Decomposition rate of organic substrates in relation to the species diversity of soil saprophytic fungi

Spatial variations impact the soil fungal communities of Larix gmelinii forests in Northeast China

Soil fungi play a critical role in the biogeochemical cycles of forest ecosystems. Larix gmelinii is a strong and important timber tree species, which forms close associations with a wide range of soil fungi. However, the temporal-spatial disparity effects on the assembly of soil fungal communities in L. gmelinii forests are poorly understood. To address these questions, a total of 120 samples, including 60 bulk soil and 60 root samples, were collected from Aershan and Genhe in July (summer) and October (autumn)2021. We obtained 7,788 operational taxonomic units (OTUs) after merging, filtering, and rarefying using high-throughput sequencing. The dominant phyla are Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota. There were 13 dominant families, among which the families with average relative abundance more than 5% included Thelephoraceae, Mortierellaceae, Archaeorhizomycoaceae, and Inocybaceae. In the functional guilds, symbiotrophic fungi had a relative advantage in the identified functions, and the relative abundances of pathotrophic and saprotrophic fungi varied significantly between sites. There were 12 families differentially expressed across compartments, 10 families differentially expressed between seasons, and 69 families were differentially expressed between sites. The variation in alpha diversity in the bulk soil was greater than that in the rhizosphere soil. Among the three parts (compartment, season, and site), the site had a crucial effect on the beta diversity of the fungal community. Deterministic processes dominated fungal community assembly in Genhe, whereas stochastic processes dominated in Aershan. Soil physicochemical properties and climatic factors significantly affected fungal community structure, among which soil total nitrogen and pH had the greatest effect. This study highlights that spatial variations play a vital role in the structure and assembly of soil fungal communities in L. gmelinii forests, which is of great significance for us in maintaining the health of the forests.

First Record of Flavocillium subprimulinum (Cordycipitaceae, Hypocreales) in Mexico: Morphological and Molecular Characterisation, Nematocidal Activity of Its Liquid Culture Filtrates against Haemonchus contortus and Protease Activity

This is the first record of the fungus Flavocillium subprimulinum in Mexico. The isolate was taxonomically characterised and cultured in potato dextrose broth (PDB), Czapek-Dox broth (CzDoxB), and sweet potato dextrose broth (SPDB) to obtain its filtrates (FLCF). The nematocidal activity (NA) of three FLCF concentrations was assessed against Haemonchus contortus L3. Protease activity (PA) was assessed with SDS-PAGE, followed by a zymogram. The NA of the FLCF reached 94.43% in PDB and 95.82% in CzDoxB, respectively, at 100 mg/mL. Lower mortality (64%) was found in SPDB at 100 mg/mL. SDS-PAGE showed bands (in PBS) of ~25, ~40, and ~55 kDa. The zymogram showed protein bands (PBs) with PA in the media, including PBs of ~14, ~40, and ~55 kDa. This study establishes the basis for exploring the potential use of this fungus against H. contortus, which is considered the most pathogenic parasite affecting lambs.

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

IMPORTANCE

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

Simultaneous removal of pharmaceuticals and heavy metals from aqueous phase via adsorptive strategy: A critical review

The coexistence of pharmaceuticals and heavy metals is regarded as a serious threat to aquatic environments. Adsorbents have been widely applied to the simultaneous removal of pharmaceuticals and metals from aqueous phase. Through a comprehensive review, behaviors that promote, inhibit, or have no effect on simultaneous adsorption of pharmaceuticals and heavy metals were found to depend on the system of contaminants and adsorbents and their environmental conditions, such as: characteristics of adsorbent and pollutant, temperature, pH, inorganic ions, and natural organic matter. Bridging and competition effects are the main reasons for promoting and inhibiting adsorption in coexisting systems, respectively. The promotion is more significant in neutral or alkaline conditions. After simultaneous adsorption, a solvent elution approach was most commonly used for regeneration of saturated adsorbents. To conclude, this work could help to sort out the theoretical knowledge in this field, and may provide new insights into the prevention and control of pharmaceuticals and heavy metals coexisting in wastewater.

Effect of Coal Mining on Soil Microorganisms from Stipa krylovii Rhizosphere in Typical Grassland

The environmental changes caused by coal mining activities caused disturbances to the plant, soil, and microbial health in the mining area. Arbuscular mycorrhizal fungi (AMF) play an important role in the ecological restoration of mining areas. However, it is less understood how soil fungal communities with multiple functional groups respond to coal mining, and the quantitative impact and risk of mining disturbance. Therefore, in this study, the effect of coal mining on soil microorganisms' composition and diversity were analyzed near the edge of an opencast coal-mine dump in the Shengli mining area, Xilingol League, Inner Mongolia. The response strategy of soil fungi to coal mining and the stability of arbuscular mycorrhizal fungi (AMF) in the soil fungal community were determined. Our results showed that coal mining affected AMF and soil fungi in areas within 900 m from the coal mine. The abundance of endophytes increased with the distance between sampling sites and the mine dump, whereas the abundance of saprotroph decreased with the distance between sampling sites and the mine dump. Saprotroph was the dominant functional flora near the mining area. The nodes percentage of Septoglomus and Claroideoglomus and AMF phylogenetic diversity near the mining area were highest. AMF responded to the mining disturbance via the variety and evolution strategy of flora. Furthermore, AMF and soil fungal communities were significantly correlated with edaphic properties and parameters. Soil available phosphorus (AP) was the main influencer of soil AMF and fungal communities. These findings evaluated the risk range of coal mining on AMF and soil fungal communities and elucidated the microbial response strategy to mining disturbance.

