Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion

Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.

Soil fungal community structure and function response to rhizoma perennial peanut cultivars

BACKGROUND

Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars.

RESULTS

This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars.

CONCLUSIONS

Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.

Changes in soil organic carbon components and microbial community following spent mushroom substrate application

While spent mushroom substrate (SMS) has shown promise in increasing soil organic carbon (SOC) and improving soil quality, research on the interplay between SOC components and microbial community following the application of diverse SMS types remains scant. A laboratory soil incubation experiment was conducted with application of two types of SMSs from cultivation of Pleurotus eryngii (PE) and Agaricus bisporus (AB), each at three application rates (3, 5.5, and 8%). Advanced techniques, including solid-state 13C nuclear magnetic resonance (NMR) and high-throughput sequencing, were employed to investigate on SOC fractions and chemical structure, microbial community composition and functionality. Compared to SMS-AB, SMS-PE application increased the relative abundances of carbohydrate carbon and O-alkyl C in SOC. In addition, SMS-PE application increased the relative abundance of the bacterial phylum Proteobacteria and those of the fungal phyla Basidiomycota and Ascomycota. The relative abundances of cellulose-degrading bacterial (e.g., Flavisolibacter and Agromyces) and fungal genera (e.g., Myceliophthora, Thermomyces, and Conocybe) were increased as well. The application of SMS-AB increased the aromaticity index of SOC, the relative abundance of aromatic C, and the contents of humic acid and heavy fraction organic carbon. In addition, SMS-AB application significantly increased the relative abundances of the bacterial phyla Firmicutes and Actinobacteria. Notably, the genera Actinomadura, Ilumatobacter, and Bacillus, which were positively correlated with humic acid, experienced an increase in relative abundance. Functional prediction revealed that SMS-PE application elevated carbohydrate metabolism and reduced the prevalence of fungal pathogens, particularly Fusarium. The application of high-rate SMS-AB (8%) enhanced bacterial amino acid metabolism and the relative abundances of plant pathogenic fungi. Our research provides strategies for utilizing SMS to enrich soil organic carbon and fortify soil health, facilitating the achievement of sustainable soil management.

Improvement and the relationship between chemical properties and microbial communities in secondary salinization of soils induced by rotating vegetables

Choosing a good crop rotation plan helps maintain soil fertility and creates a healthy soil ecosystem. However, excessive fertilization and continuous cultivation of vegetables in a greenhouse results in secondary salinization of the soil. It remains unclear how crop rotation affects Yunnan's main place for vegetable growing in the greenhouse. Six plant cultivation patterns were chosen to determine how different rotation patterns affect the chemical properties and the soil microbial communities with secondary salinization, including lettuce monoculture, lettuce-large leaf mustard, lettuce-red leaf beet, lettuce-cabbage, lettuce-romaine lettuce, and lettuce-cilantro (DZ, A1, A2, A3, A4, and A5). The results showed that all treatments increased the proportion of nutrients available in the soil, and the effect of the A1 treatment was the most significant compared to the monoculture mode. The high-throughput sequencing findings revealed that distinct crop rotation patterns exerted varying effects on the microbial communities. Microbial community diversity was significantly lower in the monoculture than in the other treatments. The number of microbial operational taxonomic units OTUs was significantly higher in the crop rotation modes (P < 0.05), and the A1 treatment had larger numbers and diversity of bacterial and fungal OTUs (Shannon's and Simpson's) than other treatments (P < 0.05). Prominent bacterial and fungal communities were readily observable in the soils planted with rotational crops. Proteobacteria had the highest relative abundance of bacteria, whereas Ascomycota was the most abundant fungus. The principal coordinate analysis at the OTU level separated soil bacterial and fungal growth communities under the different treatments. Among the six treatments, The first two axes (PC1 and PC2) described 46.44 % and 42.42 % of the bacterial and fungal communities, respectively. Network-based analysis showed that Bacteroidota and Gemmatimonadota members of the genus Bacteroidota were positively correlated with Proteobacteria. Members of Ascomycota and Chytridiomycota exhibited positive relationships. These results extend the theoretical understanding of how various crop rotation patterns affect soil chemical properties, microbial community diversity, and metabolic functions. They reveal the beneficial effects of crop rotation patterns on enhanced soil quality. This study provides theoretical guidance for the future enhancement of sustainable agriculture and soil management planning.

