor, Monascus, and Aspergillus. The dominant bacterial genera were Pseudomonas, Aneurimibacillus, Sphingobacterium, and Bacillus. Headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) combined with technology that can dynamically change flavor compounds was explored to investigate the correlation between microbiota and flavor compounds. In different stages of fermentation, 75 main volatile organic compounds were identified, including seven alcohols, four acids, 16 alkanes, 14 olefins, seven kinds of aldehydes, two kinds of ketones, 10 kinds of esters, one kind of phenol, one kind of sulfur-containing compound, one benzene, and 12 other compounds. The correlation analysis between flora and flavor compounds showed that the fungi genera Alternaria and Pichia were significantly correlated with most flavor compounds. Bacteria genera including Weissella, Hafnia-Obesumbacterium, and Leuconostoc had a strong positive correlation with ethyl oleate.

Types of vegetables shape composition, diversity, and co-occurrence networks of soil bacteria and fungi in karst areas of southwest China

BackgroundMicroorganisms are of significant importance in soil. Yet their association with specific vegetable types remains poorly comprehended. This study investigates the composition of bacterial and fungal communities in soil by employing high-throughput sequencing of 16 S rRNA genes and ITS rRNA genes while considering the cultivation of diverse vegetable varieties.ResultsThe findings indicate that the presence of cultivated vegetables influenced the bacterial and fungal communities leading to discernible alterations when compared to uncultivated soil. In particular, the soil of leafy vegetables (such as cabbage and kale) exhibited higher bacterial α-diversity than melon and fruit vegetable (such as cucumber and tomato), while fungal α-diversity showed an inverse pattern. The prevailing bacterial phyla in both leafy vegetable and melon and fruit vegetable soils were Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. In leafy vegetable soil, dominant fungal phyla included Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota whereas in melon and fruit vegetable soil. Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota held prominence. Notably, the relative abundance of Ascomycota was lower in leafy vegetable soil compared to melon and fruit vegetable soil. Moreover, leafy vegetable soil exhibited a more complex and stable co-occurrence network in comparison to melon and fruit vegetable soil.ConclusionThe findings enhance our understanding of how cultivated soil bacteria and fungi respond to human disturbance, thereby providing a valuable theoretical basis for soil health in degraded karst areas of southwest China.

Effects of Different Rotation Combinations of Cabbage, Kidney Bean and Maize on Soil Fungal Communities and Soil Nutrients

The continuous cropping of cabbage or kidney bean results in a decrease in yield by influencing the soil environment. To decrease the damage caused by continuous cropping, ten treatments of cabbage–maize–cabbage (CMC), kidney bean–maize–cabbage (BMC), cabbage–cabbage–cabbage (CCC), cabbage–maize–kidney bean (CMB), kidney bean–maize–kidney bean (BMB), kidney bean–kidney bean–kidney bean (BBB), cabbage–cabbage–maize (CCM), cabbage–kidney bean–maize (CBM), kidney bean–kidney bean–maize (BBM) and kidney bean–cabbage–maize (BCM) rotation combinations were set up. The changes in soil nutrients, fungal community structure, composition and diversity in topsoil under the ten crop rotation combinations were analyzed using Illumina NovaSeq high-throughput sequencing technology and chemical technology. Fungal species were abundant in the ten treatments. The OTUs (operational taxonomic units) showed no significant differences. The richness index values of each treatment had significant differences. The diversity index value of the CCC treatment was significantly lower than those of the other treatments. The dominant soil fungal phylum was Ascomycota, and the subordinate soil fungal phylum was Basidiomycota. No significant differences were observed in Ascomycota between the treatments. Basidiomycota in the BBM treatment was significantly higher than that in the CCM treatment. Kickxellomycota was not found in the CCM and CCC treatments. The BBM treatment had no Entorrhizomycota. The dominant soil fungal class belonged to Ascomycota. The common distinction between continuous cropping and crop rotation was Diaporthales, which might be the main fungal order causing continuous cropping disorders. As the best choice, the BBM treatment could prevent soil-borne fungal diseases and provide the basis for the rational crop rotation of cabbage, kidney bean, and maize.