Effects of different management practices on soil microbial community structure and function in alpine grassland

Management practices, such as grazing exclusion and reseeding, have been implemented to mitigate the degradation of grassland. Low grazing intensities and reseeding increase grass production. Nevertheless, few studies have investigated the effects of these measures on the soil microbial community structure and function in the Qinghai Tibetan Plateau (QTP). To reveal the effects of management practices on soil microbes and give a reference to assess and improve ecosystems functions, we here evaluated the impact of various types of grazing (exclusion, seasonal, and traditional), reseeding (annual oat (Avena fatua) grassland (RO) and perennial artificial grassland cultivated >10 y), and integrated restoration (weed control and no-tillage reseeding) measures on soil microbial community structure and function in the QTP. The Shannon-Wiener diversity indices were highest for prokaryotes under RO and for fungi under integrated grassland restoration. Relative Actinobacteria abundance was higher under seasonal grazing than that under integrated grassland restoration. The latter had relatively higher abundances of Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria and comparatively lower abundance of Thermoleophilia. There were significantly higher abundances of plant pathogens under seasonal grazing than those under other managements. There were significantly high proportions of pathotrophs and saprotrophs (10.0%) under seasonal and traditional grazing, respectively. The proportion of pathotrophs under integrated restoration (10.0%) was about seven-fold greater than that under grazing exclusion (1.5%). The relative differences among treatments in terms of soil water content, plant biomass, and soil C:N partially explained the differences in their prokaryotic community compositions. Increases in soil organic carbon and C:N may explain the observed changes in the soil fungal communities. The management practices affected soil microorganisms mainly by altering the soil nutrient profile. Grazing attracted specific pathotrophs and saprotrophs while repelling certain plant pathogens. Hence, modulations in soil microbial community structure and function must be considered in the process of planning for the implementation of grassland degradation management measures.

Experimental warming increases fungal alpha diversity in an oligotrophic maritime Antarctic soil

The climate of maritime Antarctica has altered since the 1950s. However, the effects of increased temperature, precipitation and organic carbon and nitrogen availability on the fungal communities inhabiting the barren and oligotrophic fellfield soils that are widespread across the region are poorly understood. Here, we test how warming with open top chambers (OTCs), irrigation and the organic substrates glucose, glycine and tryptone soy broth (TSB) influence a fungal community inhabiting an oligotrophic maritime Antarctic fellfield soil. In contrast with studies in vegetated soils at lower latitudes, OTCs increased fungal community alpha diversity (Simpson's index and evenness) by 102-142% in unamended soil after 5 years. Conversely, OTCs had few effects on diversity in substrate-amended soils, with their only main effects, in glycine-amended soils, being attributable to an abundance of Pseudogymnoascus. The substrates reduced alpha and beta diversity metrics by 18-63%, altered community composition and elevated soil fungal DNA concentrations by 1-2 orders of magnitude after 5 years. In glycine-amended soil, OTCs decreased DNA concentrations by 57% and increased the relative abundance of the yeast Vishniacozyma by 45-fold. The relative abundance of the yeast Gelidatrema declined by 78% in chambered soil and increased by 1.9-fold in irrigated soil. Fungal DNA concentrations were also halved by irrigation in TSB-amended soils. In support of regional- and continental-scale studies across climatic gradients, the observations indicate that soil fungal alpha diversity in maritime Antarctica will increase as the region warms, but suggest that the accumulation of organic carbon and nitrogen compounds in fellfield soils arising from expanding plant populations are likely, in time, to attenuate the positive effects of warming on diversity.

Acid deposition at higher acidity weakens the antagonistic responses during the co-decomposition of two Asteraceae invasive plants

Co-invasion by two invasive plant species (IPS) can occur in the same habitat. Diversified acid deposition may change the co-invasion process by altering litter decomposition and plant-soil feedback signalling. This study examined the co-decomposition of two Asteraceae IPS (Solidago canadensis L. and Bidens pilosa L.) on litter decomposition rate, soil enzyme activities, and soil N-fixing bacterial communities under diversified acid deposition (mixed acid deposition at pH 5.6 and at pH 4.5, sulfuric acid at pH 4.5, and nitric acid at pH 4.5). B. pilosa litter degraded faster than S. canadensis litter. Acid deposition at higher acidity accelerated the decomposition rate of both pure S. canadensis litter and the equally mixed litters from the two Asteraceae IPS. Antagonistic responses may occur during the co-decomposition of the two Asteraceae IPS with mixed acid deposition, regardless of the pH, as well as with nitric acid deposition at pH 4.5; in contrast, there may be neutral responses for the co-decomposition process with sulfuric acid at pH 4.5. The type of acid deposited may be one of the key factors affecting the intensity of the mixing effect affecting the co-decomposition. Acid deposition at higher acidity weakened the antagonistic responses for the co-decomposition of the two Asteraceae IPS compared with the response to weak acids. Together, these results indicate that acid deposition at higher acidity could facilitate the co-invasion of the two Asteraceae IPS mainly through accelerated litter decomposition as well as weakened antagonistic responses for co-decomposition.

