Composition, functional, and niche differentiation of fungal communities in the rhizosphere and root endosphere of Cinnamomum migao in southwestern China.

AIMS: Roots are key parts of plant material circulation and energy flow, creating two distinct niches for the plant microbiome, such as the rhizosphere and root endosphere, which interact to maintain plant growth and health. In this study, two niches of plant rhizosphere and root endosphere were selected to study the composition and differences of fungi communities in order to better understand how differences in the structure and function of plant fungi communities affect plant health. METHODS AND RESULTS: The community structure, diversity, and ecological function of fungi in the rhizosphere and root endosphere of Cinnamomum migao were studied using high-throughput sequencing techniques, traditional culture methods, and the FUNGuild database. The results of the analysis of alpha diversity showed that the diversity of rhizosphere fungal communities in C. migao was much higher than that of root endosphere communities. Some similarities and differences were noted between the two niche fungal communities, and some fungi had niche preferences. Functional prediction results demonstrated that fungi in the rhizosphere and root endosphere adopt multiple trophic modes, mostly saprophytic fungi. CONCLUSIONS: This study provided a basis for an in-depth understanding of the structural variation, niche differentiation, and function of plant root-related fungal microbiota. We believe that it could provide guidance on the subsequent development of beneficial fungi.

Effects of the polyhalogenated carbazoles 3-bromocarbazole and 1,3,6,8-tetrabromocarbazole on soil microbial communities.

Soil ecosystems are being more contaminated with polyhalogenated carbazoles (PHCZs), which raising much attention about their impact on soil microorganisms. 3-Bromocarbazole (3-BCZ) and 1,3,6,8-tetrabromocarbazole (1,3,6,8-TBCZ) are two typical PHCZs with high detection rates in the soil environment. However, ecological risk research on these two PHCZs in soil is still lacking. In the present study, after 80 days of exposure, the ecological influence of 3-BCZ and 1,3,6,8-TBCZ was investigated based on 16S rDNA sequencing, ITS sequencing, gene (16S rDNA, ITS, amoA, nifH, narG and cbbL) abundance and soil enzyme activity. The results showed that the bacterial 16S rDNA gene abundance significantly decreased under 3-BCZ and 1,3,6,8-TBCZ exposure after 80 days of incubation. The fungal ITS gene abundance significantly decreased under 1,3,6,8-TBCZ (10 mg/kg) exposure. PHCZs contributed to the alteration of bacteria and fungi community abundance. Bacteria Sphingomonas, RB41 and fungus Mortierella, Cercophora were identified as the most dominant genera. The two PHCZs consistently decreased the relative abundance of Sphingomonas, Lysobacter, Dokdonella, Mortierella and Cercophora etc at 80th day. These keystone taxa are related to the degradation of organic compounds, carbon metabolism, and nitrogen metabolism and may thus have influence on soil ecological functions. Bacterial and fungal functions were estimated using functional annotation of prokaryotic taxa (FAPROTAX) and fungi functional guild (FUNGuild), respectively. The nitrogen and carbon metabolism pathway were affected by 3-BCZ and 1,3,6,8-TBCZ. The soil nitrogen-related functions of aerobic ammonia oxidation were decreased but the soil carbon-related functions of methanol oxidation, fermentation, and hydrocarbon degradation were increased at 80th day. The effects of 3-BCZ and 1,3,6,8-TBCZ on the abundances of the amoA, nifH, narG, and cbbL genes showed a negative trend. These results elucidate the ecological effects of PHCZs and extend our knowledge on the structure and function of soil microorganisms in PHCZ-contaminated ecosystems.

Changes in fungal community during different phases in conventional and bioreactor composting systems according to metatranscriptomics analysis.

We determined the changes that occurred in fungal community structures and their functions in conventional and bioreactor composting systems. The Illumina MiSeq platform was employed to sequence cDNA by reverse transcription to conduct metatranscriptomics analysis of RNA, and the FUNGuild tool was applied. The α-diversity of fungi in the bioreactor composter increased throughout composting, especially in the initial three phases, but decreased in the conventional composting system. The three dominant phyla in the bioreactor system were Ascomycota (30.27%-68.50%), Mortierellomycota (3.81%-39.51%), and Basidiomycota (9.17%-30.86%). Ascomycota (76.96%-97.18%) was the main phylum in the conventional composting system. Mortierella, Guehomyces, Plectosphaerella, Chaetomium, Millerozyma, and Coprinopsis were the main genera in the bioreactor composter. In the same phase, significant differences in the fungal functions were found between the two composting methods. Available phosphorus was the main factor that affected the community structures and functions of fungi in the bioreactor composter.