Distribution of rhizosphere fungi of Kobresia humilis on the Qinghai-Tibet Plateau

Kobresia humilis is a major species in the alpine meadow communities of the Qinghai-Tibet Plateau (QTP); it plays a crucial role in maintaining the ecological balance of these meadows. Nevertheless, little is known about the rhizosphere fungi associated with K. humilis on the Qinghai Tibet Plateau. In this study, we used Illumina Miseq to investigate the fungal diversity, community structure, and ecological types in the root and rhizosphere soil of K. humilis across eight areas on the QTP and analyzed the correlation between rhizosphere fungi of K. humilis and environmental factors. A total of 19,423 and 25,101 operational taxonomic units (OTUs) were obtained from the roots and rhizosphere soil of K. humilis. These were classified into seven phyla, 25 classes, 68 orders, 138 families, and 316 genera in the roots, and nine phyla, 31 classes, 76 orders, 152 families, and 407 genera in the rhizosphere soil. There were 435 and 415 core OTUs identified in root and rhizosphere soil, respectively, which were categorized into 68 and 59 genera, respectively, with 25 shared genera. Among them, the genera with a relative abundance >1% included Mortierella, Microscypha, Floccularia, Cistella, Gibberella, and Pilidium. Compared with the rhizosphere soil, the roots showed five differing fungal community characteristics, as well as differences in ecological type, and in the main influencing environmental factors. First, the diversity, abundance, and total number of OTUs in the rhizosphere soil of K. humilis were higher than for the endophytic fungi in the roots by 11.85%, 9.85%, and 22.62%, respectively. The composition and diversity of fungal communities also differed between the eight areas. Second, although saprotroph-symbiotrophs were the main ecological types in both roots and rhizosphere soil; there were 62.62% fewer pathotrophs in roots compared to the rhizosphere soil. Thirdly, at the higher altitude sites (3,900-4,410 m), the proportion of pathotroph fungi in K. humilis was found to be lower than at the lower altitude sites (3,200-3,690 m). Fourthly, metacommunity-scale network analysis showed that during the long-term evolutionary process, ZK (EICZK = 1) and HY (EICHY = 1) were critical sites for development of the fungal community structure in the roots and rhizosphere soil of K. humilis, respectively. Fifthly, canonical correspondence analysis (CCA) showed that key driving factors in relation to the fungal community were longitude (R2 = 0.5410) for the root community and pH (R2 = 0.5226) for the rhizosphere soil community. In summary, these results show that K. humilis fungal communities are significantly different in the root and rhizosphere soil and at the eight areas investigated, indicating that roots select for specific microorganisms in the soil. This is the first time that the fungal distribution of K. humilis on the QTP in relation to long-term evolutionary processes has been investigated. These findings are critical for determining the effects of environmental variables on K. humilis fungal communities and could be valuable when developing guidance for ecological restoration and sustainable utilization of the biological resources of the QTP.

Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes

Land-use change is highly dynamic globally and there is great uncertainty about the effects of land-use legacies on contemporary environmental performance. We used a chronosequence of urban grasslands (lawns) that were converted from agricultural and forested lands from 10 to over 130 years prior to determine if land-use legacy influences components of soil biodiversity and composition over time. We used historical aerial imagery to identify sites in Baltimore County, MD (USA) with agricultural versus forest land-use history. Soil samples were taken from these sites as well as from existing well-studied agricultural and forest sites used as historical references by the National Science Foundation Long-Term Ecological Research Baltimore Ecosystem Study program. We found that the microbiomes in lawns of agricultural origin were similar to those in agricultural reference sites, which suggests that the ecological parameters on lawns and reference agricultural systems are similar in how they influence soil microbial community dynamics. In contrast, lawns that were previously forest showed distinct shifts in soil bacterial composition upon recent conversion but reverted back in composition similar to forest soils as the lawns aged over decades. Soil fungal communities shifted after forested land was converted to lawns, but unlike bacterial communities, did not revert in composition over time. Our results show that components of bacterial biodiversity and composition are resistant to change in previously forested lawns despite urbanization processes. Therefore land-use legacy, depending on the prior use, is an important factor to consider when examining urban ecological homogenization.

Integrated microbiological and metabolomics analyses to understand the mechanism that allows modified biochar to affect the alkalinity of saline soil and winter wheat growth

In order to understand the mechanism that allows modified biochar (BC) to enhance the salt tolerance and growth of crops in saline-alkali soil, we tested the effects of ordinary BC, nanoparticle-size BC, acidified BC (HBC), and acidified nanoparticle-size BC on winter wheat growth and the soil properties by combining microbiological and metabolomics analyses. The results showed that compared with the control with no BC, the plant height increased by 17.33 % under HBC and the proportion of large soil aggregates increased by 1.25-2.83 times. HBC increased the relative abundances of some dominant genera of bacteria (e.g., Streptococcus) and fungi (e.g., Mycothermus), as well as functions such as bacterial metabolic genetic information processing and cellular processes, and reduced the abundance of pathotrophic fungi. Metabolomics analysis showed that HBC upregulated various metabolites (including amino acids and their derivatives, lipids, flavonoids, and organic acids) and five main metabolic pathways. Among the KEGG pathways, the pyrimidine metabolism pathway was significantly upregulated, as well as crop leaf metabolism, β-alanine metabolism, and valine, leucine, and isoleucine metabolism, and the antioxidant levels and resistance to salt-alkali stress were enhanced in winter wheat leaves. Partial least squares-path modeling suggested that HBC affected the growth of winter wheat by significantly changing the soil physicochemical properties and microbial structure (path coefficients of 0.566 and 0.512, respectively).