Long-term nickel contamination increased soil fungal diversity and altered fungal community structure and co-occurrence patterns in agricultural soils

Nickel (Ni) contamination imposes deleterious effects on the stability of soil ecosystem. Soil fungal community as a crucial moderator of soil remediation and biochemical processes has attracted more and more research interests. In the present study, soil fungal community composition and diversity under long-term Ni contamination were investigated and fungal interaction networks were built to reveal fungal co-occurrence patterns. The results showed that moderate Ni contamination significantly increased fungal diversity and altered fungal community structure. Functional predictions based on FUNGuild suggested that the relative abundance of arbuscular mycorrhizal fungi (AMF) significantly increased at moderate Ni contamination level. Ni contamination strengthened fungal interactions. Keystone taxa at different Ni contamination levels, such as Penicillium at light contamination, were identified, which might have ecological significance in maintaining the stability of fungal community to Ni stress. The present study provided a deeper insight into the effect of long-term Ni contamination on fungal community composition and co-occurrence patterns, and was helpful to further explore ecological risk of Ni contamination in cultivated field.

Microbial biodiversity contributes to soil carbon release: A case study on fire disturbed boreal forests

Microbial communities often possess enormous diversity, raising questions about whether this diversity drives ecosystem functioning, especially the influence of diversity on soil decomposition and respiration. Although functional redundancy is widely observed in soil microorganisms, evidence that species occupy distinct metabolic niches has also emerged. In this paper, we found that apart from the environmental variables, increases in microbial diversity, notably bacterial diversity, lead to an increase in soil C emissions. This was demonstrated using structural equation modelling (SEM), linking soil respiration with naturally differing levels of soil physio-chemical properties, vegetation coverage, and microbial diversity after fire disturbance. Our SEMs also revealed that models including bacterial diversity explained more variation of soil CO2 emissions (about 45%) than fungal diversity (about 38%). A possible explanation of this discrepancy is that fungi are more multifunctional than bacteria and, therefore, an increase in fungal diversity does not necessarily change soil respiration. Further analysis on functional genes suggested that bacterial and fungal diversities mainly explain the potential decomposition of recalcitrant C than of labile C. Overall, by incorporating microbial diversity and the environmental variables, the predictive power of models on soil C emission was significantly improved, indicating microbial diversity is crucial for predicting ecosystem functions.

Changes in the Density and Composition of Rhizosphere Pathogenic Fusarium and Beneficial Trichoderma Contributing to Reduced Root Rot of Intercropped Soybean

The dynamic of soil-borne disease is closely related to the rhizosphere microbial communities. Maize–soybean relay strip intercropping has been shown to significantly control the type of soybean root rot that tends to occur in monoculture. However, it is still unknown whether the rhizosphere microbial community participates in the regulation of intercropped soybean root rot. In this study, rhizosphere Fusarium and Trichoderma communities were compared in either healthy or root-rotted rhizosphere soil from monocultured and intercropped soybean, and our results showed the abundance of rhizosphere Fusarium in intercropping was remarkably different from monoculture. Of four species identified, F. oxysporum was the most aggressive and more frequently isolated in diseased soil of monoculture. In contrast, Trichoderma was largely accumulated in healthy rhizosphere soil of intercropping rather than monoculture. T. harzianum dramatically increased in the rhizosphere of intercropping, while T. virens and T. afroharzianum also exhibited distinct isolation frequency. For the antagonism test in vitro, Trichoderma strains had antagonistic effects on F. oxysporum with the percentage of mycelial inhibition ranging from 50.59–92.94%, and they displayed good mycoparasitic abilities against F. oxysporum through coiling around and entering into the hyphae, expanding along the cell–cell lumen and even dissolving cell walls of the target fungus. These results indicate maize–soybean relay strip intercropping significantly increases the density and composition proportion of beneficial Trichoderma to antagonize the pathogenic Fusarium species in rhizosphere, thus potentially contributing to the suppression of soybean root rot under the intercropping.

Structure and diversity of fungal communities in long-term copper-contaminated agricultural soil

Copper (Cu) contamination threatens the stability of soil ecosystems. As important moderators of biochemical processes and soil remediation, the fungal community in contaminated soils has attracted much research interest. In this study, soil fungal diversity and community composition under long-term Cu contamination were investigated based on high-throughput sequencing. The co-occurrence networks were also constructed to display the co-occurrence patterns of the soil fungal community. The results showed that the richness and Chao1 index both significantly increased at 50 mg kg^-1 Cu and then significantly decreased at 1600 and 3200 mg kg^-1 Cu. Soil fungal diversity was significantly and positively correlated with plant dry weight. Specific tolerant taxa under different Cu contamination gradients were illustrated by linear discriminant analysis effect size (LEfSe). Soil Cu concentration and shoot dry weight were the strongest driving factors influencing fungal composition. The relative abundance of arbuscular mycorrhizal fungi increased first and then declined along with elevating Cu concentrations via FUNGuild analysis. The interactions among fungi were enhanced under light and moderate Cu contamination but weakened under heavy Cu contamination by random matrix theory (RMT)-based molecular ecological network analysis. Penicillium, identified as a keystone taxon in Cu-contaminated soils, had the function of removing heavy metals and detoxification, which might be vital to trigger the resistance of the fungal community to Cu contamination. The results may facilitate the identification of Cu pollution indicators and the development of in situ bioremediation technology for contaminated cultivated fields.