Soil nutrients shape the composition and function of fungal communities in abandoned ancient rice terraces.

In recent decades, terraces abandonment has been prevalent in the hilly areas of China. Soil fungi play an important role in clarifying soil ecosystematic feedback after ancient rice terraces abandonment, but how their community composition and function shift remains unclear. Soil profiles of 0-120 cm were excavated in ancient rice terraces, dry land, and forest land (formed from ancient rice terraces abandonment), respectively. The 13C NMR and high-throughput sequencing were used to determine soil organic carbon chemical groups and fungal community, respectively, and FUNGuild was used to predict functional groups. The results showed that the soil fungal community changed from Ascomycota to Basidiomycota after ancient rice terraces abandonment. The trophic modes of dry land and forest land were transformed into pathotrophic fungi and symbiotrophic fungi, respectively. The number of nodes and edges of fungal co-occurrence networks increased by 83.8% and 644.1% in dry land, and 81.3% and 431.2% in forest land, respectively. Moreover, soil nutrients (especially DOC, TN, and TP) can more affected the variation of fungal community composition and function than soil organic carbon chemical groups. These findings indicate that soil fungal community shifts in different directions in response to ancient rice terraces abandonment, which is related to the adaptive strategies for environmental changes and may be more conducive to the acquisition and turnover of soil nutrients.

Dynamic changes in rhizosphere fungi in different developmental stages of wheat in a confined and isolated environment.

As the core food crop of a bioregenerative life support system (BLSS), wheat is susceptible to pathogen infection due to the lack of effective microbial communities in the confined and isolated environment. Therefore, a thorough understanding of the dynamic changes in wheat rhizosphere fungi is of great significance for improving wheat production and ensuring the stability of the BLSS. In the current study, we collected samples of rhizosphere fungi in the four growth stages of wheat grown in the "Lunar Palace 365" experiment. We employed bioinformatics methods to analyze the samples' species composition characteristics, community network characteristics, and FUNGuild function analysis. We found that the species composition of rhizosphere fungi in the wheat at the tillering stage changed greatly in the closed and isolated environment, while the species composition in the seedling, flowering, and mature stage were relatively stable. The results of the FUNGuild function analysis showed that the functions of rhizosphere fungi changed during wheat development. The rhizosphere fungal community was centered on Ascomycota, Mortierellomycota, and Chytridiomycota, and the community showed the characteristics of a "small world" arrangement. The stage of wheat seedlings is characterized by a greater abundance, diversity, and complexity of the network of interactions in the rhizosphere mycorrhiza community, while the tillering stage exhibited a greater clustering coefficient. Based on the changes in species composition, guild function regulation, and community structure differences of the wheat rhizosphere fungi in the BLSS, our study identified the critical fungal species during wheat development, providing a reference for ensuring the health and yield of plants in the BLSS system. KEY POINTS: • The diversity, composition, FUNguild, and network structure of rhizosphere fungi were analyzed. • Ascomycota, Mortierellomycota, and Chytridiomycota were the center of the rhizosphere fungal community network. • The effects of different wheat developmental stages on the community composition, function, and network structure of rhizosphere fungi were examined.

Straw retention efficiently improves fungal communities and functions in the fallow ecosystem.

BACKGROUND: Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields. RESULT: The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity. CONCLUSIONS: Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.

Miscanthus cultivation shapes rhizosphere microbial community structure and function as assessed by Illumina MiSeq sequencing combined with PICRUSt and FUNGUIld analyses.