Diversity characterization of bacteria and fungi in water, sediments and biofilms from Songhua River in Northeast China

Water, sediments, and biofilms are the typical microbial carriers in natural water environments. However, comparative analysis of the distribution of bacterial and fungal communities in different carriers within the same habitat is relatively lacking. Therefore, this study employed 16 S and ITS rRNA gene sequencing to identify bacterial and fungal community structures in water, sediments, and biofilm. The results show that (1) the OTUs numbers revealed that the bacterial abundance, at the levels of species, genus, and family, followed the order of sediments > water > biofilms, while the fungal abundance order was water > sediments > biofilms. In addition, bacteria were mainly present in sediments, while fungi were mainly present in water. (2) The α diversity index (Shannon, ACE, Simpson, and Chao1) order, for bacteria was: sediments > water > biofilms, indicating that the diversity and homogeneity of bacteria in sediments were relatively higher; for fungi was: water > sediments > biofilms, indicating that the diversity and abundance of fungi in water were high. (3) The core phylum of bacterial in the water, sediments, and biofilms was Cyanobacteria (31.3–46.1%) and Actinobacteria (27.6–36.1%); Proteobacteria (35.0–41.8%), Cyanobacteria (14.7–36.6%); and Proteobacteria (63.3–69.2%), respectively. (4) The mainly colonized fungal phyla in biofilms in the water, sediments, and biofilms were Basidiomycota (29.3–38.7%) and Ascomycota (16.2–27.7%); Zygomycota (13.1–17.5%), Basidiomycota (5.6–17.6%); and Zygomycota (23.8–44.2%). (5) There were significant species differences in bacterial and fungal communities in water, sediments, and biofilm by NMDS analysis. Findings are useful for guiding significance for the Biogeochemical cycle of elements, the environmental fate of pollutants, and the study of water ecosystems.

Composition and Diversity of Soil Microbial Communities in Walnut Orchards at Different Altitudes in Southeastern Tibet

To understand the distribution of the soil microbial community in natural walnut orchards at different altitude gradients (3000–3500 m) and to reveal the mechanism of the soil microbial activity in natural walnut orchards adapting to high-altitude environments, soil samples from four groups of natural walnut orchards in Gyaca County, southeast Tibet, were studied. Illumina MiSeq sequencing technology was used to analyze the community composition and diversity of soil bacteria and fungi and their responses to the altitudes. The alpha diversity results showed that the vertical distribution pattern of the fungal community was more obvious than that of the bacterial community and the bacterial community diversity first increased (~3364 m) and then decreased with altitude. The number of amplicon sequence variants (ASVs) in the soil bacterial community was significantly higher than that in the fungal community, but soil bacterial and fungal communities in walnut orchards at different altitudes exhibited both inheritance and uniqueness. At the phylum level, the dominant bacterial phyla at different altitudes were Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi (relative abundances > 10.0% in each treatment). With the increase in altitude, the relative abundance of Actinobacteria increased gradually while that of Acidobacteria and Proteobacteria decreased gradually. The dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota (relative abundances >5.0% in each treatment). With the increase in altitude, the relative abundance of Ascomycota increased significantly. At the genus level, the number of dominant bacteria and fungi in the soil decreased gradually with increased altitude and showed anisotropic distribution characteristics. The relative abundances of Actinobacteria among the bacterial phyla—and Olpidiomycota and Zoopagomycota among the fungal phyla—were positively correlated with the altitude (p < 0.05). Most dominant bacterial and fungal phyla were highly significantly (p < 0.01) or significantly (p < 0.05) negatively correlated with the altitude. Soil nitrogen and phosphorus availabilities are the main limiting factors of microbial community diversity. Therefore, altitude caused changes in soil physicochemical properties which directly or indirectly affected the composition and diversity of soil bacterial and fungal communities, and our study provides a theoretical basis for the altitudinal pattern and succession changes in soil microbial communities in the natural walnut orchards of southeast Tibet.

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis.

The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.