Soil Fungal Community Structure and Function Shift during a Disease-Driven Forest Succession

Forest succession is important for sustainable forest management in terrestrial ecosystems. However, knowledge about the response of soil microbes to forest disease-driven succession is limited. In this study, we investigated the soil fungal biomass, soil enzyme activity, and fungal community structure and function in forests suffering succession processes produced by pine wilt disease from conifer to broadleaved forests using Illumina Miseq sequencing coupled with FUNGuild analysis. The results showed that the broadleaved forest had the highest fungal biomass and soil enzyme activities in C, N, and S cycles, whereas the conifer forest had the highest enzyme activity in the P cycle. Along the succession, the fungal diversity and richness significantly increased (P < 0.05). The fungal communities were dominated by Ascomycota (42.0%), Basidiomycota (38.0%), and Mortierellomycota (9.5%), among which the abundance of Ascomycota significantly increased (P < 0.05), whereas that of Basidiomycota and Mortierellomycota decreased (P < 0.05). The abundance of species Mortierella humilis, Lactarius salmonicolor, and Russula sanguinea decreased, whereas that of Mortierella minutissima increased (P < 0.05). The forests in different succession stages formed distinct fungal communities and functional structures (P < 0.05). Functionally, the saprotrophs, symbiotrophs, and pathotrophs were the dominant groups in the conifer, mixed, and broadleaved forests, respectively. Soil pH and soil organic carbon were the key factors influencing the fungal community and functional structures during the succession. These findings provide useful information for better understanding the plant-microbe interaction during forest succession caused by forest disease. IMPORTANCE The studies on soil fungal communities in disease-driven forest succession are rare. This study showed that during the disease-driven forest succession, the soil enzyme activity, soil fungal diversity, and biomass increased along succession. The disease-driven forest succession changed the soil fungal community structure and function, in which the symbiotrophs were the most dominant group along the succession. These findings provide useful information for better understanding the plant-microbe interaction during forest succession caused by forest disease.

Effects of thifluzamide on soil fungal microbial ecology

Thifluzamide, a succinate dehydrogenase inhibitor fungicide, has been used extensively for many diseases control and has the risk of accumulation in soil ecology. In order to study the ecotoxicity of thifluzamide to soil fungal communities, typical corn field soils in north (Tai'an) and south (Guoyang) China were treated with thifluzamide (0, 0.1, 1.0 and 10.0 mg/kg) and incubated for 60 days. Thifluzamide exposure promoted soil basal respiration, and significantly reduced the number of soil culturable fungi and the abundance of soil fungi (RT-qPCR) in middle and late treatment period (15, 30, 60 days). Illumina Mi-Seq sequencing revealed that thifluzamide could reduce fungal alpha diversity (Sobs, Shannon, Simpson indexes) and change fungal community structure. FUN Guild analysis showed that the relative abundance of Undefined Saprotroph increased after the thifluzamide treatment, whereas that of Plant Pathogen decreased, and we concluded that exposure to thifluzamide could change the function of soil fungi. This study evaluated the soil ecological risk caused by thifluzamide's release into soil, providing a basis for its rational application.

Elevated functional versatility of the soil microbial community associated with the invader Carpobrotus edulis across a broad geographical scale

Exotic invasive plants may shape their own rhizosphere microbial community during global invasions. Nevertheless, the impacts of such plant invasions on the functional capacities of soil microbial communities remain poorly explored. We used an approach at a broad geographical scale to estimate the composition and abundance of the fungal functional groups, as well as the bacterial metabolic functions, associated with the rhizospheres of Carpobrotus edulis (L.) L. Bolus and the predominant native plants in coastal ecosystems located in different geographical regions. We used the ASV method to infer the potential functions of the soil microbial community with the PICRUSt2 and FUNGuild tools. The predictive functional profiling of the bacterial communities differed between the rhizospheres of the invasive and native plants, regardless of the biogeographic location of the invaded soil. Some predicted pathways related to the biosynthesis of nucleotides such as ppGpp and pppGpp, lipids, carbohydrates and secondary metabolites and the degradation of organic matter were enriched in the C. edulis rhizosphere. Moreover, the invasive microbiota was characterised by a greater richness and diversity of catabolic enzymes involved in nutrients cycling and higher relative abundances of saprotrophs and pathotrophs. Invasion by C. edulis promoted a shift in the potential functional versatility of the soil microbial communities, which can cope with nutrient limitations and biotic stress, and can favour the establishment of the invasive plant, but also alter the functioning and stability of the invaded ecosystems.