Soil microbes play important roles in plant growth and in the biogeochemical cycling of earth's elements. However, the structure and functions of the microbial community associated with the growth of second-generation energy crops, such as Miscanthus, remain unclear. Thus, in this study, the composition and function of the bacterial and fungal communities associated with Miscanthus cultivation were analyzed by MiSeq sequencing combined with PICRUSt and FUNGUIld analyses. The results of community composition and diversity index analyses showed that Miscanthus cultivation significantly altered the bacterial and fungal community composition and reduced bacterial and fungal diversity. In addition, Miscanthus cultivation increased the soil organic matter (SOM) and total nitrogen (TN) contents. The correlation analysis between microbial community composition and environmental factors indicated that SOM and TN were the most important factors affecting bacterial and fungal communities. Miscanthus cultivation could enrich the abundances of Pseudomonas, Rhizobium, Luteibacter, Bradyrhizobium, Phenylobacterium and other common plant-promoting bacteria, while also increasing Cladophialophora, Hymenula, Magnaporthe, Mariannaea, etc., which predicted corresponded to the saprotrophic, plant pathogenic, and pathotrophic trophic modes. The PICRUSt predictive analysis indicated that Miscanthus cultivation altered the metabolic capabilities of bacterial communities, including the metabolism of carbon, nitrogen, and phosphorus cycle. In addition, FUNGUIld analysis indicated that Miscanthus cultivation altered the fungal trophic mode. The effects of Miscanthus on the communities and function of bacteria and fungi varied among Miscanthus species. Miscanthus specie Xiangdi NO 1 had the greatest impact on soil bacterial and fungal communities, whereas Miscanthus specie Wujiemang NO 1 had the greatest impact on soil bacteria and fungi functions. The results of this study provide a reference for the composition and function of microbial communities during the growth of Miscanthus.

Changes in structure and function of bacterial and fungal communities in open composting of Chinese herb residues.

In this study, dynamic changes in bacterial and fungal communities, metabolic characteristics, and trophic modes in Chinese herb residues open composting for 30 days were analyzed by using high-throughput sequencing, PICRUSt, and FUNGuild, respectively. Bacillaceae and Basidiomycota predominated at the early composting stage, while Proteobacteria and Ascomycota became the dominant phyla during the active phase. Aerobic composting had a significant effect on bacterial metabolic characteristics and fungal trophic modes over the composting time. The function of the bacterial communities changed from environmental information processing to metabolism. Fungal communities changed as well, with the pathogenic fungi decreasing and wood saprotrophs increasing. These results indicated that open composting of Chinese herb residues not only influenced microbial community structure but also changed metabolic characteristics and trophic modes, which became the internal dynamics of composting.

Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests.

Subtropical broadleaved forests play a crucial role in supporting terrestrial ecosystem functions, but little is known about their belowground soil fungal communities despite that they have central functions in C, N, and P cycles. This study investigated the structures and identified the drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests, using high-throughput sequencing and FUNGuild for fungal identification and assignment to the trophic guild. Fungal richness was much higher in the deciduous than in the evergreen forest. Both forests were dominated by Ascomycota and Basidiomycota phyla, but saprophytic fungi were more abundant in the deciduous forest and ectomycorrhizal fungi predominated in the evergreen forest. Fungal communities had strong links to plant and soil properties. Specifically, plant diversity and litter biomass were the main aboveground drivers of fungal diversity and composition in the deciduous forest, while host effects were prominent in the evergreen forest. The belowground factors, i.e., soil pH, water content, and nutrients especially available P, were identified as the primary drivers of soil fungal communities in the broadleaved forests. Co-occurrence network analysis revealed assembly of fungal composition in broadleaved forest soils was non-random. The smaller modularity of the network in the deciduous forest reflects lower resistance to environment changes. Concluding, these results showed that plant community attributes, soil properties, and potential interactions among fungal functional guilds operate jointly on the divergence of soil fungal community assembly in the two broadleaved forest types.

Effects of micro-/nano-hydroxyapatite and phytoremediation on fungal community structure in copper contaminated soil.