Mineral-solubilizing microbial inoculant positively affects the multifunctionality of anthropogenic soils in abandoned mining areas

The mining industry has a significant negative impact on ecosystems, and the remediation of abandoned mining sites requires effective strategies. One promising approach is the incorporation of mineral-solubilizing microorganisms into current external soil spray seeding technologies. These microorganisms possess the ability to decrease mineral particle sizes, promote plant growth, and enhance the release of vital soil nutrients. However, most previous studies on mineral-solubilizing microorganisms have been conducted in controlled greenhouse environments, and their practical application in field settings remains uncertain. To address this knowledge gap, we conducted a four-year field experiment at an abandoned mining site to investigate the efficacy of mineral-solubilizing microbial inoculants in restoring derelict mine ecosystems. We assessed soil nutrients, enzyme activities, functional genes, and soil multifunctionality. We also examined microbial compositions, co-occurrence networks, and community assembly processes. Our results demonstrated that the application of mineral-solubilizing microbial inoculants significantly enhanced soil multifunctionality. Interestingly, certain bacterial phyla or class taxa with low relative abundances were found to be key drivers of multifunctionality. Surprisingly, we observed no significant correlation between microbial alpha diversity and soil multifunctionality, but we did identify positive associations between the relative abundance and biodiversity of keystone ecological clusters (Module #1 and #2) and soil multifunctionality. Co-occurrence network analysis revealed that microbial inoculants reduced network complexity while increasing stability. Additionally, we found that stochastic processes played a predominant role in shaping bacterial and fungal communities, and the inoculants increased the stochastic ratio of microbial communities, particularly bacteria. Moreover, microbial inoculants significantly decreased the relative importance of dispersal limitations and increased the relative importance of drift. High relative abundances of certain bacterial and fungal phyla were identified as major drivers of the microbial community assembly process. In conclusion, our findings highlight the crucial role of mineral-solubilizing microorganisms in soil restoration at abandoned mining sites, shedding light on their significance in future research endeavors focused on optimizing the effectiveness of external soil spray seeding techniques.

Genetic diversity of culturable fungi associated with scleractinian corals in the Gulf of Thailand

Abstract Coral reefs are one of the most biodiverse marine ecosystems. Diverse microbes are associated with corals, including zooxanthellae, protists, prokaryotes, and viruses. This study aimed to investigate the genetic diversity of the culturable fungi associated with scleractinian corals in the Gulf of Thailand. Ribosomal DNA sequence analysis and morphological analysis of 130 fungal isolates revealed a high diversity of fungal phylotypes from three coral species: Pavona decussata, Pocillopora damicornis and Porites lutea. Ascomycota was the most abundant fungal phylum. The predominant orders included Eurotiales, Cladosporiales, Hypocreales, Mycosphaerellales, and Diaporthales. There were eight orders of the Basidiomycota dominated by Polyporales, Hymenochaetales, Agaricales, and Wallemiales. A principal component analysis was performed to compare abundance and correlation between the fungal communities, sampling locations and coral species. The results showed that the dissimilarity of fungal communities corresponded to geographic localities. On the other hand, there was a considerable overlap between the fungal communities of different coral species. The results from this research provide information on the diversity and ecology of the fungal communities associated with scleractinian corals in the Gulf of Thailand.

Response of Soil Microbial Communities and Functions to Long-Term Tea (Camellia sinensis L.) Planting in a Subtropical Region