Stem traits, compartments, and tree species affect fungal communities on decaying wood

Dead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Comparison of the Responses of Soil Fungal Community to Straw, Inorganic Fertilizer, and Compost in a Farmland in the Loess Plateau

The Loess Plateau is located in the arid and semi-arid regions in northern China. The ecosystem is particularly sensitive to natural and anthropogenic disturbances. Fungi can produce extracellular enzymes, decompose a variety of organic matter, and regulate carbon and nutrient balance. We studied the changes of soil fungal community compositions in response to straw, inorganic fertilizer, and compost in a typical farmland in the Loess Plateau. Our results demonstrated that the addition of straw significantly reduces the Shannon index of the fungal community, in addition, the participation of straw significantly affects the composition of the fungal community. Functional prediction based on FUNGuild showed that straw significantly reduced the relative abundance of saprotrophs, pathotrophs, symbiotrophs, lichenized, ectomycorrhizal, and plant pathogens. Although fertilization practices destroyed the co-occurrence pattern among the fungal species, the addition of straw alleviated this affect. No significant effect of straw, compost, and inorganic fertilizers on the co-occurrence pattern among species in the soil fungal community was observed. Compared with compost and inorganic fertilizer, the addition of straw shaped the community composition by changing the relative abundance of fungal functional taxa. Thus, in the fragile Loess Plateau environment, over-fertilizing or non-order-fertilizing may destroy the co-occurrence pattern of the fungal communities and Loess Plateau ecosystem. IMPORTANCE Determining the response of soil fungi in sensitive ecosystems to external environmental disturbances is an important, yet little-known, topic in microbial ecology. In this study, we evaluated the impact of traditional fertilization management practices on the composition, co-occurrence pattern, and functional groups of fungal communities in loessial soil. Our results show that in the fragile Loess Plateau environment, fertilizer management changed the composition of the fungal community and disrupted the co-occurrence pattern between fungi. The application of straw alleviates the destroying of the co-occurrence pattern. The current research emphasizes the necessity of rational fertilization of farmland in loessial soil.

Inferring microbiota functions from taxonomic genes: a review

Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.

Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.

Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi

The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.

Localized reshaping of the fungal community in response to a forest fungal pathogen reveals resilience of Mediterranean mycobiota

Mediterranean forests are facing the impact of pests such as the soilborne Phytophthora cambivora, the causal agent of Ink disease, and this impact is made more severe by global changes. The status and resilience of the soil microbial ecosystem in areas with such a disturbance are little known; however, the assessment of the microbial community is fundamental to preserve the ecosystem functioning under emerging challenges. We profile soil fungal communities in a chestnut stand affected by ink disease in Italy using metabarcoding, and couple high-throughput sequencing with physico-chemical parameters and dendrometric measurements. Since the site also includes an area where the disease symptoms seem to be suppressed, we performed several analyses to search for determinants that may contribute to such difference. We demonstrate that neither pathogen presence nor trees decline associate with the reduction of the residing community diversity and functions, but rather with microbial network reshaping through substitutions and new interactions, despite a conservation of core taxa. We predict interactions between taxa and parameters such as soil pH and C/N ratio, and suggest that disease incidence may also relate with disappearance of pathogen antagonists, including ericoid- and ectomycorrhizal (ECM) fungi. By combining metabarcoding and field studies, we infer the resilient status of the fungal community towards a biotic stressor, and provide a benchmark for the study of other threatened ecosystems.

Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here, we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara and Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy, and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N₅₀ = 121 Mb; L₅₀ = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one-third of BUSCO genes (390/1440) mapped to two or more scaffolds despite <2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

Safety and efficiency of sewage sludge and garden waste compost as a soil amendment based on the field application in woodland

Sewage sludge (SS) and garden waste (GW) compost can be used as soil amendments to improve the soil environment. Studies done till date have been focused on the changes of harmful substances during sludge composting, but the safety and efficacy of SS and GW composting on woodland soil environment are still unclear. In the study, a field experiment was performed using to investigate the safety and efficacy of SS and GW compost as a soil amendment on woodland soil. Soil nutrients (such as nitrogen, phosphorus and potassium), organic matter and electrical conductivity were significantly increased after the addition of the SS and GW compost, while there were no significant changes in soil heavy metals content and soil enzyme activities. From these soil properties, it was found that SS and GW compost was safe and efficacious in improving the soil environment. The application of SS and GW compost had no significant effect on microbial diversity. Co-occurrence network analysis revealed that SS and GW compost efficaciously enhanced the interaction between bacterial communities, which proved that it was safe and efficacious. Furthermore, SS and GW compost enhanced ABC transporters and carbohydrate metabolism of bacterial community, while reduced the pathotroph action (such as the plant pathogen) and wood saprotrophs. Overall, these results proved the safety and efficacy of SS and GW compost as soil amendments after being added to the soil. This study contributes to the use of harmless treatments and reutilization processes of SS and GW.