Antifungal Metabolites as Food Bio-Preservative: Innovation, Outlook, and Challenges

Perishable food spoilage caused by fungi is a major cause of discomfort for food producers. Food sensory abnormalities range from aesthetic degeneration to significant aroma, color, or consistency alterations due to this spoilage. Bio-preservation is the use of natural or controlled bacteria or antimicrobials to enhance the quality and safety of food. It has the ability to harmonize and rationalize the required safety requirements with conventional preservation methods and food production safety and quality demands. Even though synthetic preservatives could fix such issues, there is indeed a significant social need for "clean label" foods. As a result, consumers are now seeking foods that are healthier, less processed, and safer. The implementation of antifungal compounds has gotten a lot of attention in recent decades. As a result, the identification and characterization of such antifungal agents has made promising advances. The present state of information on antifungal molecules, their modes of activity, connections with specific target fungi varieties, and uses in food production systems are summarized in this review.

Cropping systems impact changes in soil fungal, but not prokaryote, alpha-diversity and community composition stability over a growing season in a long-term field trial

Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species-rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.

Soil Fungal Community in Grazed Inner Mongolian Grassland Adjacent to Coal-Mining Activity

Coal mining results in reduced soil quality and makes environments less stable. Soil fungi are suitable indicators of soil quality for monitoring purposes. Here, the objective was therefore to investigate the effects of grazing and mining on the composition of the soil fungal community at the periphery of an opencast coal-mine dump in the Shengli mining area, Xilingol League, Inner Mongolia. A total of 2,110 fungal operational taxonomic units were identified and subdivided into 81 orders and nine categories, based on trophic modes. The sensitive factor to mining was soil pH, and that to grazing were soil nitrate-nitrogen and alkaline phosphatase activity. According to the Pearson correlation and Mantel test, we propose interactions between grazing and coal-mining exist a co-effect and could regulate edaphic variables to alter the behavior of soil fungal community. Moreover, compared with coal-mining, grazing has a greater impact on it. The results provide a basis to further clarify soil fungal ecological functions, and may also contribute to the practice of soil remediation and environmental management in coal-mining areas.

Soil Nematode Communities in Managed and Natural Temperate Forest

Forest management and the stand age play key roles in determining the composition of soil biota, including nematodes. We analysed the effect of the interaction between stands of natural forest and stands influenced by human activity on nematode communities, necessary for realistically assessing the specific potentials of forest soils, plant protection, forest management, and land use management. Nematode communities were evaluated and compared in managed beech and spruce forests in three age classes (0–20, 40–60, and 100–120 years old) and an unmanaged old-growth temperate forest. A total of 51 nematode genera were found in the forests. The number of nematode genera was the highest (46) in European beech forests, dominated by Rhabditis and Filenchus. In contrast, the number of nematode genera was the lowest (37) in a Norway spruce forest, but where nematode abundance was the highest due mostly to the high abundance of bacterivorous nematodes such as Acrobeloides, Plectus, and Rhabditis. The unmanaged old-growth forest had the lowest nematode abundance and total biomass but the highest abundance of herbivorous nematodes of the order Tylenchida, especially Filenchus, Malenchus, and Paratylenchus, and a high abundance of identified genera of predators. The number of identified nematode genera, abundance, total biomass, and diversity index were the highest in young 0–20-year-old stands, and the lowest in 100–120-year-old stands. Enrichment, structure, and basal indices were influenced by both the stands and the ages of the forests.

Land-use drives the temporal stability and magnitude of soil microbial functions and modulates climate effects

Soil microbial community functions are essential indicators of ecosystem multifunctionality in managed land-use systems. Going forward, the development of adaptation strategies and predictive models under future climate scenarios will require a better understanding of how both land-use and climate disturbances influence soil microbial functions over time. Between March and November 2018, we assessed the effects of climate change on the magnitude and temporal stability of soil basal respiration, soil microbial biomass and soil functional diversity across a range of land-use types and intensities in a large-scale field experiment. Soils were sampled from five common land-use types including conventional and organic croplands, intensive and extensive meadows, and extensive pastures, under ambient and projected future climate conditions (reduced summer precipitation and increased temperature) at the Global Change Experimental Facility (GCEF) in Bad Lauchstädt, Germany. Land-use and climate treatment interaction effects were significant in September, a month when precipitation levels slightly rebounded following a period of drought in central Germany: compared to ambient climate, in future climate treatments, basal respiration declined in pastures and increased in intensive meadows, functional diversity declined in pastures and croplands, and respiration-to-biomass ratio increased in intensive and extensive meadows. Low rainfall between May and August likely strengthened soil microbial responses toward the future climate treatment in September. Although microbial biomass showed declining levels in extensive meadows and pastures under future climate treatments, overall, microbial function magnitudes were higher in these land-use types compared to croplands, indicating that improved management practices could sustain high microbial ecosystem functioning in future climates. In contrast to our hypothesis that more disturbed land-use systems would have destabilized microbial functions, intensive meadows and organic croplands showed stabilized soil microbial biomass compared to all other land-use types, suggesting that temporal stability, in addition to magnitude-based measurements, may be useful for revealing context-dependent effects on soil ecosystem functioning.

How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics

Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.