Soil microbes are the key to revealing the mechanisms driving variation in soil biogeochemical processes. In recent decades, forests in Southeast China have been widely transformed into tea plantations due to the drivers of economic benefits. However, the changes in the soil microbial community and their potential function during the transition from a typical forest ecosystem to tea plantations remain poorly understood. This study investigated the soil microbial community in tea plantation soils with different planting ages, i.e., 6, 12, 23 and 35 years, and in an adjacent woodland control. We discovered that tea planting significantly increased soil bacterial richness (ACE and Chao1) and decreased fungal richness, the diversity of bacteria (Simpson and Shannon) show a trend of initially decreasing and then increasing while there was no significant effect on fungal diversity. After tea planting, the relative abundances of Actinobacteria and Proteobacteria increased by 180.9%–386.6% and 62.3%–97.5%, respectively; the relative abundances of Acidobacteria decreased by 11.4%–66.8%. However, the fungal phyla were not significantly different among different aged tea plantations and woodlands. FAPROTAX and FUNGuild revealed that the transition of natural woodland to tea plantations significantly increased the relative abundances of aerobic_chemoheterotrophy (14.66%–22.69%), chemoheterotrophy (34.36%–37.04%), ureolysis (0.68%–1.35%) and pathogenic fungi (26.17%–37.02%). db-RDA proved that the bacterial community structure was more strongly related to soil pH and available nitrogen (AN), while the main determinants of the fungal community composition were soil pH and soil organic matter (SOM). These findings indicate that tea planting has a strong effect on the soil microbial community and potential function. The change in soil pH during tea planting was the most important factor affecting the soil microbial community, while soil bacteria were more sensitive to tea planting than fungi.

Effect of peach trichome removal on post-harvest brown rot and on the fruit surface microbiome

Postharvest peaches undergo rapid soft ripening and are susceptible to fungal diseases, which often result in severe losses during storage. The peach epidermis contains trichomes that form a specific structure on the peach surface. However, the relationship between trichomes and postharvest disease and involved mechanisms has not been well studied. In this study, the removal of trichomes reduced the disease incidence of peach brown rot caused by Monilinia fructicola. Cryo-scanning electron microscope observations showed that the fungal hyphae were found attached to the surface of trichomes. The fungal and bacterial communities on the peach surface at 0 d and 6 d were obtained by amplicon sequencing technology. Fungal communities on the peach surface contained a total of 1089 amplicon sequence variants (ASVs), which were demarcated into eight fungal phyla, 25 classes, 66 orders, 137 families, and 228 genera. The bacterial communities contained 10,821 ASVs assigned to 25 phyla, 50 classes, 114 orders, 220 families, and 507 genera. Higher bacterial diversity than fungal diversity was recorded on the peach epidermis. Trichome removal changed the microbial diversity and community on the peach surface. Compared with peach epidermis samples, the peach epidermis excluded trichomes samples contained similar fungal alpha diversity but significantly lower bacterial diversity. Seventeen different fungal genera and twenty-eight different bacterial genera were identified between peach trichome and peach epidermis excluded trichomes samples. The fungal and bacterial diversity on the peach epidermis showed a decreasing trend during storage. Beta diversity analysis revealed that the microbial communities of the peach epidermis and trichomes show different change trends between 0 d and 6 d. Trichome removal decreased relative abundance of Monilinia spp. and increased relative abundance of potential yeast and bacterial biocontrol agents. This study suggested that trichomes might modulate the microbial communities on fruit surfaces, and trichome removal technology after harvest might be developed to control peach postharvest decay.

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina.

The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. Taxonomic novelties: New classes: Alloascoideomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Dipodascomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Lipomycetes M. Groenew., Hittinger, Opulente, A. Rokas, Pichiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Sporopachydermiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Trigonopsidomycetes M. Groenew., Hittinger, Opulente & A. Rokas. New orders: Alloascoideomycetes: Alloascoideales M. Groenew., Hittinger, Opulente & A. Rokas; Dipodascomycetes: Dipodascales M. Groenew., Hittinger, Opulente & A. Rokas; Lipomycetes: Lipomycetales M. Groenew., Hittinger, Opulente & A. Rokas; Pichiomycetes: Alaninales M. Groenew., Hittinger, Opulente & A. Rokas, Pichiales M. Groenew., Hittinger, Opulente & A. Rokas, Serinales M. Groenew., Hittinger, Opulente & A. Rokas; Saccharomycetes: Phaffomycetales M. Groenew., Hittinger, Opulente & A. Rokas, Saccharomycodales M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiomycetes: Sporopachydermiales M. Groenew., Hittinger, Opulente & A. Rokas; Trigonopsidomycetes: Trigonopsidales M. Groenew., Hittinger, Opulente & A. Rokas. New families: Alaninales: Pachysolenaceae M. Groenew., Hittinger, Opulente & A. Rokas; Pichiales: Pichiaceae M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiales: Sporopachydermiaceae M. Groenew., Hittinger, Opulente & A. Rokas. Citation: Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Čadež N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105: 1-22. doi: 10.3114/sim.2023.105.01 This study is dedicated to the memory of Cletus P. Kurtzman (1938-2017), a pioneer of yeast taxonomy.