Micro-/nano-hydroxyapatite (MHA/NHA) has been used to reduce the concentration of available heavy metals and increase soil pH in the remediation of heavy metal-contaminated soils. However, little is known about the effects of MHA and NHA on soil fungal communities and function. In this study, fungal community composition was characterized from copper-contaminated soils amended with MHA, NHA and three other classic amendments combined with Elsholtzia splendens during a 3-year immobilization experiment. High-throughput sequencing results showed that applications of MHA increased the richness and diversity of the fungal community, which was opposite the results of NHA. SIMPER analysis indicated that both the relative abundance of fungi associated with biosorption and plant growth promotion increased, whereas the relative abundance of fungi related to bioleaching and potential pathogens decreased after applying MHA. Redundancy (RDA) analysis revealed that the soil pH was a crucial environmental factor in the succession of fungal communities. In addition, the results of functional prediction via FUNGuild suggested that the application of MHA had the potential to reduce the risk of pathogens infecting animals and plants in the soil but that NHA had some environmental risks. Overall, fungal community showed a synergistic effect of immobilization with the test amendments, and MHA was better for the remediation of heavy metal-contaminated soils than the other test amendments.

Exploiting community structure, interactions and functional characteristics of fungi involved in the biodrying of storage sludge and beer lees.

In this study, the dynamic changes in fungal biodiversity, community structure, fungal associations and functional characteristics were investigated in the biodrying of storage sludge and beer lees by using high throughput sequencing, network and correlation matrix analyses, and FUNGuild database. Additionally, a hypothetical model was provided to better understand the biodrying system. The results showed that fungal diversity decreased after biodrying, while community richness increased in the mesophilic stage and decreased as biodrying progressed. Fungal communities differed in different stages of the biodrying process. Ascomycota and Basidiomycota were the dominant phyla throughout the biodrying process, while Pichia was the dominant genus in the thermophilic stage. Network and correlation matrix analyses provided useful tools for insight into the fungal interactions, allowing us to propose a conceptual model of how succession in fungal associations regulates the dynamics of biodrying systems. Biodrying treatment had a significant effect on fungal trophic modes, with most pathogenic fungi fading away over the process, illustrating that biodrying is an effective bio-treatment method to eliminate pathogenic fungi. These findings provide information that elucidates the fungal interactions and functional characteristics during the biodrying process.

Interguild fungal competition in litter and soil inversely modulate microbial necromass accumulation during Loess Plateau forest succession.

Microbial interactions determine ecosystem carbon (C) and nutrient cycling, yet it remains unclear how interguild fungal interactions modulate microbial residue contribution to soil C pools (SOC) during forest succession. Here, we present a region-wide investigation of the relative dominance of saprophytic versus symbiotic fungi in litter and soil compartments, exploring their linkages to soil microbial residue pools and potential drivers along a chronosequence of secondary Chinese pine (Pinus tabulaeformis) forests on the Loess Plateau. Despite minor changes in C and nitrogen (N) stocks in the litter or soil layers across successional stages, we found significantly lower soil phosphorus (P) stocks, higher ratios of soil C: N, soil N: P and soil C: P but lower ratios of litter C: N and litter C: P in old (>75 years) than young stands (<30 years). Pine stand development altered the saprotroph: symbiotroph ratios of fungal communities to favor the soil symbiotrophs versus the litter saprotrophs. The dominance of saprotrophs in litter is positively related to microbial necromass contribution to SOC, which is negatively related to the dominance of symbiotrophs in soils. Antagonistic interguild fungal competition in litter and soil layers, in conjunction with increased fungal but decreased bacterial necromass contribution to SOC, jointly contribute to unchanged total necromass contribution to SOC with stand development. The saprotroph: symbiotroph ratios in litter and soil layers are mainly driven by soil P stocks and stand parameters (e.g., stand age and slope), respectively, while substrate stoichiometries primarily regulate microbial necromass accumulation and fungal: bacterial necromass ratios. These results provide novel insights into how microbial interactions at local spatial scales modulate temporal changes in SOC pools, with management implications for mitigating regional land degradation.

Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact.