Decay stages of wood and associated fungal communities characterise diversity-decomposition relationships

The biodiversity–ecosystem function relationship is a central topic in ecology. Fungi are the dominant decomposers of organic plant material in terrestrial ecosystems and display tremendous species diversity. However, little is known about the fungal diversity–decomposition relationship. We evaluated fungal community assemblies and substrate quality in different stages of wood decay to assess the relationships between fungal species richness and weight loss of wood substrate under laboratory conditions. Wood-inhabiting fungal communities in the early and late stages of pine log decomposition were used as a model. Colonisation with certain species prior to inoculation with other species resulted in four-fold differences in fungal species richness and up to tenfold differences in the rate of wood substrate decomposition in both early- and late-decaying fungal communities. Differences in wood substrate quality had a significant impact on species richness and weight loss of wood and the relationships between the two, which were negative or neutral. Late communities showed significantly negative species richness–decay relationships in wood at all decay stages, whereas negative relationships in early communities were significant only in the intermediate decay stage. Our results suggest that changes in fungal communities and wood quality during wood decomposition affect the fungal diversity–decomposition relationship.

Fungal Community and Biodeterioration Analysis of Hull Wood and Its Storage Environment of the Nanhai No. 1 Shipwreck

The Nanhai No. 1 shipwreck is a Chinese merchant ship in the Southern Song Dynasty, and now it is stored in a huge enclosed glass warehouse in Maritime Silk Road Museum in Guangdong Province. At present, the hull of the Nanhai No. 1 shipwreck is still being excavated, and a small part of the hull wood is soaked in a specific solution to desalt. Through long-term exploration, we found that the above two states of hull wood had undergone biodeterioration, so the purpose of this study is to analyze the fungal community of exposed and soaked wood from the Nanhai No. 1 shipwreck. We sampled 10 exposed hull wood and sea mud samples, two wood storage water samples, and air samples in the glass warehouse. We used scanning electron microscope and optical microscope to find that there were obvious fungal structures in exposed wood and wood storing water samples. High-throughput sequencing of fungi revealed that the most abundant genera in exposed and soaked wood were Fusarium sp., and Scedosporium sp., respectively. In addition, Fusarium solani and Scedosporium apiospermum were successfully isolated from the hull wood surface and wood storing water samples, and the degradation tests of lignin and cellulose, the sensitivity tests of biocides and growth curve assay were carried out. We also found that Penicillium sp. and Cladosporium sp. are the most abundant in the glass warehouse air. Our research results show that F. solani and S. apiospermum should be regarded as a major threat to the preservation of the Nanhai No. 1 shipwreck. These results provide a reference for our protection of shipwrecks and other similar artifacts.

Regional Diversity of Maritime Antarctic Soil Fungi and Predicted Responses of Guilds and Growth Forms to Climate Change

We report a metabarcoding study documenting the fungal taxa in 29 barren fellfield soils sampled from along a 1,650 km transect encompassing almost the entire maritime Antarctic (60-72°S) and the environmental factors structuring the richness, relative abundance, and taxonomic composition of three guilds and growth forms. The richness of the lichenised fungal guild, which accounted for 19% of the total fungal community, was positively associated with mean annual surface air temperature (MASAT), with an increase of 1.7 operational taxonomic units (OTUs) of lichenised fungi per degree Celsius rise in air temperature. Soil Mn concentration, MASAT, C:N ratio, and pH value determined the taxonomic composition of the lichenised guild, and the relative abundance of the guild was best predicted by soil Mn concentration. There was a 3% decrease in the relative abundance of the saprotrophic fungal guild in the total community for each degree Celsius rise in air temperature, and the OTU richness of the guild, which accounted for 39% of the community, was negatively associated with Mn concentration. The taxonomic composition of the saprotrophic guild varied with MASAT, pH value, and Mn, NH4 +-N, and SO4 2- concentrations. The richness of the yeast community, which comprised 3% of the total fungal community, was positively associated with soil K concentration, with its composition being determined by C:N ratio. In contrast with a similar study in the Arctic, the relative abundance and richness of lichenised fungi declined between 60°S and 69°S, with those of saprotrophic Agaricales also declining sharply in soils beyond 63°S. Basidiomycota, which accounted for 4% of reads, were much less frequent than in vegetated soils at lower latitudes, with the Ascomycota (70% of reads) being the dominant phylum. We conclude that the richness, relative abundance, and taxonomic composition of guilds and growth forms of maritime Antarctic soil fungi are influenced by air temperature and edaphic factors, with implications for the soils of the region as its climate changes during the 21st century.

Biogeographic pattern of bacterioplanktonic community and potential function in the Yangtze River: Roles of abundant and rare taxa

Bacterioplanktonic communities, consisting of a few abundant taxa (AT) and many rare taxa (RT), are essential component of riverine ecosystems. Nonetheless, the biogeographic patterns of bacterioplankton and roles of AT and RT in community structuring and functional composition remain uncertain in large rivers. Here, we employ the Yangtze River, which is the third-longest river in the world, as model system. By using high-throughput sequencing and bioinformatics tool of Tax4Fun, the geographical patterns of bacterioplanktonic taxonomic and predicted functional communities are investigated, and the relative importance of abundant and rare subcommunities in community structuring are explored. Results showed a clear spatial variation that the bacterioplanktonic communities of upper, middle and lower reaches of the river are significantly different from each other. Besides, the Three Gorges Dam exhibited impact on the bacterioplankton of upper reach whose community is relatively closer to that of the Poyang Lake. Both the abundant and rare subcommunities showed spatial variation along the river, which is similar to the total bacterioplanktonic community. The rare subcommunity comprised a majority of community diversity with 23.6% of the total sequences and 94.2% of the total OTUs. The rare subcommunity contributes a major part (56.8%) versus abundant subcommunity (16.3%) of the spatial variation of the total community. In addition, the non-RT exhibits more interactions with RT than with themselves, and all of the 33 keystone species are belonged to RT. Hence, the RT is critical for community structuring and assembling. By contrast, no obvious spatial effect was observed for the predicted functional community. The predicted functions of abundant and rare subcommunities are consistent with that of total community, despite their contrasting community composition. In summary, the rare subcommunity show significantly impact on the community structure and assembling, and play an important role in predicted function as 'seed bank' in the Yangtze River.