Comparative analysis of gut fungal composition and structure of the yaks under different feeding models.

The yaks that inhabit the Tibetan plateau are a rare breed that is closely related to local economic development and human civilization. This ancient breed may have evolved a unique gut microbiota due to the hypoxic high-altitude environment. The gut microbiota is susceptible to external factors, but research regarding the effects of different feeding models on the gut fungal community in yaks remains scarce. In this study, we compared and analyzed the composition and variability of the gut fungal community among wild yaks (WYG), house-feeding domestic yaks (HFG), and grazing domestic yaks (GYG). The results revealed that Basidiomycota and Ascomycota were the most preponderant phyla in the gut fungal community, regardless of feeding models. Although the types of dominant fungal phyla did not change, their abundances did. Intergroup analysis of fungal diversity showed that the Shannon and Simpson indices of WYG and GYG were significantly higher than those of HFG. Fungal taxonomic analysis showed that there were 20 genera (Sclerostagonospora and Didymella) that were significantly different between WYG and GYG, and 16 genera (Thelebolus and Cystobasidium) that were significantly different between the WYG and HFG. Furthermore, the proportions of 14 genera (Claussenomyces and Papiliotrema) significantly decreased, whereas the proportions of eight genera (Stropharia and Lichtheimia) significantly increased in HFG as compared to GYG. Taken together, this study indicated that the gut fungal composition and structure differ significantly between yaks raised in different breeding groups.

The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties.

Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.

Nutrient availability and acid erosion determine the early colonization of limestone by lithobiontic microorganisms.

Microorganisms, including the pioneer microorganisms that play a role in the early colonization of rock, are extremely important biological factors in rock deterioration. The interaction of microorganisms with limestone leads to biodeterioration, accelerates soil formation, and plays an important role in the restoration of degraded ecosystems that cannot be ignored. However, the process of microbial colonization of sterile limestone in the early stages of ecological succession is unclear, as are the factors that affect the colonization. Acid erosion (both organic and inorganic), nutrient availability, and water availability are thought to be key factors affecting the colonization of lithobiontic microorganisms. In this study, organic acid (Oa), inorganic acid (Ia), inorganic acid + nutrient solution (Ia + Nut), nutrient solution (Nut), and rain shade (RS) treatments were applied to sterilized limestone, and the interaction between microorganisms and limestone was investigated using high-throughput sequencing techniques to assess the microorganisms on the limestone after 60 days of natural placement. The results were as follows: (1) The abundance of fungi was higher than that of bacteria in the early colonization of limestone, and the dominant bacterial phyla were Proteobacteria, Bacteroidota, and Actinobacteriota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Chytridiomycota. (2) Acid erosion and nutrient availability shaped different microbial communities in different ways, with bacteria being more sensitive to the environmental stresses than fungi, and the higher the acidity (Ia and Oa)/nutrient concentration, the greater the differences in microbial communities compared to the control (based on principal coordinate analysis). (3) Fungal communities were highly resistant to environmental stress and competitive, while bacterial communities were highly resilient to environmental stress and stable. In conclusion, our results indicate that limestone exhibits high bioreceptivity and can be rapidly colonized by microorganisms within 60 days in its natural environment, and both nutrient availability and acid erosion of limestone are important determinants of early microbial colonization.