Influence of Intraspecific Competition Stress on Soil Fungal Diversity and Composition in Relation to Tree Growth and Soil Fertility in Sub-Tropical Soils under Chinese Fir Monoculture

Soil microorganisms provide valuable ecosystem services, such as nutrient cycling, soil remediation, and biotic and abiotic stress resistance. There is increasing interest in exploring total belowground biodiversity across ecological scales to understand better how different ecological aspects, such as stand density, soil properties, soil depth, and plant growth parameters, influence belowground communities. In various environments, microbial components of belowground communities, such as soil fungi, respond differently to soil features; however, little is known about their response to standing density and vertical soil profiles in a Chinese fir monoculture plantation. This research examined the assemblage of soil fungal communities in different density stands (high, intermediate, and low) and soil depth profiles (0–20 cm and 20–40 cm). This research also looked into the relationship between soil fungi and tree canopy characteristics (mean tilt angle of the leaf (MTA), leaf area index (LAI), and canopy openness index (DIFN)), and general growth parameters, such as diameter, height, and biomass. The results showed that low-density stand soil had higher fungal alpha diversity than intermediate- and high-density stand soils. Ascomycota, Basidiomycota, Mucromycota, and Mortierellomycota were the most common phyla of the soil fungal communities, in that order. Saitozyma, Penicillium, Umbelopsis, and Talaromyces were the most abundant fungal genera. Stand density composition was the dominant factor in changing fungal community structure compared to soil properties and soil depth profiles. The most significant soil elements in soil fungal community alterations were macronutrients. In addition, the canopy openness index and fungal community structure have a positive association in the low-density stand. Soil biota is a nutrient cycling driver that can promote better plant growth in forest ecosystems by supporting nutrient cycling. Hence, this research will be critical in understanding soil fungal dynamics, improving stand growth and productivity, and improving soil quality in intensively managed Chinese fir plantations.

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network

Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.

Response of Fungal Diversity, Community Composition, and Functions to Nutrients Management in Red Soil

Soil fungi play a critical role in plant performance and soil nutrient cycling. However, the understanding of soil fungal community composition and functions in response to different nutrients management practices in red soils remains largely unknown. Here, we investigated the responses of soil fungal communities and functions under conventional farmer fertilization practice (FFP) and different nutrient management practices, i.e., optimization of NPK fertilizer (O) with soil conditioner (O + C), with lime and mushroom residue (O + L + M), and with lime and magnesium fertilizer (O + L + Mg). Illumina high-throughput sequencing was used for fungal identification, while the functional groups were inferred with FUNGuild. Nutrient management practices significantly raised the soil pH to 4.79–5.31 compared with FFP (3.69), and soil pH had the most significant effect (0.989 ***) on fungal communities. Predominant phyla, including Ascomycota, Basidiomycota, and Mortierellomycota were identified in all treatments and accounted for 94% of all fungal communities. The alpha diversity indices significantly increased under nutrients management practices compared with FFP. Co-occurrence network analysis revealed the keystone fungal species in the red soil, i.e., Ascomycota (54.04%), Basidiomycota (7.58%), Rozellomycota (4.55%), and Chytridiomycota (4.04%). FUNGuild showed that the relative abundance of arbuscular mycorrhizal fungi and ectomycorrhizal fungi was higher, while pathogenic fungi were lower under nutrient management practices compared with FFP. Our findings have important implications for the understanding of improvement of acidic soils that could significantly improve the soil fungal diversity and functioning in acidic soils.

Invasion-induced root-fungal disruptions alter plant water and nitrogen economies

Despite widespread evidence that biological invasion influences both the biotic and abiotic soil environments, the extent to which these two pathways underpin the effects of invasion on plant traits and performance remains unknown. Leveraging a long-term (14-year) field experiment, we show that an allelochemical-producing invader affects plants through biotic mechanisms, altering the soil fungal community composition, with no apparent shifts in soil nutrient availability. Changes in belowground fungal communities resulted in high costs of nutrient uptake for native perennials and a shift in plant traits linked to their water and nutrient use efficiencies. Some plants in the invaded community compensate for the disruption of nutritional symbionts and reduced nutrient provisioning by sanctioning more nitrogen to photosynthesis and expending more water, which demonstrates a trade-off in trait investment. For the first time, we show that the disruption of belowground nutritional symbionts can drive plants towards alternative regions of their trait space in order to maintain water and nutrient economics.