Characterising the effect of crop species and fertilisation treatment on root fungal communities

Information about the root mycobiome may improve the overall quality of the plants and contribute to a valuable strategy to enhance sustainable agriculture. Therefore, we assessed differences in fungal community diversity and composition in the roots of potato, wheat and barley grown under mineral nitrogen fertilisation at five rates, with and without farmyard manure amendment. The same factorial combination of treatments has been used since 1989. Species richness and diversity, as well as community composition, of different fungal guilds were characterised using Illumina MiSeq sequencing of the ITS2 region. Crop species was the main factor determining overall fungal richness and diversity, with wheat showing the highest, and potato the lowest, richness and diversity. Pathogen diversity indices were highest in wheat plots amended with farmyard manure, whereas the lowest values were observed for potato roots. Fertilisation treatments and the interaction between crop species and fertilisation had the strongest impact on arbuscular mycorrhiza and saprotroph diversity. Crop species also determined the composition of the overall fungal community and that of fungal guilds, whereas fertilisation treatment had only a minor effect. This study highlights crop species as the main driver in shaping root fungal diversity and composition under the same environmental conditions.

Identification of Fungal Dynamics Associated With Black Locust Leaves Mineralization and Their Correlations With Physicochemical Factors

In this study, the fungal dynamics associated with black locust (BL) mineralization and its correlation with various environmental factors were evaluated across three different vegetation types along a gradient of temperature and humidity. The results confirmed that Ascomycota and Basidiomycota were the dominant phyla in each habitat, with average relative abundance of 86.57 and 11.42%, respectively. But both phylum abundance varied significantly among different BL leaves' decomposing habitats. Black locust changed the most significantly in the forest habitat and the least in the steppe. In addition, the litter characteristics of BL decreased with total carbon and total nitrogen mineralization and underground water level in water-rich region, while this result was significantly consistent with the fungal diversity. Co-occurrence network studies revealed that significant correlations were found between fungal community composition and environmental factors, the decrease of underground water level influence the fungal structure in forest habitat. Finally, the present study results provide important insights about the biological invasion of new ecosystems.

Divergent responses of taxonomic and predicted functional profiles of bacterioplankton to reservoir impoundment

Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%-58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.

Soil functional responses to drought under range-expanding and native plant communities

Current climate warming enables plant species and soil organisms to expand their range to higher latitudes and altitudes. At the same time, climate change increases the incidence of extreme weather events such as drought. While it is expected that plants and soil organisms originating from the south are better able to cope with drought, little is known about the consequences of their range shifts on soil functioning under drought events.Here, we test how range-expanding plant species and soil communities may influence soil functioning under drought. We performed a full-factorial outdoor mesocosm experiment with plant communities of range expanders or related natives, with soil inocula from the novel or the original range, with or without summer drought. We measured litter decomposition, carbon mineralization and enzyme activities, substrate-induced respiration and the relative abundance of soil saprophytic fungi immediately after drought and at 6 and 12 weeks after rewetting.Drought decreased all soil functions regardless of plant and soil origin except one; soil respiration was less reduced in soils of range-expanding plant communities, suggesting stronger resistance to drought. After rewetting, soil functioning responses depended on plant and soil origin. Soils of native plant communities with a history of drought had more litter mass loss and higher relative abundance of saprophytic fungi than soils without drought and soils of range expanders. Functions of soil from range expanders recovered in a more conservative manner than soils of natives, as litter mass loss did not exceed the control rates. At the end of the experiment, after rewetting, most soil functions in mesocosms with drought history did not differ anymore from the control.We conclude that functional consequences of range-expanding plants and soil biota may interact with effects of drought and that these effects are most prominent during the first weeks after rewetting of the soil. A free http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13453/suppinfo can be found within the Supporting Information of this article.

Fungi in the Canopy: How Soil Fungi and Extracellular Enzymes Differ Between Canopy and Ground Soils

Tropical montane cloud forests contain a large abundance and diversity of canopy epiphytes, which depend on canopy soil to retain water and nutrients. We lack an in depth understanding of how these soils contribute to ecosystem processes and soil diversity and how sensitive they may be to projected climate change. We compared canopy and ground soils in Monteverde, Costa Rica, to determine how these two soil types differ in their extracellular enzyme activity (EEA) and fungal communities. Samples were also collected along two elevation gradients to reveal if canopy soils differed in how EEA and fungal communities responded to elevation compared to ground soils. We found that canopy soils had higher EEA than ground soils. Fungal communities were less diverse and differed significantly between the two soil types. These differences were associated with higher relative abundances of yeasts and endophytes in canopy soils. The relative abundances of free-living filamentous fungi and yeasts shifted more dramatically with elevation in canopy soils compared to ground soils. Our study suggests that canopy soils may be a reservoir for endophytes. Epiphytes may invest in symbionts that promote stress tolerance over mycorrhizal fungi whose high resource demands are costly and less beneficial. Overall, soils harbor distinct fungal communities that may be altered under projected climate change.

Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China

Recent studies have detected strong phylogenetic signals in tree-fungus associations for diseased leaves and mycorrhizal symbioses. However, the extent of plant phylogenetic constraints on the free-living soil mycobiome remains unknown, especially at broad geographic scales. Here, 343 soil samples were collected adjacent to individual tree trunks, representing 58 woody plant species located in five mountain forests of eastern China. Integrating plant species identity and phylogenetic information, we aimed to unravel the relative contributions of phylogenetic relationships among tree species, abiotic environmental filtering, and geographic isolation to the geographic distribution of soil mycobiome. We found that the community dissimilarities of total fungi and each dominant guild (viz. saprotrophs, plant pathogens, and ectomycorrhizal fungi) significantly increased with increasing plant phylogenetic distance. Plant phylogenetic eigenvectors explained 11.4% of the variation in community composition, whereas environmental and spatial factors explained 24.1% and 7.2% of the variation, respectively. The communities of ectomycorrhizal fungi and plant pathogens were relatively more strongly affected by plant phylogeny than those of saprotrophs (13.7% and 10.4% vs. 8.5%). Overall, our results demonstrate how plant phylogeny, environment, and geographic space contribute to forest soil fungal distributions and suggest that the influence of plant phylogeny on fungal association may differ by guilds.

Response of Soil Fungal Community Structure to Long-Term Continuous Soybean Cropping

Long-term continuous soybean cropping can lead to the aggravation of soil fungal disease. However, the manner in which the fungal community and functional groups of fungi are affected by continuous soybean cropping remains unclear. We investigated the fungal abundance, composition and diversity during soybean rotation (RS), 2-year (SS) and long-term (CS) continuous soybean cropping systems using quantitative real-time PCR and high-throughput sequencing. The results showed that the fungal abundance was significantly higher in CS than in SS and RS. CS altered the fungal composition. Compared with RS, SS had an increase of 29 and a decrease of 12 genera in fungal relative abundance, and CS increased 38 and decreased 17 genera. The Shannon index was significantly higher in CS and SS than in RS. The result of principal coordinate analysis (PCoA) showed that CS and SS grouped together and were clearly separated from RS on the PCoA1. A total of 32 features accounted for the differences in fungal composition across RS, SS, and CS. The relative abundance of 10 potentially pathogenic and 10 potentially beneficial fungi changed, and most of their relative abundances dramatically increased in SS and CS compared with RS. Our study indicated that CS results in selective stress on pathogenic and beneficial fungi and causes the development of the fungal community structure that is antagonistic to plant health.

Decomposition responses to climate depend on microbial community composition

Bacteria and fungi drive decomposition, a fundamental process in the carbon cycle, yet the importance of microbial community composition for decomposition remains elusive. Here, we used an 18-month reciprocal transplant experiment along a climate gradient in Southern California to disentangle the effects of the microbial community versus the environment on decomposition. Specifically, we tested whether the decomposition response to climate change depends on the microbial community. We inoculated microbial decomposers from each site onto a common, irradiated leaf litter within "microbial cages" that prevent microbial exchange with the environment. We characterized fungal and bacterial composition and abundance over time and investigated the functional consequences through litter mass loss and chemistry. After 12 months, microbial communities altered both decomposition rate and litter chemistry. Further, the functional measurements depended on an interaction between the community and its climate in a manner not predicted by current theory. Moreover, microbial ecologists have traditionally considered fungi to be the primary agents of decomposition and for bacteria to play a minor role. Our results indicate that not only does climate change and transplantation have differential legacy effects among bacteria and fungi, but also that bacterial communities might be less functionally redundant than fungi with regards to decomposition. Thus, it may be time to reevaluate both the role of microbial community composition in its decomposition response to climate and the relative roles of bacterial and fungal communities in decomposition.

Comparison of fungal communities among ten macrophyte rhizospheres

The fungal community composition, size and several physico-chemical properties were individually investigated in ten macrophyte rhizospheric substrates using nested PCR-denaturing gradient gel electrophoresis and soil chemical methods. Results indicated that both Dothideomycetes and Sordariomycetes were dominant fungi in macrophyte rhizospheric substrates, and denitrifying fungi (Fusarium graminearum) was found in nine of ten macrophyte rhizospheres. Fungal Shannon-Wiener diversity index (H) and richness (S) in Thalia dealbata, Typha latifolia, Iris hexagona and Hemerocallis aurantiaca rhizospheres were higher than those in other six rhizospheres. Fungal number and biomass were 1.91 × 10³ CFUs g^-1 dw and 1.53 μg ergosterol g^-1 dw in Iris pseudacor rhizosphere, and were greater than in other nine rhizospheres. The correlation analysis showed that fungal number and biomass significantly and positively correlated to total soil phosphorus, while fungal H and S were significantly and negatively correlated to total organic carbon. The principal components analysis (PCA) showed that the fungal community significantly divided ten macrophyte rhizospheres into four groups, showing the significant difference of fungal communities among ten rhizospheric substrates. The current study revealed for the first time the importance of rhizospheric fungal community in distinguishing macrophyte rhizospheres, thus will undoubtedly widen our insight into fungal communities in aquatic rhizospheres.