BACKGROUND: Soil microorganisms play an extensive role in the biogeochemical cycles providing the nutrients necessary for plant growth. Root-associated bacteria and fungi, originated from soil, are also known to influence host health. In response to environmental stresses, the plant roots exude specific molecules influencing the composition and functioning of the rhizospheric and root microbiomes. This response is host genotype-dependent and is affected by the soil microbiological and chemical properties. It is essential to unravel the influence of grapevine rootstock and scion genotypes on the composition of this microbiome, and to investigate this relationship with plant growth and adaptation to its environment. Here, the composition and the predicted functions of the microbiome of the root system were studied using metabarcoding on ten grapevine scion-rootstock combinations, in addition to plant growth and nutrition measurements. RESULTS: The rootstock genotype significantly influenced the diversity and the structure of the bacterial and fungal microbiome, as well as its predicted functioning in rhizosphere and root compartments when grafted with the same scion cultivar. Based on ß-diversity analyses, 1103P rootstock showed distinct bacterial and fungal communities compared to the five others (RGM, SO4, 41B, 3309 C and Nemadex). The influence of the scion genotype was more variable depending on the community and the investigated compartment. Its contribution was primarily observed on the ß-diversity measured for bacteria and fungi in both root system compartments, as well as for the arbuscular mycorrhizal fungi (AMF) in the rhizosphere. Significant correlations were established between microbial variables and the plant phenotype, as well as with the plant mineral status measured in the petioles and the roots. CONCLUSION: These results shed light on the capacity of grapevine rootstock and scion genotypes to recruit different functional communities of microorganisms, which affect host growth and adaptation to the environment. Selecting rootstocks capable of associating with positive symbiotic microorganisms is an adaptation tool that can facilitate the move towards sustainable viticulture and help cope with environmental constraints.

Degradation of betaine aldehyde dehydrogenase transgenic maize BZ-136 straw and its effects on soil nutrients and fungal community.

The development of salt-alkali tolerant genetically modified crops represents an important approach to increase grain production in saline-alkali soils. However, there is a paucity of research on the impact of such genetically modified crops on soil microbial diversity. This study aims to investigate the straw degradation of betaine aldehyde dehydrogenase (BADH) transgenic maize BZ-136 and its effects on soil chemical properties, fungal community composition, community diversity and ecological function compared to non-transgenic maize Zheng58 straw. The degradation experiments of BZ-136 straw were carried out under a simulated burying condition with saline-alkali soil for 210 days. The results showed that the degradation rate of C and N of BZ-136 straw was significantly faster than that of Zheng58 in the early stage (p < 0.05). Compared to Zheng58, the straw degradation of BZ-136 increased the soil available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) in the early stage (p < 0.05). The AN content of soil with BZ-136 straw was 18.16 and 12.86% higher than that of soil with Zheng58 at day 60 and 120 (p < 0.05). The TP content of soil with BZ-136 was higher 20.9 and 20.59% than that with Zheng58 at day 30 and 90 (p < 0.05). The AP content of soil with BZ-136 was 53.44% higher than that with Zheng58 at day 60 (p < 0.05). The straw degradation of BZ-136 increased the OTU number of soil fungal community by 127 (p < 0.05) at day 60, and increased Chao1 and Shannon index at day 60 and 180 (p < 0.05). The degradation rate of C and N in BZ-136 straw was higher than that in Zheng58 at early stage, which led to the phased increase of soil AN and TP contents, and the obvious changes of relative abundances (RA) of some genera and guilds. These findings are important as they provide insight into the potential benefits of BADH transgenic crops in upgrading the soil fertility and the fungal community diversity.

Soil fungal community characteristics vary with bamboo varieties and soil compartments.

Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal α diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not affected by bamboo variety or interactions between the soil compartment and bamboo variety. Soil compartment and bamboo variety together explained 31.74% of the variation in fungal community diversity. Soil compartment and bamboo variety were the key factors affecting the relative abundance of the major fungal taxa at the phylum and genus levels. Soil compartment mainly affected the relative abundance of the dominant fungal phylum, while bamboo variety primarily influenced the dominant fungal genus. Network analysis showed that the fungal network in rhizosphere soil was more complex, stable, and connected than that in bulk soil. A FUNGuild database analysis indicated that both soil compartment and bamboo variety affect fungal functions. Our findings provide new insights into the roles of both soil compartments and plant species (including variety) in shaping soil fungal communities.

Effects of micro-positive pressure environment on nitrogen conservation and humification enhancement during functional membrane-covered aerobic composting.