Spartina alterniflora invasions reduce soil fungal diversity and simplify co-occurrence networks in a salt marsh ecosystem

Soil fungal communities drive diverse ecological processes and are critical in maintaining ecosystems' stability, but the effects of plant invasion on soil fungal diversity, community composition, and functional groups are not well understood. Here, we investigated soil fungal communities in a salt marsh ecosystem with both native (Suaeda salsa) and exotic (Spartina alterniflora) species in the Yellow River Delta. We characterized fungal diversity based on the PCR-amplified Internal Transcribed Spacer 2 (ITS2) DNA sequences from soil extracted total DNA. The plant invasion evidently decreased fungal richness and phylogenetic diversity and significantly altered the taxonomic community composition (indicated by the permutation test, P < 0.001). Co-occurrence networks between fungal species showed fewer network links but were more assembled because of the high modularity after the invasion. As indicated by the fungal Bray-Curtis and weighted UniFrac distances, the fungal community became homogenized with the invasion. FUNGuild database analyses revealed that the invaded sites had a higher proportion of saprophytic fungi, suggesting higher organic matter decomposition potential with the invasion. The plant invasion dramatically inhibited the growth of pathogenic fungi, which may facilitate the expansion of invasive plants in the intertidal habitats. Soil pH and salinity were identified as the most important edaphic factors in shaping the fungal community structures in the context of Spartina alterniflora invasion. Overall, this study elucidates the linkage between plant invasion and soil fungal communities and poses potential consequences for fungal contribution to ecosystem function, including the decomposition of soil organic substrates.

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.

Plant invasion impacts on fungal community structure and function depend on soil warming and nitrogen enrichment

The impacts of invasive species on biodiversity may be mitigated or exacerbated by abiotic environmental changes. Invasive plants can restructure soil fungal communities with important implications for native biodiversity and nutrient cycling, yet fungal responses to invasion may depend on numerous anthropogenic stressors. In this study, we experimentally invaded a long-term soil warming and simulated nitrogen deposition experiment with the widespread invasive plant Alliaria petiolata (garlic mustard) and tested the responses of soil fungal communities to invasion, abiotic factors, and their interaction. We focused on the phytotoxic garlic mustard because it suppresses native mycorrhizae across forests of North America. We found that invasion in combination with warming, but not under ambient conditions or elevated nitrogen, significantly reduced soil fungal biomass and ectomycorrhizal relative abundances and increased relative abundances of general soil saprotrophs and fungal genes encoding for hydrolytic enzymes. These results suggest that warming potentially exacerbates fungal responses to plant invasion. Soils collected from uninvaded and invaded plots across eight forests spanning a 4 °C temperature gradient further demonstrated that the magnitude of fungal responses to invasion was positively correlated with mean annual temperature. Our study is one of the first empirical tests to show that the impacts of invasion on fungal communities depends on additional anthropogenic pressures and were greater in concert with warming than under elevated nitrogen or ambient conditions.

Effects of bird aggregation on the soil properties and microbial community diversity of urban forest fragments

Forest fragments in urban parks provide important habitat for birds. However, the guano deposited by large aggregations of birds in such fragments can dramatically change soil properties, which in turn, can alter soil microbial community composition, potentially affecting the forests' composition and survival. To investigate the effects of bird aggregations on the soil of fragmented urban forests, we compared the soil properties and microbial communities of two forested islands, one in Liuhuahu park and the other in Wanzuitou park, Guangzhou, where large numbers of birds aggregate yearly to nest. Comparison to sites without bird aggregations suggests that decades of guano deposition appears to have caused soil acidification and an increase in soil nutrients. The relative abundance of the soil bacterial phylum Actinobacteria and the soil fungal phylum Ascomycota were significantly lower in soil under bird aggregations. The aerobic nitrite oxidation, nitrate reduction and cellulolysis bacterial guilds were significantly less abundant under bird aggregations in Liuhuahu park. The wood saprotroph fungi guild was significantly less abundant under the bird aggregation in Liuhuahua park and the pathogenic fungi guild significantly more abundant in Wanzuitou park. Soil properties, including TN, NO₃^--N, TOC and pH, explained the variation in Ascomycota and Basidiomycota abundance, and the alpha-diversity of the fungal community. Microbial community variation could potentially slow the rate of decomposition and disease resistance of plant in these forests. We suggest that sufficient contiguous forest should be maintained in urban areas to reduce the density of bird aggregations in isolated forest fragments.