High Microbial Diversity Promotes Soil Ecosystem Functioning

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO₂ emission by up to 40%, and (ii) shaped the source of CO₂ emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil.IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.

High Microbial Diversity Promotes Soil Ecosystem Functioning

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO₂ emission by up to 40%, and (ii) shaped the source of CO₂ emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil.IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.

Diversity of cultivable fungal endophytes in Paullinia cupana (Mart.) Ducke and bioactivity of their secondary metabolites

Paullinia cupana is associated with a diverse community of pathogenic and endophytic microorganisms. We isolated and identified endophytic fungal communities from the roots and seeds of P. cupana genotypes susceptible and tolerant to anthracnose that grow in two sites of the Brazilian Amazonia forest. We assessed the antibacterial, antitumor and genotoxic activity in vitro of compounds isolated from the strains Trichoderma asperellum (1BDA) and Diaporthe phaseolorum (8S). In concert, we identified eight fungal species not previously reported as endophytes; some fungal species capable of inhibiting pathogen growth; and the production of antibiotics and compounds with bacteriostatic activity against Pseudomonas aeruginosa in both susceptible and multiresistant host strains. The plant genotype, geographic location and specially the organ influenced the composition of P. cupana endophytic fungal community. Together, our findings identify important functional roles of endophytic species found within the microbiome of P. cupana. This hypothesis requires experimental validation to propose management of this microbiome with the objective of promoting plant growth and protection.

Mixed cropping regimes promote the soil fungal community under zero tillage

Fungi of yield soils represent a significant portion of the microbial biomass and reflect sensitivity to changes in the ecosystem. Our hypothesis was that crops included in cropping regimes under the zero tillage system modify the structure of the soil fungi community. Conventional and molecular techniques provide complementary information for the analysis of diversity of fungal species and successful information to accept our hypothesis. The composition of the fungal community varied according to different crops included in the cropping regimes. However, we detected other factors as sources of variation among them, season and sampling depth. The mixed cropping regimes including perennial pastures and one crop per year promote fungal diversity and species with potential benefit to soil and crop. The winter season and 0-5 cm depth gave the largest evenness and fungal diversity. Trichoderma aureoviride and Rhizopus stolonifer could be used for monitoring changes in soil under zero tillage.

Functional Diversity of Fungal Communities in Soil Contaminated with Diesel Oil

The widespread use and consumption of crude oil draws the public's attention to the fate of petroleum hydrocarbons in the environment, as they can permeate the soil environment in an uncontrollable manner. Contamination of soils with petroleum products, including diesel oil (DO), can cause changes in the microbiological soil properties. The effect of diesel oil on the functional diversity of fungi was tested in a model experiment during 270 days. Fungi were isolated from soil and identified. The functional diversity of fungal communities was also determined. Fungi were identified with the MALDI-TOF method, while the functional diversity was determined using FF-plates made by Biolog®, with 95 carbon sources. Moreover, the diesel oil degradation dynamics was assessed. The research showed that soil contaminated with diesel oil is characterized by a higher activity of oxireductases and a higher number of fungi than soil not exposed to the pressure of this product. The DO pollution has an adverse effect on the diversity of fungal community. This is proved by significantly lower values of the Average Well-Color Development, substrates Richness (R) and Shannon-Weaver (H) indices at day 270 after contamination. The consequences of DO affecting soil not submitted to remediation are persistent. After 270 days, only 64% of four-ringed, 28% of five-ringed, 21% of 2-3-ringed and 16% of six-ringed PAHs underwent degradation. The lasting effect of DO on communities of fungi led to a decrease in their functional diversity. The assessment of the response of fungi to DO pollution made on the basis of the development of colonies on Petri dishes [Colony Development (CD) and Eco-physiological Diversity (EP) indices] is consistent with the analysis based on the FF MicroPlate system by Biolog®. Thus, a combination of the FF MicroPlate system by Biolog® with the simultaneous calculation of CD and EP indices alongside the concurrent determination of the content of PAHs and activity of oxireductases provides an opportunity to achieve relatively complete characterization of the consequences of a long-term impact of diesel oil on soil fungi.

Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity

Previous studies have revealed inconsistent correlations between fungal diversity and plant diversity from local to global scales, and there is a lack of information about the diversity-diversity and productivity-diversity relationships for fungi in alpine regions. Here we investigated the internal relationships between soil fungal diversity, plant diversity and productivity across 60 grassland sites on the Tibetan Plateau, using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region for fungal identification. Fungal alpha and beta diversities were best explained by plant alpha and beta diversities, respectively, when accounting for environmental drivers and geographic distance. The best ordinary least squares (OLS) multiple regression models, partial least squares regression (PLSR) and variation partitioning analysis (VPA) indicated that plant richness was positively correlated with fungal richness. However, no correlation between plant richness and fungal richness was evident for fungal functional guilds when analyzed individually. Plant productivity showed a weaker relationship to fungal diversity which was intercorrelated with other factors such as plant diversity, and was thus excluded as a main driver. Our study points to a predominant effect of plant diversity, along with other factors such as carbon : nitrogen (C : N) ratio, soil phosphorus and dissolved organic carbon, on soil fungal richness.