Aerobic composting is a humification process accompanied by nitrogen loss. This study is the first research systematically investigating and elucidating the mechanism by which functional membrane-covered aerobic composting (FMCAC) reduces nitrogen loss and enhances humification. The variations in bioavailable organic nitrogen (BON) and humic substances (HSs) in different composting systems were quantitatively studied, and the functional succession patterns of fungal groups were determined by high-throughput sequencing and FUNGuild. The FMCAC improved oxygen utilization and pile temperature, increased BON by 29.95 %, reduced nitrogen loss by 34.00 %, and enhanced humification by 26.09 %. Meanwhile, the FMCAC increased the competitive advantage of undefined saprotroph and significantly reduced potential pathogenic fungi (<0.10 %). Structural equation modeling indicated that undefined saprotroph facilitated the humification process by increasing the production of BON and storing BON in stable humic acid. Overall, the FMCAC increased the safety, stability, and quality of the final compost product.

Endophytic Fungal and Bacterial Microbiota Shift in Rice and Barnyardgrass Grown under Co-Culture Condition.

Although barnyardgrass (Echinochloa crus-galli L.) is more competitive than rice (Oryza sativa L.) in the aboveground part, little is known about whether barnyardgrass is still competitive in recruiting endophytes and the root microbiota composition variation of rice under the barnyardgrass stress. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during co-planted barnyardgrass stress and a comparison with the microbiomes of unplanted soil, we found that the bacterial community diversity of rice was dramatically higher while the fungal community richness was significantly lower than that of barnyardgrass at BBCH 45 and 57. More importantly, rice recruited more endophytic bacteria at BBCH 45 and 57, and more endophytic fungi at BBCH 17, 24, 37 to aginst the biotic stress from barnyardgrass. Principal coordinates analysis (PCoA) showed that rice and barnyardgrass had different community compositions of endophytic bacteria and fungi in roots. The PICRUSt predictive analysis indicated that majority of metabolic pathways of bacteria were overrepresented in barnyardgrass. However, eleven pathways were significantly presented in rice. In addition, rice and barnyardgrass harbored different fungal trophic modes using FUNGuild analysis. A negative correlation between bacteria and fungi in rice and barnyardgrass roots was found via network analysis. Actinobacteria was the vital bacteria in rice, while Proteobacteria dominated in barnyardgrass, and Ascomycota was the vital fungi in each species. These findings provided data and a theoretical basis for the in-depth understanding of the competition of barnyardgrass and endophytes and have implications relevant to weed prevention and control strategies using root microbiota.

Composition and Ecological Functionality of Fungal Communities Associated with Smokeless Tobacco Products Mainly Consumed in India.

The microbial communities present in smokeless tobacco products (STPs) perform critical steps in the synthesis of carcinogens, mainly tobacco-specific nitrosamines (TSNAs). Most studies emphasize the bacterial component, and the mycobiome of STPs has not been well characterized. In this study, we investigated the fungal communities in the different categories of STPs by sequencing the internal transcribed spacer (ITS) rRNA region of the fungal genome. The ecological character of the fungal community associated with STPs was determined by using FUNGuild. Our results indicated that Ascomycota and Basidiomycota were the most abundant fungal phyla across all STPs. The predominant fungal genera in STPs were Pichia, Sterigmatomyces, and Mortierella. The α-diversity varied significantly across the STPs based on observed, Fisher, and Shannon indices. Using SparCC cooccurrence network analysis, significant positive correlations of 58.5% and negative connections of 41.5% were obtained among fungal genera identified in STPs. Furthermore, the functional predictions by FUNGuild determined that STPs possessed high abundances of saprotroph and pathotroph-saprotroph-symbiotroph fungal trophic groups. At the functional guild level, the qiwam samples contained high abundances of soil saprotrophs, while plant pathogens were prevalent in pan-masala samples. These results suggest that various fungal populations reside in STPs and interrelate with each other and can contribute to the synthesis of TSNAs. This study has established the basis for future large-scale investigations of STP-associated mycobiota and the impact of such mycobiota in oral carcinogenesis in STP users via inflammation and carcinogens (TSNAs and mycotoxins). IMPORTANCE Smokeless tobacco products (STPs) contain complex microbial communities that influence the synthesis of carcinogens, such as tobacco-specific nitrosamines (TSNAs). Research on STP-associated bacterial populations revealed connections between bacterial metabolism and TSNA synthesis. The abundance of the fungal population may also have an impact on the production of TSNAs. This study examined STPs popularly used in India, and diverse fungal communities were identified in these STPs. Pichia, Sterigmatomyces, and Mortierella were the predominant fungal genera in the STPs. High abundances of saprotroph and pathotroph-saprotroph-symbiotroph trophic groups in STPs could affect the degradation of tobacco products and the synthesis of TSNAs.