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities

Soil microbiomes could play a major role in ecosystem responses to escalating anthropogenic global change. However, we currently have a poor understanding of how soil microbes will respond to interacting global change factors and if responses will be mediated by changes in plant community structure. We used a field experiment to assess changes in soil fungal and bacterial communities in response to plant invasion, experimental drought, and their combination. In addition, we evaluated the relative importance of direct versus indirect pathways of invasion and drought through changes in associated plant communities with structural equation models. We found that fungal communities were interactively structured by invasion and drought, where fungal richness was lowest with invasion under ambient conditions but highest with invasion under drought conditions. Bacterial richness was lower under drought but unaffected by invasion. Changes in the plant community, including lower plant richness and higher root biomass, moderated the direct effects of invasion on microbial richness. Fungal and bacterial functional groups, including pathogens, mutualists, and nitrogen metabolizers, were also influenced by plant community changes. In sum, plant communities mediated the effects of interacting global change drivers on soil microbial community structure, with significant potential consequences for community dynamics and ecosystem functions.

Contrasting Patterns of Functional Diversity in Coffee Root Fungal Communities Associated with Organic and Conventionally Managed Fields

The structure and function of fungal communities in the coffee rhizosphere are influenced by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities under markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic, or transitional management in two regions of Costa Rica. We amplified the internal transcribed spacer 2 (ITS2) region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, and more leaf litter and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium availability than conventionally managed fields, although differences between organic and conventionally managed fields in shade and calcium and magnesium availability depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally managed fields were also correlated with shade, soil acidity, and nitrate and copper availability. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse, and plant pathogens were more abundant, in organic than in conventionally managed fields, while saprotroph-plant pathogens were more abundant in conventionally managed fields. These differences reflected environmental differences and depended on region.IMPORTANCE Rhizosphere fungi play key roles in ecosystems as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management may influence rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but it also maintains a greater richness of saprotrophic, plant-pathogenic, and mycoparasitic fungi that has implications for the efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.

Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism

Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.

Studies on fungal communities and functional guilds shift in tea continuous cropping soils by high-throughput sequencing

Purpose

Although soil fungal communities are considered important in tea orchard ecosystems, experimental research on their responses to the long-term continuous ratooning cultivation of tea plants are limited.

Methods

In this study, Illumina high-throughput sequencing technology was employed to investigate soil fungal communities in tea orchards with continuous cropping histories of 0, 1, 10, and 20 years.

Results

Results indicated that the predominant phyla were Ascomycota and Basidiomycota in all tea soil samples. Plant pathogen fungi Alternaria was the most predominant genus in the 10- and 20-year soils and significantly higher than that in the 0- and 1-year soils. FUNGuild revealed that the symbiotrophs in the 1-year soil (8.00%) was markedly higher than those in the 0-, 10-, and 20-year soils (1.43%~2.47%). The saprotrophs in the 20-year soils was approximately two-fold higher than those identified in the 0-, 1-, and 10-year soils. The pathotroph–saprotroph–symbiotroph fungi were higher in the 10- and 20-year soils in comparison to the 0- and 1-year soils as expected. Diversity analysis showed that the indices of Shannon and Simpson in the 1-year soils were higher than those in other treatments. Redundancy analysis suggested that fungal community structure and function were evidently interrelated to pH and exchangeable aluminum in the soils, respectively.

Conclusion

In summary, the long-term continuous ratooning cultivation of tea plants changed the fungal communities in the rhizosphere, enriched saprotrophs and plant pathogens (Alternaria spp.), and reduced beneficial fungi (symbiotrophs). Results of this work can be used to explore reasonable management measures, such as microbial fertilizer application, and eventually relieve the long-term monoculture problems of tea plants.

Silicate Fertilizer Amendment Alters Fungal Communities and Accelerates Soil Organic Matter Decomposition

Soil microorganisms play a crucial role in organic matter decomposition and nutrient cycling in cropping systems. Compared to bacteria, fungal community composition and the role of fungi in organic matter decomposition and nutrient cycling in agro-systems are, however, elusive. Silicon (Si) fertilization is essential to improve agronomic performance of rice. The effects of the Si fertilizer application on the soil fungal community composition and their contribution in soil organic matter (SOM) decomposition are not yet studied. We investigated the short-term (120 days) slag silicate fertilizer (SSF) amendment impacts on plant photosynthesis and soil biochemical changes, soil fungal communities (assessed by ITS amplicon illumina sequencing), hydrolytic and oxidase enzyme activities, CO₂ emissions, and bacterial and fungal respiration in diverse eco-geographic races of rice (Oryza sativa L.), i.e., Japonica rice (O. sativa japonica) and Indica rice (O. sativa indica). The short-term SSF amendment significantly increased the relative abundance of saprotrophic fungi and accelerated organic matter decomposition. The increase in saprotrophic fungi was mostly attributed to greater labile C availability and Si availability. Higher organic matter decomposition was accompanied by an increase in both hydrolytic and oxidative enzyme activities in response to the SSF amendment. The stimulation of oxidative enzyme activities was explained by an increase in root oxidase activities and iron redox cycling, whereas stimulation of hydrolytic enzyme activities was explained by the greater labile C availability under SSF fertilization. We conclude that the short-term SSF amendment increases saprotrophic fungal communities and soil hydrolytic and oxidative enzyme activities, which in turn stimulates SOM mineralization and thus could have negative feedback impacts on soil C storage in submerged rice paddies.