Natural restoration alters soil microbial community structure, but has contrasting effects on the diversity of bacterial and fungal assemblages in salinized grasslands

Natural restoration has often been considered an effective measure for rehabilitating degraded ecosystems. However, its impact on the structure and diversity of soil microbial communities, particularly within a salinized grassland during its restoration succession, remains unclear. In this study, we examined the effects of natural restoration on the Shannon-Wiener diversity index, Operational Taxonomic Units (OTU) richness, and structure of the soil microbial community of a sodic-saline grassland in China using high-throughput amplicon sequencing data from representative successional chronosequences. Our results indicated that natural restoration resulted in a significant mitigation of the grassland salinization (pH from 9.31 to 8.32 and electrical conductivity from 393.33 to 136.67 μs·cm−1) and a significant alteration of the soil microbial community structure of the grassland (p < 0.01). However, the effects of natural recovery differed in terms of the abundance and diversity of bacteria and fungi. For example, the relative abundance of the bacterial phyla Acidobacteria increased by 116.45 % in the topsoil and 339.03 % in the subsoil, while that of the fungal phyla Ascomycota decreased by 8.86 % in the topsoil and 30.18 % in the subsoil. There was no significant effect of restoration on bacterial diversity, but fungal diversity increased by 15.02 % in the Shannon-Wiener index and 62.20 % in the OTU richness in the topsoil. Model-selection analysis further corroborated that the alteration of the soil microbial structure by natural restoration may be due to the fact that the bacteria could adapt to the alleviated salinized grassland soil and the fungi could adapt to the improved soil fertility of the grasslands. Overall, our results contribute to an in-depth understanding of the impacts of natural restoration on soil microbial diversity and community structure in salinized grasslands during the long-term successional course. This may also help to apply natural restoration as a greener practice option for managing degraded ecosystems.

Variations in soil microbial community structure and extracellular enzymatic activities along a forest-wetland ecotone in high-latitude permafrost regions.

Permafrost degradation by global warming is expected to alter the hydrological processes, which results in changes in vegetation species composition and gives rise to community succession. Ecotones are sensitive transition areas between ecosystem boundaries, attract particular interest due to their ecological importance and prompt responses to the environmental variables. However, the characteristics of soil microbial communities and extracellular enzymes along the forest-wetland ecotone in high-latitude permafrost region remain poorly understood. In this study, we evaluated the variations of soil bacterial and fungal community structures and soil extracellular enzymatic activities of 0-10 cm and 10-20 cm soil layers in five different wetland types along environmental gradients, including Larix gmelinii swamp (LY), Betula platyphylla swamp (BH), Alnus sibirica var. hirsute swamp (MCY), thicket swamp (GC), and tussock swamp (CC). The relative abundances of some dominant bacterial (Actinobacteria and Verrucomicrobia) and fungal (Ascomycota and Basidiomycota) phyla differed significantly among different wetlands, while bacterial and fungal alpha diversity was not strongly affected by soil depth. PCoA results showed that vegetation type, rather than soil depth explained more variation of soil microbial community structure. β-glucosidase and β-N-acetylglucosaminidase activities were significantly lower in GC and CC than in LY, BH, and MCY, while acid phosphatase activity was significantly higher in BH and GC than LY and CC. Altogether, the data suggest that soil moisture content (SMC) was the most important environmental factor contributing to the bacterial and fungal communities, while extracellular enzymatic activities were closely related to soil total organic carbon (TOC), nitrate nitrogen () and total phosphorus (TP).

Variations in litter-soil properties between planted and naturally restored forests drive microbial community structure and function

How forest restoration can affect soil microbial composition and functionality remains unclear, limiting our ability to evaluate restoration approaches. Here, we used metagenomes, 16S rRNA, and ITS gene sequencing to distinguish the composition and functional attributes of soil microbial communities between plantation forest of Pinus massoniana (PF) and naturally restored secondary forest (SF) in their organic horizon and mineral soil from a typical karst region in Southwest China. Our results showed that fungal communities differed more than bacterial communities between PF and SF, while the differences in archaeal communities were not significant. The most abundant fungal phylum in both mineral soil and organic horizon was Ascomycota at SF and Basidiomycota at PF, respectively. The PF soil had lower nitrogen (N) cycling gene abundance and lower inorganic N availability compared to SF soil probably because of the poor soil and lower litter quality. The SF soil had higher abundances of genes associated with labile carbon (C) (i.e., starch, hemicellulose, cellulose, pectin, and chitin) degradation compared with PF soil, but lower abundances of genes responsible for recalcitrant C (i.e., lignin and aromatics) degradation, which was strongly correlated with the litter properties. Simultaneous effects of soil and litter variables explained >50 % of the variation in microbial community structure and functional gene composition; soil nitrate-N had the strongest effect on the soil bacterial and fungal community structure. Our results highlight the superiority of naturally restored secondary forests for improving both soil fertility and soil microbial-mediated C and N cycling functions, which can support forest managers in selecting forest restoration approaches that optimize C and N storage in forest stands.