Responses of soil fungal communities and functional guilds to ~160 years of natural revegetation in the Loess Plateau of China.

Natural revegetation has been widely confirmed to be an effective strategy for the restoration of degraded lands, particularly in terms of rehabilitating ecosystem productivity and soil nutrients. Yet the mechanisms of how natural revegetation influences the variabilities and drivers of soil residing fungal communities, and its downstream effects on ecosystem nutrient cycling are not well understood. For this study, we investigated changes in soil fungal communities along with ~160 years of natural revegetation in the Loess Plateau of China, employing Illumina MiSeq DNA sequencing analyses. Our results revealed that the soil fungal abundance was greatly enhanced during the later stages of revegetation. As revegetation progresses, soil fungal richness appeared first to rise and then decline at the climax Quercus liaotungensis forest stage. The fungal Shannon and Simpson diversity indexes were the lowest and highest at the climax forest stage among revegetation stages, respectively. Principal component analysis, Bray-Curtis similarity indices, and FUNGuild function prediction suggested that the composition, trophic modes, and functional groups for soil fungal communities gradually shifted along with natural revegetation. Specifically, the relative abundances of Basidiomycota, Agaricomycetes, Eurotiomycetes, and ectomycorrhizal fungi progressively increased, while that of Ascomycota, Sordariomycetes, Dothideomycetes, Tremellomycetes, saprotrophic, pathotrophic, arbuscular mycorrhizal fungi, and endophyte fungi gradually decreased along with natural revegetation, respectively. The most enriched members of Basidiomycota (e.g., Agaricomycetes, Agaricales, Cortinariaceae, Cortinarius, Sebacinales, Sebacinaceae, Tricholomataceae, Tricholoma, Russulales, and Russulaceae) were found at the climax forest stage. As important carbon (C) sources, the most enriched symbiotic fungi (particularly ectomycorrhizal fungi containing more recalcitrant compounds) can promote organic C and nitrogen (N) accumulation in soils of climax forest. However, the most abundant of saprotrophic fungi in the early stages of revegetation decreased soil organic C and N accumulation by expediting the decomposition of soil organic matter. Our results suggest that natural revegetation can effectively restore soil fungal abundance, and modify soil fungal diversity, community composition, trophic modes, and functional groups by altering plant properties (e.g., plant species richness, diversity, evenness, litter quantity and quality), quantity and quality of soil nutrient substrates, soil moisture and pH. These changes in soil fungal communities, particularly their trophic modes and functional groups along with natural revegetation, impact the accumulation and decomposition of soil C and N and potentially affect ecosystem C and N cycling in the Loess Plateau of China.

Fungal community succession contributes to product maturity during the co-composting of chicken manure and crop residues.

The succession of the fungal community during the co-composting of chicken manure and crop residues and its role in relation to compost maturity was deciphered using Illumina sequencing and FUNGuild (Fungi + Functional + Guild) tool. In the maturation phase of composting, the relative abundance of pathogenic and symbiotrophic fungi decreased by 68%-85% and 145%-622%, respectively, as compared to the initial phase, which showed 574%-720% increase in the saprotrophic guild. The pathogenic and saprotrophic fungi abundance was correlated to compost maturity represented by germination index and humic spectroscopic ratio (p < 0.05). Random forest analysis and structural equation modeling elucidated the positive effects of the aforementioned fungal taxa on compost maturity, and these effects were mediated by the micro-environmental variables, such as temperature, NH4+-N/NO3--N ratio and total organic carbon content. Our study outlines the importance of fungal community succession for improving composting performance and efficiency.