Selenium (Se) reduces Sclerotinia stem rot disease incidence of oilseed rape by increasing plant Se concentration and shifting soil microbial community and functional profiles

Sclerotinia stem rot (SSR), a soil-borne plant disease, cause the yield loss of oilseed rape. Selenium (Se), a beneficial element of plant, improves plant resistance to pathogens, and regulates microbial communities in soil. Soil microbial communities has been identified to play an important role in plant health. We studied whether the changes in soil microbiome under influence of Se associated with oilseed rape health. SSR disease incidence of oilseed rape and soil biochemical properties were investigated in Enshi district, "The World Capital of Selenium", and soil bacterial and fungal communities were analyzed by 16S rRNA and ITS sequencing, respectively. Results showed that Se had a strong effect on SSR incidence, and disease incidence inversely related with plant Se concentration. Besides, soil Se enhanced the microbiome diversities and the relative abundance of PGPR (plant growth promoting rhizobacteria), such as Bryobacter, Nitrospirae, Rhizobiales, Xanthobacteraceae, Nitrosomonadaceae and Basidiomycota. Furthermore, Soil Se decreased the relative abundance of pathogenic fungi, such as Olpidium, Armillaria, Coniosporium, Microbotryomycetes and Chytridiomycetes. Additionally, Se increased nitrogen metabolism, carbohydrate metabolism and cell processes related functional profiles in soil. The enrichment of Se in plants and improvement of soil microbial community were related to increased plant resistance to pathogen infection. These findings suggested that Se has potential to be developed as an ecological fungicide for biological control of SSR.

Short-Term Effects of Different Organic Amendments on Soil Fungal Composition

Fungi play an essential role in recovering the quality and fertility of soil. There is a limited understating of the complex response of fungal diversity to different organic materials in clay loam soil. Here, we report the response of soil fungi toward the short-term application of manure (M), sugarcane straw (S), and sugarcane straw plus manure (MS), including no organic material control (CK) at two different time points (50 and 100 days after application). Illumina sequencing was used to examine the fungal communities. Our results reveal a significant shift among the soil fungal community structure associated with each organic material application. After both time points, amendments—especially M and MS—decreased the fungal richness and stimulated the copiotrophic fungal group (Ascomycota) compared to the control soil (CK) and S-amended soil. On the contrary, as compared to the M and MS-amended soils, the CK and S-amended soils at both time points increased the fungal richness and stimulated the oligotrophic fungal groups. Organic material use, especially M and MS, showed variable results regarding pathogenic fungi enhancing the abundance of Lophodermium and Cercophora and decreasing Fusarium. Concerning the abundance of plant-beneficial fungi, Mortierella was reduced, and Podospora was increased by M and MS input. FUNGuild showed that the amendment of organic materials efficiently declined the abundance of endophytes and plant pathogens, but also enhanced the animal pathogens in terms of abundance with respect to CK at two time points. This study could be useful to provide a novel understanding of the management of soil-borne pathogens by organic amendments for the sustainable production of short-term crops.

High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests.

Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota

Immune‐mediated diseases have increased during the last decades in urban environments. The hygiene hypothesis suggests that increased hygiene level and reduced contacts with natural biodiversity are related to the increase in immune‐mediated diseases. We tested whether short‐time contact with microbiologically diverse nature‐based materials immediately change bacterial diversity on human skin. We tested direct skin contact, as two volunteers rubbed their hands with sixteen soil and plant based materials, and an exposure via fabric packets filled with moss material. Skin swabs were taken before and after both exposures. Next‐generation sequencing showed that exposures increased, at least temporarily, the total diversity of skin microbiota and the diversity of Acidobacteria, Actinobacteria, Bacteroidetes, Proteobacteria and Alpha‐, Beta‐ and Gammaproteobacteria suggesting that contact with nature‐based materials modify skin microbiome and increase skin microbial diversity. Until now, approaches to cure or prevent immune system disorders using microbe‐based treatments have been limited to use of a few microbial species. We propose that nature‐based materials with high natural diversity, such as the materials tested here, might be more effective in modifying human skin microbiome, and eventually, in reducing immune system disorders. Future studies should investigate how long‐term changes in skin microbiota are achieved and if the exposure induces beneficial changes in the immune system markers.