Poplar Sawdust Biochar Altered Community Composition of Dominant Soil Fungi but Not Bacteria Depending on Pyrolysis Temperature

There is a growing focus on the production of biochar from organic wastes and its forestry use. However, it is unclear how applying biochar pyrolyzed at different temperatures influences both soil bacterial and fungal communities. In this study, two kinds of biochar were pyrolyzed at 350 °C and 600 °C, from poplar sawdust, and then applied as an auxiliary substrate material (15% addition by volume) for the container seedling cultivation of Cyclocarya paliurus, a native timber and medically used tree species, to compare the response of the soil’s microbial traits. The results showed that after 5 months of cultivation, the addition of the biochar application improved the soil’s physical and chemical properties to a certain extent by decreasing its bulk density and increasing its field water-holding capacity, pH and organic carbon content. The soil’s pH and content of organic C, available N and available P were significantly higher in the substrate with the addition of the biochar pyrolyzed at 600 °C (Bioc600) than in that of the substrate with added pyrolyzed biochar at 350 °C (Bioc350). The biochar application also enhanced the soil’s microbial N (MBN) but showed no changes in the MBC/MBN ratio. The biochar application had no effect on the diversity and composition of the soil’s bacterial community, but showed a certain effect on its fungal community composition and had different influences between low and high pyrolysis temperatures. The relative abundance of several of the dominant fungal phyla and genera increased with the addition of biochar due to the increase in the soil’s pH when compared to the CK (no biochar or sawdust addition). When compared with Bioc350, the dominant phylum Basidiomycota and genus Vanrija further increased in abundance with Bioc600. These findings reveal the consistent effects of biochar pyrolysis temperature and demonstrate the different regulatory roles of biochar application in soil bacterial and fungal communities, providing valuable information on how biochar can effectively be used as a substrate for seedling cultivation.

Effects of plastic film mulching and legume rotation on soil nutrients and microbial communities in the Loess Plateau of China

BackgroundPotato (Solanum tuberosum L.) continuous cropping causes the decrease of tuber yield, deterioration of quality and soil degradation in the semi-arid area. These negative effects can generally be mitigated by legume rotation and mulching. However, little is known about how can mulching and legume rotation alleviate the above damage through altering soil environment.MethodsA field experiment was conducted to investigate changes in soil properties and microbial community in response to legume rotation and mulching under six planting patterns: potato continuous cropping without film mulching (PC), potato continuous cropping with film mulching (PCF), potato–broad bean rotation without film mulching (R1), potato–broad bean rotation with film mulching (R1F), potato–pea rotation without film mulching (R2) and potato–pea rotation with film mulching (R2F).ResultsCompared with the PC, the R1F and R2F had significantly enhanced the contents of alkaline nitrogen (AN), available phosphorus (AP), available potassium (AK), total carbon (TC) and total nitrogen (TN), but reduced soil pH and electrical conductivity (EC). The Shannon index of fungi in R1F and R2 was significantly higher than other treatments. The dominant bacterial and fungal phyla of each treatment was Proteobacteria and Ascomycota. R1, R1F, R2 and R2F enhanced the relative abundance of metabolic fungi and altered key differential microbial species. Soil EC, AN and AK were major factors influencing the soil bacterial and fungal communities.ConclusionOverall, the study demonstrated that potato-broad bean/pea rotation with mulching can be adopted as the preferred cropping systems to alleviate potato continuous cropping obstacles through enhancing soil fertility and regulating soil microbial communities in the semi-arid of Loess Plateau, China.Graphical